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  1. Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus.

    Science.gov (United States)

    Takahata, Satoshi; Yago, Takumi; Iwabuchi, Keisuke; Hirakawa, Hideki; Suzuki, Yutaka; Onodera, Yasuyuki

    2016-01-01

    Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Comparative Genomics of the Mating-Type Loci of the Mushroom Flammulina velutipes Reveals Widespread Synteny and Recent Inversions

    Science.gov (United States)

    van Peer, Arend F.; Park, Soon-Young; Shin, Pyung-Gyun; Jang, Kab-Yeul; Yoo, Young-Bok; Park, Young-Jin; Lee, Byoung-Moo; Sung, Gi-Ho; James, Timothy Y.; Kong, Won-Sik

    2011-01-01

    Background Mating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs. Methodology/Principal Findings We report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters. Conclusions/Significance In our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as

  3. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis.

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    Yang, Luming; Koo, Dal-Hoe; Li, Dawei; Zhang, Tao; Jiang, Jiming; Luan, Feishi; Renner, Susanne S; Hénaff, Elizabeth; Sanseverino, Walter; Garcia-Mas, Jordi; Casacuberta, Josep; Senalik, Douglas A; Simon, Philipp W; Chen, Jinfeng; Weng, Yiqun

    2014-01-01

    In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the

  4. Jumbled genomes: missing Apicomplexan synteny.

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    DeBarry, Jeremy D; Kissinger, Jessica C

    2011-10-01

    Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes found on the same chromosome and in the same order within 25 kb up- and downstream of any orthologous genes. Conserved synteny between major lineages is limited to small regions in Plasmodium and Theileria/Babesia species, and within these conserved regions, there are a number of proteins putatively targeted to organelles. The observed overall lack of synteny is surprising considering the divergence times and the apparent absence of transposable elements (TEs) within any of the species examined. TEs are ubiquitous in all other groups of eukaryotes studied to date and have been shown to be involved in genomic rearrangements. It appears that there are different criteria governing genome evolution within the Apicomplexa relative to other well-studied unicellular and multicellular eukaryotes.

  5. Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over seven million years

    Science.gov (United States)

    Genome evolution influences a parasite’s’s pathogenicity, host-pathogen interactions, environmental constraints, and invasion biology, while genome assemblies form the basis of comparative sequence analyses. Given that closely related organisms typically maintain appreciable synteny, the genome asse...

  6. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

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    Rebekah E Oliver

    Full Text Available A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42 has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

  7. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

    Science.gov (United States)

    Chao, Shiaoman; Jellen, Eric N.; Carson, Martin L.; Rines, Howard W.; Obert, Donald E.; Lutz, Joseph D.; Shackelford, Irene; Korol, Abraham B.; Wight, Charlene P.; Gardner, Kyle M.; Hattori, Jiro; Beattie, Aaron D.; Bjørnstad, Åsmund; Bonman, J. Michael; Jannink, Jean-Luc; Sorrells, Mark E.; Brown-Guedira, Gina L.; Mitchell Fetch, Jennifer W.; Harrison, Stephen A.; Howarth, Catherine J.; Ibrahim, Amir; Kolb, Frederic L.; McMullen, Michael S.; Murphy, J. Paul; Ohm, Herbert W.; Rossnagel, Brian G.; Yan, Weikai; Miclaus, Kelci J.; Hiller, Jordan; Maughan, Peter J.; Redman Hulse, Rachel R.; Anderson, Joseph M.; Islamovic, Emir

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. PMID:23533580

  8. Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea

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    Gujaria-Verma, Neha; Vail, Sally L.; Carrasquilla-Garcia, Noelia; Penmetsa, R. Varma; Cook, Douglas R.; Farmer, Andrew D.; Vandenberg, Albert; Bett, Kirstin E.

    2014-01-01

    Lentil (Lens culinaris Medik.) is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum) and pea (Pisum sativum), and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil. PMID:25538716

  9. Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea.

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    Neha eGujaria-Verma

    2014-12-01

    Full Text Available Lentil (Lens culinaris Medik. is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum and pea (Pisum sativum, and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1,107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil.

  10. In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate

    DEFF Research Database (Denmark)

    Li, Hang; Li, Mingshun; Huang, Yinyan

    2013-01-01

    In order to construct a more universal model for understanding the genetic requirements for bacterial AsIII oxidation, an in silico examination of the available sequences in the GenBank was assessed and revealed 21 conserved 5-71 kb arsenic islands within phylogenetically diverse bacterial genomes...... in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s) yet to be discovered. Phylogenetic analysis of the aio, ars, pst, and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer (HGT). It is therefore likely the arsenic...

  11. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

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    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  12. A Plasmodium Whole-Genome Synteny Map: Indels and Synteny Breakpoints as Foci for Species-Specific Genes.

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    2005-12-01

    Full Text Available Whole-genome comparisons are highly informative regarding genome evolution and can reveal the conservation of genome organization and gene content, gene regulatory elements, and presence of species-specific genes. Initial comparative genome analyses of the human malaria parasite Plasmodium falciparum and rodent malaria parasites (RMPs revealed a core set of 4,500 Plasmodium orthologs located in the highly syntenic central regions of the chromosomes that sharply defined the boundaries of the variable subtelomeric regions. We used composite RMP contigs, based on partial DNA sequences of three RMPs, to generate a whole-genome synteny map of P. falciparum and the RMPs. The core regions of the 14 chromosomes of P. falciparum and the RMPs are organized in 36 synteny blocks, representing groups of genes that have been stably inherited since these malaria species diverged, but whose relative organization has altered as a result of a predicted minimum of 15 recombination events. P. falciparum-specific genes and gene families are found in the variable subtelomeric regions (575 genes, at synteny breakpoints (42 genes, and as intrasyntenic indels (126 genes. Of the 168 non-subtelomeric P. falciparum genes, including two newly discovered gene families, 68% are predicted to be exported to the surface of the blood stage parasite or infected erythrocyte. Chromosomal rearrangements are implicated in the generation and dispersal of P. falciparum-specific gene families, including one encoding receptor-associated protein kinases. The data show that both synteny breakpoints and intrasyntenic indels can be foci for species-specific genes with a predicted role in host-parasite interactions and suggest that, besides rearrangements in the subtelomeric regions, chromosomal rearrangements may also be involved in the generation of species-specific gene families. A majority of these genes are expressed in blood stages, suggesting that the vertebrate host exerts a greater

  13. A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes.

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    Taco W A Kooij

    2005-12-01

    Full Text Available Whole-genome comparisons are highly informative regarding genome evolution and can reveal the conservation of genome organization and gene content, gene regulatory elements, and presence of species-specific genes. Initial comparative genome analyses of the human malaria parasite Plasmodium falciparum and rodent malaria parasites (RMPs revealed a core set of 4,500 Plasmodium orthologs located in the highly syntenic central regions of the chromosomes that sharply defined the boundaries of the variable subtelomeric regions. We used composite RMP contigs, based on partial DNA sequences of three RMPs, to generate a whole-genome synteny map of P. falciparum and the RMPs. The core regions of the 14 chromosomes of P. falciparum and the RMPs are organized in 36 synteny blocks, representing groups of genes that have been stably inherited since these malaria species diverged, but whose relative organization has altered as a result of a predicted minimum of 15 recombination events. P. falciparum-specific genes and gene families are found in the variable subtelomeric regions (575 genes, at synteny breakpoints (42 genes, and as intrasyntenic indels (126 genes. Of the 168 non-subtelomeric P. falciparum genes, including two newly discovered gene families, 68% are predicted to be exported to the surface of the blood stage parasite or infected erythrocyte. Chromosomal rearrangements are implicated in the generation and dispersal of P. falciparum-specific gene families, including one encoding receptor-associated protein kinases. The data show that both synteny breakpoints and intrasyntenic indels can be foci for species-specific genes with a predicted role in host-parasite interactions and suggest that, besides rearrangements in the subtelomeric regions, chromosomal rearrangements may also be involved in the generation of species-specific gene families. A majority of these genes are expressed in blood stages, suggesting that the vertebrate host exerts a greater

  14. OrthoClusterDB: an online platform for synteny blocks

    National Research Council Canada - National Science Library

    Ng, Man-Ping; Vergara, Ismael A; Frech, Christian; Chen, Qingkang; Zeng, Xinghuo; Pei, Jian; Chen, Nansheng

    2009-01-01

    .... However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes-synteny blocks-as well as databases, which host synteny blocks...

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

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    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

  16. Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.

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    Lv, Jie; Havlak, Paul; Putnam, Nicholas H

    2011-10-05

    Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c. A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

  17. Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

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    Paczia Nicole

    2012-09-01

    Full Text Available Abstract Overflow metabolism is well known for yeast, bacteria and mammalian cells. It typically occurs under glucose excess conditions and is characterized by excretions of by-products such as ethanol, acetate or lactate. This phenomenon, also denoted the short-term Crabtree effect, has been extensively studied over the past few decades, however, its basic regulatory mechanism and functional role in metabolism is still unknown. Here we present a comprehensive quantitative and time-dependent analysis of the exometabolome of Escherichia coli, Corynebacterium glutamicum, Bacillus licheniformis, and Saccharomyces cerevisiae during well-controlled bioreactor cultivations. Most surprisingly, in all cases a great diversity of central metabolic intermediates and amino acids is found in the culture medium with extracellular concentrations varying in the micromolar range. Different hypotheses for these observations are formulated and experimentally tested. As a result, the intermediates in the culture medium during batch growth must originate from passive or active transportation due to a new phenomenon termed “extended” overflow metabolism. Moreover, we provide broad evidence that this could be a common feature of all microorganism species when cultivated under conditions of carbon excess and non-inhibited carbon uptake. In turn, this finding has consequences for metabolite balancing and, particularly, for intracellular metabolite quantification and 13C-metabolic flux analysis.

  18. SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence

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    Lewin Harris A

    2009-07-01

    Full Text Available Abstract Background The recent availability of genomic sequences and BAC libraries for a large number of mammals provides an excellent opportunity for identifying comparatively-anchored markers that are useful for creating high-resolution radiation-hybrid (RH and BAC-based comparative maps. To use these maps for multispecies genome comparison and evolutionary inference, robust bioinformatic tools are required for the identification of chromosomal regions shared between genomes and to localize the positions of evolutionary breakpoints that are the signatures of chromosomal rearrangements. Here we report an automated tool for the identification of homologous synteny blocks (HSBs between genomes that tolerates errors common in RH comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution. Findings We developed an algorithm and software tool (SyntenyTracker that can be used for automated definition of HSBs using pair-wise RH or gene-based comparative maps as input. To verify correct implementation of the underlying algorithm, SyntenyTracker was used to identify HSBs in the cattle and human genomes. Results demonstrated 96% agreement with HSBs defined manually using the same set of rules. A comparison of SyntenyTracker with the AutoGRAPH synteny tool was performed using identical datasets containing 14,380 genes with 1:1 orthology in human and mouse. Discrepancies between the results using the two tools and advantages of SyntenyTracker are reported. Conclusion SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies. The utility of SyntenyTracker will become more important for comparative genomics as the number of mapped and sequenced genomes increases.

  19. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes.

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    Staton, Margaret; Zhebentyayeva, Tetyana; Olukolu, Bode; Fang, Guang Chen; Nelson, Dana; Carlson, John E; Abbott, Albert G

    2015-10-05

    Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome

  20. A high-resolution map of synteny disruptions in gibbon and human genomes.

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    Lucia Carbone

    2006-12-01

    Full Text Available Gibbons are part of the same superfamily (Hominoidea as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52 (Nomascus leucogenys leucogenys as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon-human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state.

  1. [Extensive cutaneous candidiasis revealing cutaneous T-cell lymphoma: 2 cases].

    Science.gov (United States)

    Duong, T; Ingen-Housz-Oro, S; Gaulier, A; Petit, A; Dubertret, L; Sigal-Grinberg, M

    2006-01-01

    During the course of immunodeficiency diseases, severe candidiasis can occur with extensive cutaneous and mucous membrane lesions. However, blood dyscrasias are very rarely revealed by diffuse candidiasis. We report two case of cutaneous T-cell lymphoma revealed by extensive and atypical cutaneous candidiasis. Case No. 1:A 72-year-old woman presented a pruritic rash of circinate, serpiginous patches on glabrous skin and skinfolds with multiple intertrigo and rapidly worsening palmoplantar keratoderma. All mycological skin specimens tested positive for Candida albicans. Histological examination of a biopsy sample from a serpiginous patch revealed the presence of fungal elements while palmoplantar keratoderma biopsy showed an epidermotropic lymphocytic infiltrate in the superficial dermis evocative of mycosis fungoides. Blood tests showed a white cell count of 28 600/mm3 with 14% circulating Sezary cells and a T-cell clone. The T-cell lymphoma was treated with methotrexate, but the disease worsened a few months later, progressing to CD30- large T-cell pleomorphic lymphoma. The patient died of severe sepsis. Case No 2:A 60-year-old man presented a macular rash over the face, trunk and skinfolds as well as erythematous scaly annular plaques of the glabrous skin with lymphadenopathy. Cultures of skin scrapings were all positive for Candida albicans. Blood tests showed a white cell count of 15 000/mm3 with 30% circulating Sezary cells. A trunk patch biopsy revealed the histological appearance of mycosis fungoides. There was a T-cell clone in the peripheral blood and skin. In both cases, the patients presented with widespread annular and erythematous scaly lesions of the glabrous skin and skinfolds with evidence of Candida albicans on fungal tests of all skin scrapings. The discovery of circulating Sezary cells on a systematic smear for hyperleukocytosis led us to suspect underlying cutaneous T-cell lymphoma, which was confirmed by biopsy of the skin lesions accompanying

  2. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

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    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  3. The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification

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    Vinogradov Serge N

    2008-10-01

    Full Text Available Abstract Background Globin isoforms with variant properties and functions have been found in the pseudocoel, body wall and cuticle of various nematode species and even in the eyespots of the insect-parasite Mermis nigrescens. In fact, much higher levels of complexity exist, as shown by recent whole genome analysis studies. In silico analysis of the genome of Caenorhabditis elegans revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles. Results In the present study we have analyzed whole genomic data from C. briggsae, C. remanei, Pristionchus pacificus and Brugia malayi and EST data from several other nematode species to study the evolutionary history of the nematode globin gene family. We find a high level of conservation of the C. elegans globin complement, with even distantly related nematodes harboring orthologs to many Caenorhabditis globins. Bayesian phylogenetic analysis resolves all nematode globins into two distinct globin classes. Analysis of the globin intron-exon structures suggests extensive loss of ancestral introns and gain of new positions in deep nematode ancestors, and mainly loss in the Caenorhabditis lineage. We also show that the Caenorhabditis globin genes are expressed in distinct, mostly non-overlapping, sets of cells and that they are all under strong purifying selection. Conclusion Our results enable reconstruction of the evolutionary history of the globin gene family in the nematode phylum. A duplication of an ancestral globin gene occurred before the divergence of the Platyhelminthes and the Nematoda and one of the duplicated genes radiated further in the nematode phylum before the split of the Spirurina and Rhabditina and was followed by further radiation in the lineage leading to Caenorhabditis. The resulting globin genes were subject to processes of subfunctionalization and diversification leading to cell

  4. Extensive hydrothermal activity in the NE Lau basin revealed by ROV dives

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    Embley, R. W.; Resing, J. A.; Tebo, B.; Baker, E. T.; Butterfield, D. A.; Chadwick, B.; Davis, R.; de Ronde, C. E. J.; Lilley, M. D.; Lupton, J. E.; Merle, S. G.; Rubin, K. H.; Shank, T. M.; Walker, S. L.; Arculus, R. J.; Bobbitt, A. M.; Buck, N. J.; Caratori Tontini, F.; Crowhurst, P. V.; Mitchell, E.; Olson, E. J.; Ratmeyer, V.; Richards, S.; Roe, K. K.; Kenner-Chavis, P.; Martinez-Lyons, A.; Sheehan, C.; Brian, R.

    2014-12-01

    Dives with the QUEST 4000 ROV (Remotely Operated Vehicle) in September 2012 discovered nine hydrothermal sites in the arc and rear-arc region of the NE Lau Basin in 1150 m to 2630 m depth. These sites, originally detected by water column and seafloor surveys conducted in 2008-2011, include: (1) a paired sulfur-rich/black smoker field on the summit of a tectonically deformed magmatic arc volcano (Niua), (2) fracture-controlled black smoker venting on several small en echelon seamounts (north Matas) that lie between the magmatic arc and the backarc spreading center and (3) a magmatic degassing site on the summit of a dacite cone within a large (~12 km diameter) caldera volcano (Niuatahi). Dives at West Mata Seamount, which was undergoing strombolian volcanic activity and effusive rift-zone eruptions from 2008 to 2010, revealed a dormant volcanic phase in September 2012, with continued low-temperature diffuse venting. The high-temperature venting is likely driven by magmatic heat indicative of underlying partial melt zones and/or melt pockets distributed through the region. The occurrence of the youngest known boninite eruptions on the Mata volcanoes is consistent with subduction fluid flux melting extending into the rear-arc zone. Extension related to the transition from subduction to strike-slip motion of the northern Tonga Arc over the active Subduction-Transform Edge Propagator (STEP) fault probably contributes to the enhanced volcanism/hydrothermal activity in the NE Lau Basin. Chemosynthetic ecosystems at these sites range from mostly motile, lower diversity ecosystems at the eruptive/magmatically-degassing sites to higher diversity ecosystems with less mobile faunal components at the black-smoker systems. The wide range of fluid chemistry, water depth and geologic settings of the hydrothermal systems in this area provides an intriguing template to study the interaction of hydrothermal fluid chemistry, chemosynthetic habitats and their geologic underpinning

  5. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae.

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    Xiujuan Wang

    Full Text Available Two major transitions in animal evolution--the origins of multicellularity and bilaterality--correlate with major changes in mitochondrial DNA (mtDNA organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida. Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements

  6. High extensibility of stress fibers revealed by in vitro micromanipulation with fluorescence imaging

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    Matsui, Tsubasa S. [Department of Biomolecular Sciences, Tohoku University (Japan); Sato, Masaaki [Department of Biomedical Engineering, Tohoku University (Japan); Department of Bioengineering and Robotics, Tohoku University (Japan); Deguchi, Shinji, E-mail: deguchi@nitech.ac.jp [Department of Bioengineering and Robotics, Tohoku University (Japan)

    2013-05-10

    Highlights: •We isolate contractile stress fibers from vascular smooth muscle cells. •We measure the extensibility of individual stress fibers. •We present the first direct evidence that individual stress fibers are highly extensible. •We quantitatively determine the local strain along the length of stress fibers. •The high extensibility we found is beyond that explained by a conventional model. -- Abstract: Stress fibers (SFs), subcellular bundles of actin and myosin filaments, are physically connected at their ends to cell adhesions. The intracellular force transmitted via SFs plays an essential role in cell adhesion regulation and downstream signaling. However, biophysical properties intrinsic to individual SFs remain poorly understood partly because SFs are surrounded by other cytoplasmic components that restrict the deformation of the embedded materials. To characterize their inherent properties independent of other structural components, we isolated SFs from vascular smooth muscle cells and mechanically stretched them by in vitro manipulation while visualizing strain with fluorescent quantum dots attached along their length. SFs were elongated along their entire length, with the length being approximately 4-fold of the stress-free length. This surprisingly high extensibility was beyond that explained by the tandem connection of actin filaments and myosin II bipolar filaments present in SFs, thus suggesting the involvement of other structural components in their passive biophysical properties.

  7. VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

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    Yiqing Xu

    2016-01-01

    Full Text Available Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG and vector graphic (SVG, EPS, and PDF. Result. Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.

  8. Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini

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    Cristiani Gifalli-Iughetti

    2009-01-01

    Full Text Available In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus, Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62. The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates.

  9. GSV: a web-based genome synteny viewer for customized data

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    Bierschank Ezekiel

    2011-08-01

    Full Text Available Abstract Background The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis. Results We have developed the web-based Genome Synteny Viewer (GSV that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation. Conclusions GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas-bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations.

  10. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

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    Brown, Kim H.; Dobrinski, Kimberly P.; Gokcumen, Omer; Mills, Ryan E.; Shi, Xinghua; Chong, Wilson W. S.; Chen, Jin Yun Helen; Yoo, Paulo; David, Sthuthi; Peterson, Samuel M.; Raj, Towfique; Choy, Kwong Wai; Stranger, Barbara E.; Williamson, Robin E.; Zon, Leonard I.; Freeman, Jennifer L.; Lee, Charles

    2012-01-01

    Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases. PMID:22203992

  11. Crystal structure of Venezuelan hemorrhagic fever virus fusion glycoprotein reveals a class 1 postfusion architecture with extensive glycosylation.

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    Parsy, Marie-Laure; Harlos, Karl; Huiskonen, Juha T; Bowden, Thomas A

    2013-12-01

    Guanarito virus (GTOV) is an emergent and deadly pathogen. We present the crystal structure of the glycosylated GTOV fusion glycoprotein to 4.1-Å resolution in the postfusion conformation. Our structure reveals a classical six-helix bundle and presents direct verification that New World arenaviruses exhibit class I viral membrane fusion machinery. The structure provides visualization of an N-linked glycocalyx coat, and consideration of glycan dynamics reveals extensive coverage of the underlying protein surface, following virus-host membrane fusion.

  12. Conserved synteny in rat and mouse for a blood pressure QTL on human chromosome 17.

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    Zimdahl, Heike; Kreitler, Thomas; Gösele, Claudia; Ganten, Detlev; Hübner, Norbert

    2002-06-01

    Evidence for blood pressure quantitative trait loci (QTLs) on rat chromosome 10 has been found in multiple independent studies. Analysis of the homologous region on human chromosome 17 revealed significant linkage to blood pressure. The critical segment on human chromosome 17 spans a large interval containing the genes Itga2b, Gfap, and Itgb3. Therefore, findings in the rat may help to refine the position of blood pressure-regulating loci, assuming a common molecular cause across species. However, it has recently been suggested that the gene order in human, rat, and mouse is not conserved in this region, leaving uncertainty about the overlap of the blood pressure- regulating region between human chromosome 17 and rat chromosome 10. We have performed a detailed comparative analysis among human, mouse, and rat, defining the segment in question, by obtaining gene structure information in silico and by radiation hybrid mapping. It is of interest that this region also contains Wnk4, a gene previously identified to cause pseudohypoaldosteronism type II and human hypertension. Our results definitively show that the conserved synteny extends among human chromosome 17, rat chromosome 10, and mouse chromosome 11, demonstrating an overlap between previously localized blood pressure QTLs in humans and rats.

  13. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae.

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    Kiley A Hicks

    Full Text Available We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.

  14. Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae, a genus that has undergone rapid radiation.

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    Dongshi Wan

    Full Text Available BACKGROUND: During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively. CONCLUSIONS: These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.

  15. Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma.

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    Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F; Breen, Matthew

    2014-09-01

    Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.

  16. Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.

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    Dolja, Valerian V; Koonin, Eugene V

    2017-11-08

    Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  17. Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper.

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    Stefanie Kaufmann

    Full Text Available High-quality mapping of genomic regions and genes between two organisms is an indispensable prerequisite for evolutionary analyses and comparative genomics. Existing approaches to this problem focus on either delineating orthologs or finding extended sequence regions of common evolutionary origin (syntenic blocks. We propose SyntenyMapper, a novel tool for refining predefined syntenic regions. SyntenyMapper creates a set of blocks with conserved gene order between two genomes and finds all minor rearrangements that occurred since the evolutionary split of the two species considered. We also present TrackMapper, a SyntenyMapper-based tool that allows users to directly compare genome features, such as histone modifications, between two organisms, and identify genes with highly conserved features. We demonstrate SyntenyMapper's advantages by conducting a large-scale analysis of micro-rearrangements within syntenic regions of 25 eukaryotic species. Unsurprisingly, the number and length of syntenic regions is correlated with evolutionary distance, while the number of micro-rearrangements depends only on the size of the harboring region. On the other hand, the size of rearranged regions remains relatively constant regardless of the evolutionary distance between the organisms, implying a length constraint in the rearrangement process. SyntenyMapper is a useful software tool for both large-scale and gene-centric genome comparisons.

  18. In Vivo Microscopy Reveals Extensive Embedding of Capillaries within the Sarcolemma of Skeletal Muscle Fibers

    Science.gov (United States)

    Glancy, Brian; Hsu, Li-Yueh; Dao, Lam; Bakalar, Matthew; French, Stephanie; Chess, David J.; Taylor, Joni L.; Picard, Martin; Aponte, Angel; Daniels, Mathew P.; Esfahani, Shervin; Cushman, Samuel; Balaban, Robert S.

    2013-01-01

    Objective To provide insight into mitochondrial function in vivo, we evaluated the 3D spatial relationship between capillaries, mitochondria, and muscle fibers in live mice. Methods 3D volumes of in vivo murine Tibialis anterior muscles were imaged by multi-photon microscopy (MPM). Muscle fiber type, mitochondrial distribution, number of capillaries, and capillary-to-fiber contact were assessed. The role of myoglobin-facilitated diffusion was examined in myoglobin knockout mice. Distribution of GLUT4 was also evaluated in the context of the capillary and mitochondrial network. Results MPM revealed that 43.6 ± 3.3% of oxidative fiber capillaries had ≥ 50% of their circumference embedded in a groove in the sarcolemma, in vivo. Embedded capillaries were tightly associated with dense mitochondrial populations lateral to capillary grooves and nearly absent below the groove. Mitochondrial distribution, number of embedded capillaries, and capillary-to-fiber contact were proportional to fiber oxidative capacity and unaffected by myoglobin knockout. GLUT4 did not preferentially localize to embedded capillaries. Conclusions Embedding capillaries in the sarcolemma may provide a regulatory mechanism to optimize delivery of oxygen to heterogeneous groups of muscle fibers. We hypothesize that mitochondria locate to paravascular regions due to myofibril voids created by embedded capillaries, not to enhance the delivery of oxygen to the mitochondria. PMID:25279425

  19. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    Science.gov (United States)

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

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    Huang Yong

    2009-11-01

    Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

  1. Biocytin filling of adult gonadotropin-releasing hormone neurons in situ reveals extensive, spiny, dendritic processes.

    Science.gov (United States)

    Campbell, Rebecca E; Han, Seong-Kyu; Herbison, Allan E

    2005-03-01

    Ultrastructural studies suggest that GnRH neurons receive relatively few synaptic inputs. However, these techniques are biased toward the analysis of portions of the neuron containing GnRH peptide. Using acute brain slices prepared from transgenic GnRH-green fluorescent protein mice, individual fluorescing GnRH neurons were identified, patched, and filled with the small-molecular-weight dye biocytin. Cells were subsequently visualized with an avidin-conjugated fluorophore, and their morphological characteristics were analyzed by confocal microscopy. In total, 45 GnRH neurons from seven adult male and eight diestrus female mice were examined. Unexpectedly, we found that GnRH neurons possess remarkably long dendritic processes, in some cases extending over 1000 microm distal to the cell body. The somata and dendrites of all GnRH neurons were decorated with an assortment of spine-like protrusions, including filopodia, in an heterogeneous manner. Overall, GnRH neurons had a mean dendritic spine density of 0.4 spines/microm, with the highest densities found in the first 50 microm of the dendrite. GnRH neurons with dendrites running in a horizontal orientation had significantly (P < 0.05) more spines than dendrites with a vertical orientation. The comparison of male and female GnRH neurons revealed no sexually differentiated characteristics of somal or dendritic spine density. Using a technique in which the full extent of the GnRH neuron can be visualized, we demonstrate here a previously unrecognized GnRH neuron morphology of long dendrites covered in spines. These observations suggest that GnRH neurons are not poorly innervated and that they receive abundant excitatory synaptic inputs.

  2. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    Directory of Open Access Journals (Sweden)

    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  3. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

    Directory of Open Access Journals (Sweden)

    Jason Carnes

    2015-01-01

    Full Text Available Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA. In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  4. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

    Science.gov (United States)

    Carnes, Jason; Anupama, Atashi; Balmer, Oliver; Jackson, Andrew; Lewis, Michael; Brown, Rob; Cestari, Igor; Desquesnes, Marc; Gendrin, Claire; Hertz-Fowler, Christiane; Imamura, Hideo; Ivens, Alasdair; Kořený, Luděk; Lai, De-Hua; MacLeod, Annette; McDermott, Suzanne M; Merritt, Chris; Monnerat, Severine; Moon, Wonjong; Myler, Peter; Phan, Isabelle; Ramasamy, Gowthaman; Sivam, Dhileep; Lun, Zhao-Rong; Lukeš, Julius; Stuart, Ken; Schnaufer, Achim

    2015-01-01

    Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  5. FISH mapping of 57 BAC clones reveals strong conservation of synteny between Galliformes and Anseriformes

    NARCIS (Netherlands)

    Fillon, V.; Vignoles, M.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Zoorob, R.; Vignal, A.

    2007-01-01

    Karyotypes of chicken (Gallus gallus domesticus; 2n = 78) and mallard duck (Anas platyrhynchos; 2n = 80) share the typical organization of avian karyotypes including a few macrochromosome pairs, numerous indistinguishable microchromosomes, and Z and W sex chromosomes. Previous banding studies

  6. Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.

    Science.gov (United States)

    Semeria, Magali; Tannier, Eric; Guéguen, Laurent

    2015-01-01

    Most models of genome evolution concern either genetic sequences, gene content or gene order. They sometimes integrate two of the three levels, but rarely the three of them. Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content. We propose a probabilistic evolutionary model for gene neighborhoods, allowing genes to be inserted, duplicated or lost. It uses reconciled phylogenies, which integrate sequence and gene content evolution. We are then able to optimize parameters such as phylogeny branch lengths, or probabilistic laws depicting the diversity of susceptibility of syntenic regions to rearrangements. We reconstruct a structure for ancestral genomes by optimizing a likelihood, keeping track of all evolutionary events at the level of gene content and gene synteny. Ancestral syntenies are associated with a probability of presence.

  7. A synteny-based draft genome sequence of the forage grass Lolium perenne

    OpenAIRE

    Byrne Stephen L.; Nagy Istvan; Pfeifer Matthisas; Armstead Ian; Swain Suresh; Studer Bruno; Mayer Klaus; Campbell Jacqueline D.; Czaban Adrian; Hentrup Stephan; Paniz Frank; Bendixen Christian; Hedegaard Jakob; Caccamo Mario; Asp Torben

    2015-01-01

    Here we report the draft genome sequence of perennial ryegrass (Lolium perenne) an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It is classified along with wheat barley oats and Brachypodium distachyon in the Pooideae sub family of the grass family (Poaceae). Transcriptome data was used to identify 28 455 gene models and we utilized macro co linearity between perennial ryegrass and barley and synteny within the grass family to ...

  8. Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.

    Science.gov (United States)

    Waszak, Sebastian M; Hasin, Yehudit; Zichner, Thomas; Olender, Tsviya; Keydar, Ifat; Khen, Miriam; Stütz, Adrian M; Schlattl, Andreas; Lancet, Doron; Korbel, Jan O

    2010-11-11

    Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95-99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ~15% and ~20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high

  9. Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis.

    Science.gov (United States)

    Liu, Shuai; Zhou, Xiaosu; Hao, Lili; Piao, Xianyu; Hou, Nan; Chen, Qijun

    2017-01-01

    Alternative splicing (AS), as one of the most important topics in the post-genomic era, has been extensively studied in numerous organisms. However, little is known about the prevalence and characteristics of AS in Echinococcus species, which can cause significant health problems to humans and domestic animals. Based on high-throughput RNA-sequencing data, we performed a genome-wide survey of AS in two major pathogens of echinococcosis-Echinococcus granulosus and Echinococcus multilocularis. Our study revealed that the prevalence and characteristics of AS in protoscoleces of the two parasites were generally consistent with each other. A total of 6,826 AS events from 3,774 E. granulosus genes and 6,644 AS events from 3,611 E. multilocularis genes were identified in protoscolex transcriptomes, indicating that 33-36% of genes were subject to AS in the two parasites. Strikingly, intron retention instead of exon skipping was the predominant type of AS in Echinococcus species. Moreover, analysis of the Kyoto Encyclopedia of Genes and Genomes pathway indicated that genes that underwent AS events were significantly enriched in multiple pathways mainly related to metabolism (e.g., purine, fatty acid, galactose, and glycerolipid metabolism), signal transduction (e.g., Jak-STAT, VEGF, Notch, and GnRH signaling pathways), and genetic information processing (e.g., RNA transport and mRNA surveillance pathways). The landscape of AS obtained in this study will not only facilitate future investigations on transcriptome complexity and AS regulation during the life cycle of Echinococcus species, but also provide an invaluable resource for future functional and evolutionary studies of AS in platyhelminth parasites.

  10. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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    Alexander H. Li

    2017-10-01

    Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

  11. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns.

    Science.gov (United States)

    Li, Alexander H; Hanchard, Neil A; Furthner, Dieter; Fernbach, Susan; Azamian, Mahshid; Nicosia, Annarita; Rosenfeld, Jill; Muzny, Donna; D'Alessandro, Lisa C A; Morris, Shaine; Jhangiani, Shalini; Parekh, Dhaval R; Franklin, Wayne J; Lewin, Mark; Towbin, Jeffrey A; Penny, Daniel J; Fraser, Charles D; Martin, James F; Eng, Christine; Lupski, James R; Gibbs, Richard A; Boerwinkle, Eric; Belmont, John W

    2017-10-31

    Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5-6.5). Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene

  12. A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits.

    Science.gov (United States)

    Książkiewicz, Michał; Nazzicari, Nelson; Yang, Hua'an; Nelson, Matthew N; Renshaw, Daniel; Rychel, Sandra; Ferrari, Barbara; Carelli, Maria; Tomaszewska, Magdalena; Stawiński, Stanisław; Naganowska, Barbara; Wolko, Bogdan; Annicchiarico, Paolo

    2017-11-10

    White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L. angustifolius L.) genomes. Mapping of white lupin quantitative trait loci (QTLs) revealed polygenic control of vernalization responsiveness and anthracnose resistance, as well as a single locus regulating seed alkaloid content. We found high sequence collinearity between white and narrow-leafed lupin genomes. Interestingly, the white lupin QTLs did not correspond to previously mapped narrow-leafed lupin loci conferring vernalization independence, anthracnose resistance, low alkaloids and Phomopsis stem blight resistance, highlighting different genetic control of these traits. Our suite of allele-sequenced and PCR validated markers tagging these QTLs is immediately applicable for marker-assisted selection in white lupin breeding. The consensus map constitutes a platform for synteny-based gene cloning approaches and can support the forthcoming white lupin genome sequencing efforts.

  13. Integrated maps in quail (Coturnix japonica confirm the high degree of synteny conservation with chicken (Gallus gallus despite 35 million years of divergence

    Directory of Open Access Journals (Sweden)

    Vignoles Matthieu

    2006-05-01

    Full Text Available Abstract Background By comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected. From a more practical point of view, the definition of conserved syntenies helps to predict the position of genes in quail, based on information taken from the chicken sequence, thus enhancing the utility of this species in biological studies through a better knowledge of its genome structure. A microsatellite and an Amplified Fragment Length Polymorphism (AFLP genetic map were previously published for quail, as well as comparative cytogenetic data with chicken for macrochromosomes. Quail genomics will benefit from the extension and the integration of these maps. Results The integrated linkage map presented here is based on segregation analysis of both anonymous markers and functional gene loci in 1,050 quail from three independent F2 populations. Ninety-two loci are resolved into 14 autosomal linkage groups and a Z chromosome-specific linkage group, aligned with the quail AFLP map. The size of linkage groups ranges from 7.8 cM to 274.8 cM. The total map distance covers 904.3 cM with an average spacing of 9.7 cM between loci. The coverage is not complete, as macrochromosome CJA08, the gonosome CJAW and 23 microchromosomes have no marker assigned yet. Significant sequence identities of quail markers with chicken enabled the alignment of the quail linkage groups on the chicken genome sequence assembly. This, together with interspecific Fluorescence In Situ Hybridization (FISH, revealed very high similarities in marker order between the two species for the eight macrochromosomes and the 14 microchromosomes studied. Conclusion Integrating the two microsatellite and the AFLP quail genetic maps greatly enhances the quality of the resulting information and will thus facilitate the identification of Quantitative Trait Loci (QTL. The alignment with the

  14. Extensive Direct Subcortical Cerebellum-Basal Ganglia Connections in Human Brain as Revealed by Constrained Spherical Deconvolution Tractography.

    Science.gov (United States)

    Milardi, Demetrio; Arrigo, Alessandro; Anastasi, Giuseppe; Cacciola, Alberto; Marino, Silvia; Mormina, Enricomaria; Calamuneri, Alessandro; Bruschetta, Daniele; Cutroneo, Giuseppina; Trimarchi, Fabio; Quartarone, Angelo

    2016-01-01

    The connections between the cerebellum and basal ganglia were assumed to occur at the level of neocortex. However evidences from animal data have challenged this old perspective showing extensive subcortical pathways linking the cerebellum with the basal ganglia. Here we tested the hypothesis if these connections also exist between the cerebellum and basal ganglia in the human brain by using diffusion magnetic resonance imaging and tractography. Fifteen healthy subjects were analyzed by using constrained spherical deconvolution technique obtained with a 3T magnetic resonance imaging scanner. We found extensive connections running between the subthalamic nucleus and cerebellar cortex and, as novel result, we demonstrated a direct route linking the dentate nucleus to the internal globus pallidus as well as to the substantia nigra. These findings may open a new scenario on the interpretation of basal ganglia disorders.

  15. A synteny-based draft genome sequence of the forage grass Lolium perenne.

    Science.gov (United States)

    Byrne, Stephen L; Nagy, Istvan; Pfeifer, Matthias; Armstead, Ian; Swain, Suresh; Studer, Bruno; Mayer, Klaus; Campbell, Jacqueline D; Czaban, Adrian; Hentrup, Stephan; Panitz, Frank; Bendixen, Christian; Hedegaard, Jakob; Caccamo, Mario; Asp, Torben

    2015-11-01

    Here we report the draft genome sequence of perennial ryegrass (Lolium perenne), an economically important forage and turf grass species that is widely cultivated in temperate regions worldwide. It is classified along with wheat, barley, oats and Brachypodium distachyon in the Pooideae sub-family of the grass family (Poaceae). Transcriptome data was used to identify 28,455 gene models, and we utilized macro-co-linearity between perennial ryegrass and barley, and synteny within the grass family, to establish a synteny-based linear gene order. The gametophytic self-incompatibility mechanism enables the pistil of a plant to reject self-pollen and therefore promote out-crossing. We have used the sequence assembly to characterize transcriptional changes in the stigma during pollination with both compatible and incompatible pollen. Characterization of the pollen transcriptome identified homologs to pollen allergens from a range of species, many of which were expressed to very high levels in mature pollen grains, and are potentially involved in the self-incompatibility mechanism. The genome sequence provides a valuable resource for future breeding efforts based on genomic prediction, and will accelerate the development of new varieties for more productive grasslands. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  16. A perennial ryegrass CBF gene cluster is located in a region predicted by conserved synteny between Poaceae species.

    Science.gov (United States)

    Tamura, K; Yamada, T

    2007-01-01

    CBF/DREB1 proteins are the most important regulators of the cold temperature signaling pathway in many plants. CBF genes are candidates for low-temperature tolerance QTL in wheat and barley. Ten novel putative CBF cDNAs of perennial ryegrass (Lolium perenne L.) have been isolated from cold-treated leaf tissue. Their primary structures contain some conserved motifs, characteristic of the gene class. Phylogenetic analysis revealed that LpCBF genes were attributable to the HvCBF3-, and HvCBF4-subgroups following the previously proposed classification of barley CBF genes. RT-PCR analysis revealed that the expression of LpCBF genes was rapidly induced in response to low temperature and that the expression pattern under the low-temperature conditions for a long period was different between the various LpCBF genes. Five of the ten LpCBF genes were assigned to the genetic linkage map using the p150/112 reference mapping population. LpCBFIb, LpCBFII, LpCBFIIIb and LpCBFIIIc were mapped on LG5 forming a cluster within 2.2 cM, while LpCBFVb was located on LG1. Based on comparative genetic studies, conserved synteny for CBF gene family was observed between the Triticeae cereals and perennial ryegrass. Information on the perennial ryegrass CBF genes at both the molecular and genetic level obtained in this study would be useful for the further study on the role of CBF genes and low-temperature tolerance in grasses.

  17. Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC.

    Science.gov (United States)

    Totten, Sarah M; Feasley, Christa L; Bermudez, Abel; Pitteri, Sharon J

    2017-03-03

    Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.

  18. Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua - Conserved synteny between fish monolobal and tetrapod bilobal transferrin loci

    Directory of Open Access Journals (Sweden)

    Tooming-Klunderud Ave

    2011-05-01

    Full Text Available Abstract Background The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. Results The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2, a melanotransferrin gene (MTf, and a monolobal transferrin gene (Omp. Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE and Northwest (NW Atlantic populations revealed 22 single nucleotide polymorphisms (SNP causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. Conclusions The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest

  19. Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua)--conserved synteny between fish monolobal and tetrapod bilobal transferrin loci.

    Science.gov (United States)

    Andersen, Øivind; De Rosa, Maria Cristina; Pirolli, Davide; Tooming-Klunderud, Ave; Petersen, Petra E; André, Carl

    2011-05-25

    The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in

  20. Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua) - Conserved synteny between fish monolobal and tetrapod bilobal transferrin loci

    Science.gov (United States)

    2011-01-01

    Background The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. Results The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. Conclusions The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive

  1. The initiation and tectonic regimes of the Cenozoic extension in the Bohai Bay Basin, North China revealed by numerical modelling

    Science.gov (United States)

    Li, Lu; Qiu, Nansheng

    2017-06-01

    In this study the dynamic aspects of the Cenozoic extension in the Bohai Bay Basin are considered in the context of initial thickness of the crust and lithosphere, tectonic force, strain rate and thermal rheology, which are directly or indirectly estimated from a pure shear extensional model. It is accordingly reasonable to expect that, in the Bohai Bay Basin, the thickness variation could be present prior to the initiation of extension. The extensional deformation is localized by a thickness variation of the crust and lithosphere and the heterogeneity of the initial thickness plays an important role in rifting dynamics. The onset of rifting requires a critical tectonic force (initial tectonic force) to be applied, which then immediately begins to decay gradually. Rifting will only occur when the total effective buoyancy force of the subducting slab reaches a critical level, after a certain amount of subduction taking place. The magnitude of the tectonic force decreases with time in the early phase of rifting, which indicates the weakening due to the increase in geothermal gradient. In order to deform the continental lithosphere within the currently accepted maximum magnitude of the force derived from subducted slab roll-back, the following conditions should be satisfied: (1) the thickness of the continental lithosphere is significantly thin and less than 125 km and (2) the lithosphere has a wet and hot rheology, which provides implications for rheological layering in continental lithosphere. Our results are strongly supported by the ;crème brûlée; model, in which the lower crust and mantle are relatively ductile.

  2. A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts.

    Science.gov (United States)

    Guyomard, René; Boussaha, Mekki; Krieg, Francine; Hervet, Caroline; Quillet, Edwige

    2012-03-16

    Rainbow trout is an economically important fish and a suitable experimental organism in many fields of biology including genome evolution, owing to the occurrence of a salmonid specific whole-genome duplication (4th WGD). Rainbow trout is among some of the most studied teleosts and has benefited from substantial efforts to develop genomic resources (e.g., linkage maps. Here, we first generated a synthetic map by merging segregation data files derived from three independent linkage maps. Then, we used it to evaluate genome conservation between rainbow trout and three teleost models, medaka, stickleback and zebrafish and to further investigate the extent of the 4th WGD in trout genome. The INRA linkage map was updated by adding 211 new markers. After standardization of marker names, consistency of marker assignment to linkage groups and marker orders was checked across the three different data sets and only loci showing consistent location over all or almost all of the data sets were kept. This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM. Blastn searches against medaka, stickleback, and zebrafish genomic databases resulted in 778, 824 and 730 significant hits respectively while blastx searches yielded 505, 513 and 510 significant hits. Homology search results revealed that, for most rainbow trout chromosomes, large syntenic regions encompassing nearly whole chromosome arms have been conserved between rainbow trout and its closest models, medaka and stickleback. Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor. These syntenies consolidated the known homeologous affinities between rainbow trout chromosomes due to the 4th WGD and suggested new ones. The synthetic map constructed herein further highlights the stability of the teleost genome over long evolutionary time scales. This map can be easily extended by incorporating new data sets and should

  3. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

    Science.gov (United States)

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

    2016-12-01

    A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Live cell linear dichroism imaging reveals extensive membrane ruffling within the docking structure of natural killer cell immune synapses

    DEFF Research Database (Denmark)

    Benninger, Richard K P; Vanherberghen, Bruno; Young, Stephen

    2009-01-01

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted...... into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming...

  5. Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes

    Science.gov (United States)

    Sherman, David J.; Martin, Tiphaine; Nikolski, Macha; Cayla, Cyril; Souciet, Jean-Luc; Durrens, Pascal

    2009-01-01

    The Génolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of Hemiascomycete yeasts. The 2008 update to the Génolevures database provides four new genomes in complete (subtelomere to subtelomere) chromosome sequences, 50 000 protein-coding and tRNA genes, and in silico analyses for each gene element. A key element is a novel classification of conserved multi-species protein families and their use in detecting synteny, gene fusions and other aspects of genome remodeling in evolution. Our purpose is to release high-quality curated data from complete genomes, with a focus on the relations between genes, genomes and proteins. PMID:19015150

  6. Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.

    Science.gov (United States)

    Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues; Louis, Alexandra

    2018-01-04

    Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants, in an integrated evolutionary context. New analyses and visualization tools have recently been implemented in Genomicus Vertebrate. Karyotype structures from several genomes can now be compared along an evolutionary pathway (Multi-KaryotypeView), and synteny blocks can be computed and visualized between any two genomes (PhylDiagView). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Science.gov (United States)

    Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

    2015-01-01

    Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  8. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Directory of Open Access Journals (Sweden)

    Colin Southwell

    Full Text Available Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  9. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.

    Science.gov (United States)

    Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I

    2011-09-15

    Perturbations of the composition of the symbiotic intestinal microbiota can have profound consequences for host metabolism and immunity. In mice, segmented filamentous bacteria (SFB) direct the accumulation of potentially proinflammatory Th17 cells in the intestinal lamina propria. We present the genome sequence of SFB isolated from monocolonized mice, which classifies SFB phylogenetically as a unique member of Clostridiales with a highly reduced genome. Annotation analysis demonstrates that SFB depend on their environment for amino acids and essential nutrients and may utilize host and dietary glycans for carbon, nitrogen, and energy. Comparative analyses reveal that SFB are functionally related to members of the genus Clostridium and several pathogenic or commensal "minimal" genera, including Finegoldia, Mycoplasma, Borrelia, and Phytoplasma. However, SFB are functionally distinct from all 1200 examined genomes, indicating a gene complement representing biology relatively unique to their role as a gut commensal closely tied to host metabolism and immunity. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates

    Directory of Open Access Journals (Sweden)

    Bergthorsson Ulfar

    2011-09-01

    Full Text Available Abstract Background Duplicated genes frequently experience asymmetric rates of sequence evolution. Relaxed selective constraints and positive selection have both been invoked to explain the observation that one paralog within a gene-duplicate pair exhibits an accelerated rate of sequence evolution. In the majority of studies where asymmetric divergence has been established, there is no indication as to which gene copy, ancestral or derived, is evolving more rapidly. In this study we investigated the effect of local synteny (gene-neighborhood conservation and codon usage on the sequence evolution of gene duplicates in the S. cerevisiae genome. We further distinguish the gene duplicates into those that originated from a whole-genome duplication (WGD event (ohnologs versus small-scale duplications (SSD to determine if there exist any differences in their patterns of sequence evolution. Results For SSD pairs, the derived copy evolves faster than the ancestral copy. However, there is no relationship between rate asymmetry and synteny conservation (ancestral-like versus derived-like in ohnologs. mRNA abundance and optimal codon usage as measured by the CAI is lower in the derived SSD copies relative to ancestral paralogs. Moreover, in the case of ohnologs, the faster-evolving copy has lower CAI and lowered expression. Conclusions Together, these results suggest that relaxation of selection for codon usage and gene expression contribute to rate asymmetry in the evolution of duplicated genes and that in SSD pairs, the relaxation of selection stems from the loss of ancestral regulatory information in the derived copy.

  11. A functional screen reveals an extensive layer of transcriptional and splicing control underlying RAS/MAPK signaling in Drosophila.

    Directory of Open Access Journals (Sweden)

    Dariel Ashton-Beaucage

    2014-03-01

    Full Text Available The small GTPase RAS is among the most prevalent oncogenes. The evolutionarily conserved RAF-MEK-MAPK module that lies downstream of RAS is one of the main conduits through which RAS transmits proliferative signals in normal and cancer cells. Genetic and biochemical studies conducted over the last two decades uncovered a small set of factors regulating RAS/MAPK signaling. Interestingly, most of these were found to control RAF activation, thus suggesting a central regulatory role for this event. Whether additional factors are required at this level or further downstream remains an open question. To obtain a comprehensive view of the elements functionally linked to the RAS/MAPK cascade, we used a quantitative assay in Drosophila S2 cells to conduct a genome-wide RNAi screen for factors impacting RAS-mediated MAPK activation. The screen led to the identification of 101 validated hits, including most of the previously known factors associated to this pathway. Epistasis experiments were then carried out on individual candidates to determine their position relative to core pathway components. While this revealed several new factors acting at different steps along the pathway--including a new protein complex modulating RAF activation--we found that most hits unexpectedly work downstream of MEK and specifically influence MAPK expression. These hits mainly consist of constitutive splicing factors and thereby suggest that splicing plays a specific role in establishing MAPK levels. We further characterized two representative members of this group and surprisingly found that they act by regulating mapk alternative splicing. This study provides an unprecedented assessment of the factors modulating RAS/MAPK signaling in Drosophila. In addition, it suggests that pathway output does not solely rely on classical signaling events, such as those controlling RAF activation, but also on the regulation of MAPK levels. Finally, it indicates that core splicing

  12. Transcriptional Profiling of Coxiella burnetii Reveals Extensive Cell Wall Remodeling in the Small Cell Variant Developmental Form

    Science.gov (United States)

    Sandoz, Kelsi M.; Popham, David L.; Beare, Paul A.; Sturdevant, Daniel E.; Hansen, Bryan; Nair, Vinod; Heinzen, Robert A.

    2016-01-01

    A hallmark of Coxiella burnetii, the bacterial cause of human Q fever, is a biphasic developmental cycle that generates biologically, ultrastructurally, and compositionally distinct large cell variant (LCV) and small cell variant (SCV) forms. LCVs are replicating, exponential phase forms while SCVs are non-replicating, stationary phase forms. The SCV has several properties, such as a condensed nucleoid and an unusual cell envelope, suspected of conferring enhanced environmental stability. To identify genetic determinants of the LCV to SCV transition, we profiled the C. burnetii transcriptome at 3 (early LCV), 5 (late LCV), 7 (intermediate forms), 14 (early SCV), and 21 days (late SCV) post-infection of Vero epithelial cells. Relative to early LCV, genes downregulated in the SCV were primarily involved in intermediary metabolism. Upregulated SCV genes included those involved in oxidative stress responses, arginine acquisition, and cell wall remodeling. A striking transcriptional signature of the SCV was induction (>7-fold) of five genes encoding predicted L,D transpeptidases that catalyze nonclassical 3–3 peptide cross-links in peptidoglycan (PG), a modification that can influence several biological traits in bacteria. Accordingly, of cross-links identified, muropeptide analysis showed PG of SCV with 46% 3–3 cross-links as opposed to 16% 3–3 cross-links for LCV. Moreover, electron microscopy revealed SCV with an unusually dense cell wall/outer membrane complex as compared to LCV with its clearly distinguishable periplasm and inner and outer membranes. Collectively, these results indicate the SCV produces a unique transcriptome with a major component directed towards remodeling a PG layer that likely contributes to Coxiella’s environmental resistance. PMID:26909555

  13. Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

    Science.gov (United States)

    Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying; Liu, Chang; Lv, Aiping; Deng, Youping; Larson-Rabin, Zachary; Wilkinson, Mike; Chen, Shilin

    2012-01-01

    Background Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. Methodology/Principal Findings In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. Conclusions Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification. PMID:22952830

  14. Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs.

    Science.gov (United States)

    Khubrani, Yahya M; Wetton, Jon H; Jobling, Mark A

    2018-03-01

    Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler ® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler ® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler ® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for

  15. What do fault patterns reveal about the latest phase of extension within the Northern Snake Range metamorphic core complex, Nevada, USA?

    Science.gov (United States)

    Ismat, Zeshan; Riley, Paul; Lerback, Jory

    2016-08-01

    The Northern Snake Range is a classic example of a metamorphic core complex, Basin-and-Range province, United States. It is composed of a plastically deformed footwall and a brittlely deformed hanging wall, separated by the Northern Snake Range low-angle detachment (NSRD). Brittle deformation, however, is not confined to the hanging wall. This paper focuses on exposures in Cove Canyon, located on the SE flank of the Northern Snake Range, where penetrative, homogeneous faults are well exposed throughout the hanging wall, footwall and NSRD, and overprint early plastic deformation. These late-stage fault sets assisted Eocene-Miocene extension. Detailed analysis of the faults reveals the following: (1) The shortening direction defined by faults is similar to the shortening direction defined by the stretching lineation in the footwall mylonites, indicating that the extensional kinematic history remained unchanged as the rocks were uplifted into the elastico-frictional regime. (2) After ∼17 Ma, extension may have continued entirely within elastic-frictional regime via cataclastic flow. (3) This latest deformation phase may have been accommodated by a single, continuous event. (3) Faults within NSRD boudins indicate that deformation within the detachment zone was non-coaxial during the latest phase of extension.

  16. Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus

    Directory of Open Access Journals (Sweden)

    Matthew C. Hale

    2017-11-01

    Full Text Available Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq to generate a marker-dense genetic map for Brook Trout (Salvelinus fontinalis. The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.

  17. Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

    Energy Technology Data Exchange (ETDEWEB)

    Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis; Rubin, EdwardM.; Couronne, Olivier

    2005-06-13

    Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.

  18. A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

    Directory of Open Access Journals (Sweden)

    Tsalavouta Matina

    2007-02-01

    Full Text Available Abstract Background Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae. Results An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST that give a significant similarity hit to Tetraodon. Conclusion The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well

  19. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement

    Science.gov (United States)

    Hexaploid oat (Avena sativa, 2n = 6x = 42) is a member of the Poaceae family with a very large genome (~13 Gb) containing 21 chromosome pairs: seven from each of two similar ancestral diploids (A and D) and seven from a more diverged ancestral diploid (C). Physical rearrangements among ancestral oat...

  20. Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-01-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. PMID:21816873

  1. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-10-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction-mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.

  2. Comparison of different cells of Haematococcus pluvialis reveals an extensive acclimation mechanism during its aging process: from a perspective of photosynthesis.

    Directory of Open Access Journals (Sweden)

    Wenhui Gu

    Full Text Available Both biomass dominated green vegetative cells (GV and astaxanthin-dominated orange resting cells (OR affect the final astaxanthin yield in industry. Examination of Haematococcus pluvialis revealed that the OR cells greatly varied from the GV cells at both cellular and subcellular levels. In particular, the thylakoid membranes in the OR were disassembled and fragmented. Furthermore, the OR conserved most of the photosynthetic pigments, with elevated concentrations of violaxanthin, antheraxanthin, and neoxanthin. Notably, moderate photosynthesis was detected in OR, even though most of the thylakoid membranes were disassembled, when compared with those in the GV. However, the energy distribution pattern between photosystem I and II (PSI and PSII in the OR favored PSI, which was also confirmed by 77-K fluorescence. As zeaxanthin was not detected in the OR, we attribute the acclimation role to astaxanthin, instead of xanthophyll cycle. Additionally, proteomic-scale comparison analysis of thylakoids of the OR and GV indicated no photosynthetically remarkable variations. However, an extensive acclimation mechanism of H. pluvialis was proposed, in which proteins in thylakoid of GV were noted to be involved in biomass accumulation and those in OR were involved in stress response. Conclusions of the comparative analysis might provide some physiological background of OR for astaxanthin production by using H. pluvialis.

  3. Comparison of different cells of Haematococcus pluvialis reveals an extensive acclimation mechanism during its aging process: from a perspective of photosynthesis.

    Science.gov (United States)

    Gu, Wenhui; Xie, Xiujun; Gao, Shan; Zhou, Wei; Pan, Guanghua; Wang, Guangce

    2013-01-01

    Both biomass dominated green vegetative cells (GV) and astaxanthin-dominated orange resting cells (OR) affect the final astaxanthin yield in industry. Examination of Haematococcus pluvialis revealed that the OR cells greatly varied from the GV cells at both cellular and subcellular levels. In particular, the thylakoid membranes in the OR were disassembled and fragmented. Furthermore, the OR conserved most of the photosynthetic pigments, with elevated concentrations of violaxanthin, antheraxanthin, and neoxanthin. Notably, moderate photosynthesis was detected in OR, even though most of the thylakoid membranes were disassembled, when compared with those in the GV. However, the energy distribution pattern between photosystem I and II (PSI and PSII) in the OR favored PSI, which was also confirmed by 77-K fluorescence. As zeaxanthin was not detected in the OR, we attribute the acclimation role to astaxanthin, instead of xanthophyll cycle. Additionally, proteomic-scale comparison analysis of thylakoids of the OR and GV indicated no photosynthetically remarkable variations. However, an extensive acclimation mechanism of H. pluvialis was proposed, in which proteins in thylakoid of GV were noted to be involved in biomass accumulation and those in OR were involved in stress response. Conclusions of the comparative analysis might provide some physiological background of OR for astaxanthin production by using H. pluvialis.

  4. Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.

    Science.gov (United States)

    Singh, Param Priya; Arora, Jatin; Isambert, Hervé

    2015-07-01

    Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.

  5. Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.

    Directory of Open Access Journals (Sweden)

    Param Priya Singh

    2015-07-01

    Full Text Available Whole genome duplications (WGD have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.

  6. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in

  7. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

    OpenAIRE

    Mahadevan Padmanabhan; Seto Donald

    2010-01-01

    Abstract Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the v...

  8. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes.

    Directory of Open Access Journals (Sweden)

    Alexis P Yelton

    2011-10-01

    Full Text Available During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application.

  9. Genomic characterization of putative allergen genes in peach/almond and their synteny with apple

    Directory of Open Access Journals (Sweden)

    Weg Eric

    2008-11-01

    /almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other Prunus species.

  10. Variations in fault-slip data and cooling history reveal corridor of heterogeneous backarc extension in the eastern Aegean Sea region

    Science.gov (United States)

    Ring, Uwe; Gessner, Klaus; Thomson, Stuart

    2017-03-01

    We report fault-slip data across the boundary between the highly extended and largely submerged crust underlying the Aegean Sea from Samos in the north to eastern Crete in the south, and the much less extended and emergent crust of western Anatolia. We identify three brittle deformation increments, a late Miocene (mainly Pliocene) to Recent crustal stretching increment, an intermittent early to late Miocene shortening increment concurrent with extension and magmatism, and a Miocene extensional event. The youngest increment documents late Miocene to Recent NNE extension over large areas, but can locally also be oriented SE (Amorgos and Astipalea Islands), and ESE (eastern Crete) suggesting overall oblate strain geometry. The intermittent Miocene ( 24-5 Ma) fault-slip records suggest overall prolate strain geometry, where NNE stretching is accompanied by E-W shortening. The older extension event is mainly NNE directed but on Samos Island extension is E-W, probably reflecting local extension in a sinistral wrench corridor in the early/mid Miocene. Overall it seems that since the early Miocene NNE-trending extension is the dominant regime in the eastern Aegean with an intermittent component of short-lived E-W shortening. The existence of a corridor of heterogeneous crustal deformation - which is spatially associated with uncharacteristically old fission track ages - and the apparent change in strain geometry in time challenge concepts that propose that the eastern Aegean Sea and western Anatolia have been deformed as a continuous tectonic domain since the Miocene. We propose that the regional variation in extensional strain geometry resulted from a sinistral wrench component that was superimposed on the regional 'background' NNE extension by translation across a diffuse plate boundary. We conclude that the eastern shoreline of the Aegean Sea is controlled by a Miocene to Recent sinistral wrench corridor that accommodated movement between different lithospheric domains.

  11. LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Depuydt, Geert G.; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

    2014-02-20

    The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity and metabolism in C. elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass-spectrometry (LC-MS) based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2); daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the up-regulation of many core intermediary metabolic pathways. These include, glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complex I, II, III and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative for spatio-temporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves, possibly also shunting metabolites through alternative energy-generating pathways, in order to sustain longevity.

  12. LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Depuydt, Geert; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

    2014-04-04

    The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. Finally, this restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity.

  13. Creep, flow, and phase slippage regimes: an extensive view of the sliding charge-density wave revealed by coherent X-ray diffraction.

    Science.gov (United States)

    Pinsolle, E; Kirova, N; Jacques, V L R; Sinchenko, A A; Le Bolloc'h, D

    2012-12-21

    Coherent x-ray diffraction experiments have been used to probe the dynamics of the charge density wave (CDW) in the quasi-1D system NbSe(3). The 2k(F) satellite reflection associated with the CDW has been measured with respect to external dc currents, below and above the depinning current. These measurements illustrate for the first time the extensive behavior of a moving electronic crystal: the creep regime, with nucleation of CDW dislocations, the flow regime, with motional ordering, along with phase slippage and the role of strong pinning due to an extrinsic defect.

  14. Collision of extensive exocrine and neuroendocrine neoplasms in multiple endocrine neoplasia type 1 revealed by cytogenetic analysis of loss of heterozygosity: a case report.

    Science.gov (United States)

    Moriyoshi, Koki; Minamiguchi, Sachiko; Miyagawa-Hayashino, Aya; Fujimoto, Masakazu; Kawaguchi, Michiya; Haga, Hironori

    2013-09-01

    The combination of exocrine and neuroendocrine neoplasms is rarely found in the pancreas. These combined lesions vary from a clonal tumor with mixed differentiation to the incidental co-existence of two or more independent tumors, but the differential diagnosis is sometimes difficult. Here we report a case of multiple endocrine neoplasia type 1 (MEN1) with extensive ductal and neuroendocrine neoplastic changes. These two types of tumors admixed markedly in some parts, which made it difficult to determine the pathological diagnosis based on histological findings. Cytogenetic analysis showed that loss of heterozygosity (LOH) of the MEN1 locus exists in neuroendocrine but not in exocrine neoplasms, indicating that independent mechanisms of tumorigenesis may occur in these two types of tumors. This case shows the usefulness of cytogenetic analysis for the diagnosis of combined tumors of the pancreas. Extensive exocrine neoplastic change, including pancreatic intraepithelial neoplasia (PanIN) in virtually all pancreatic ducts and a focus of intraductal papillary mucinous neoplasm (IPMN) with focal invasion, was a distinguishing feature of the present case. The possible association of ductal tumorigenesis and a MEN1 background is discussed. © 2013 The Authors. Pathology International © 2013 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

  15. Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures

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    Vogel Hans J

    2008-01-01

    Full Text Available Abstract Background Opium poppy (Papaver somniferum produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a model system to study plant alkaloid metabolism. The plant is cultivated as the only commercial source of the narcotic analgesics morphine and codeine, but also produces many other alkaloids including the antimicrobial agent sanguinarine. Modulations in plant secondary metabolism as a result of environmental perturbations are often associated with the altered regulation of other metabolic pathways. As a key component of our functional genomics platform for opium poppy we have used proton nuclear magnetic resonance (1H NMR metabolomics to investigate the interplay between primary and secondary metabolism in cultured opium poppy cells treated with a fungal elicitor. Results Metabolite fingerprinting and compound-specific profiling showed the extensive reprogramming of primary metabolic pathways in association with the induction of alkaloid biosynthesis in response to elicitor treatment. Using Chenomx NMR Suite v. 4.6, a software package capable of identifying and quantifying individual compounds based on their respective signature spectra, the levels of 42 diverse metabolites were monitored over a 100-hour time course in control and elicitor-treated opium poppy cell cultures. Overall, detectable and dynamic changes in the metabolome of elicitor-treated cells, especially in cellular pools of carbohydrates, organic acids and non-protein amino acids were detected within 5 hours after elicitor treatment. The metabolome of control cultures also showed substantial modulations 80 hours after the start of the time course, particularly in the levels of amino acids and phospholipid pathway intermediates. Specific flux modulations were detected throughout primary metabolism, including glycolysis, the tricarboxylic acid cycle, nitrogen assimilation, phospholipid/fatty acid synthesis and the shikimate pathway, all of which

  16. A rapid, high-throughput viability assay for Blastocystis spp. reveals metronidazole resistance and extensive subtype-dependent variations in drug susceptibilities.

    Science.gov (United States)

    Mirza, Haris; Teo, Joshua D W; Upcroft, Jacqui; Tan, Kevin S W

    2011-02-01

    Blastocystis is an emerging protistan parasite of controversial pathogenesis. Although metronidazole (Mz) is standard therapy for Blastocystis infections, there have been accumulating reports of treatment failure, suggesting the existence of drug-resistant isolates. Furthermore, very little is known about Blastocystis susceptibility to standard antimicrobials. In the present study, we established resazurin and XTT viability microassays for Blastocystis spp. belonging to subtypes 4 and 7, both of which have been suggested to represent pathogenic zoonotic subtypes. The optimized resazurin assay was used to screen a total of 19 compounds against both subtypes. Interestingly, subtype 7 parasites were resistant to Mz, a 1-position-substituted 5-nitroimidazole (5-NI), while subtype 4 parasites were sensitive. Some cross-resistance was observed to tinidazole, another 1-position 5-NI. Conversely, subtype 4 parasites were resistant to emetine, while subtype 7 parasites were sensitive. Position 2 5-NIs were effective against both subtypes, as were ornidazole, nitazoxanide, furazolidone, mefloquine, quinicrine, quinine, cotrimoxazole (trimethoprim-sulfamethoxazole), and iodoacetamide. Both subtypes were resistant to chloroquine, doxycycline, paromomycin, ampicillin, and pyrimethamine. This is the first study to report extensive variations in drug sensitivities among two clinically important subtypes. Our study highlights the need to reevaluate established treatment regimens for Blastocystis infections and offers clear new treatment options for Mz treatment failures.

  17. Systematic examination of publicly-available information reveals the diverse and extensive corporate political activity of the food industry in Australia.

    Science.gov (United States)

    Mialon, Melissa; Swinburn, Boyd; Allender, Steven; Sacks, Gary

    2016-03-22

    The political influence of the food industry, referred to as corporate political activity (CPA), represents a potential barrier to the development and implementation of effective public health policies for non-communicable diseases prevention. This paper reports on the feasibility and limitations of using publicly-available information to identify and monitor the CPA of the food industry in Australia. A systematic search was conducted for information from food industry, government and other publicly-available data sources in Australia. Data was collected in relation to five key food industry actors: the Australian Food and Grocery Council; Coca Cola; McDonald's; Nestle; and Woolworths, for the period January 2012 to February 2015. Data analysis was guided by an existing framework for classifying CPA strategies of the food industry. The selected food industry actors used multiple CPA strategies, with 'information and messaging' and 'constituency building' strategies most prominent. The systematic analysis of publicly-available information over a limited period was able to identify diverse and extensive CPA strategies of the food industry in Australia. This approach can contribute to accountability mechanisms for NCD prevention.

  18. Systematic examination of publicly-available information reveals the diverse and extensive corporate political activity of the food industry in Australia

    Directory of Open Access Journals (Sweden)

    Melissa Mialon

    2016-03-01

    Full Text Available Abstract Background The political influence of the food industry, referred to as corporate political activity (CPA, represents a potential barrier to the development and implementation of effective public health policies for non-communicable diseases prevention. This paper reports on the feasibility and limitations of using publicly-available information to identify and monitor the CPA of the food industry in Australia. Methods A systematic search was conducted for information from food industry, government and other publicly-available data sources in Australia. Data was collected in relation to five key food industry actors: the Australian Food and Grocery Council; Coca Cola; McDonald’s; Nestle; and Woolworths, for the period January 2012 to February 2015. Data analysis was guided by an existing framework for classifying CPA strategies of the food industry. Results The selected food industry actors used multiple CPA strategies, with ‘information and messaging’ and ‘constituency building’ strategies most prominent. Conclusions The systematic analysis of publicly-available information over a limited period was able to identify diverse and extensive CPA strategies of the food industry in Australia. This approach can contribute to accountability mechanisms for NCD prevention.

  19. Abnormal microRNA-16 locus with synteny to human 13q14 linked to CLL in NZB mice.

    Science.gov (United States)

    Raveche, Elizabeth S; Salerno, Erica; Scaglione, Brian J; Manohar, Vijaya; Abbasi, Fatima; Lin, Yi-Chu; Fredrickson, Torgny; Landgraf, Pablo; Ramachandra, Sumant; Huppi, Konrad; Toro, Jorge R; Zenger, Vincent E; Metcalf, Robert A; Marti, Gerald E

    2007-06-15

    New Zealand black (NZB) mice with autoimmune and B lymphoproliferative disease (B-LPD) are a model for human chronic lymphocytic leukemia (CLL). A genomewide linkage scan of the NZB loci associated with lymphoma was conducted in F1 backcrosses of NZB and a control strain, DBA/2. Of 202 mice phenotyped for the presence or absence of LPD, surface maker expression, DNA content, and microsatellite polymorphisms, 74 had disease. The CD5(+), IgM(+), B220(dim), hyperdiploid LPD was linked to 3 loci on chromosomes 14, 18, and 19 that are distinct from previously identified autoimmunity-associated loci. The region of synteny with mouse D14mit160 is the human 13q14 region, associated with human CLL, containing microRNAs mir-15a16-1. DNA sequencing of multiple NZB tissues identified a point mutation in the 3' flanking sequence of the identical microRNA, mir-16-1, and this mutation was not present in other strains, including the nearest neighbor, NZW. Levels of miR-16 were decreased in NZB lymphoid tissue. Exogenous miR-16 delivered to an NZB malignant B-1 cell line resulted in cell-cycle alterations and increased apoptosis. Linkage of the mir-15a/16-1 complex and the development of B-LPD in this spontaneous mouse model suggest that the altered expression of the mir-15a/16-1 is the molecular lesion in CLL.

  20. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-03-01

    Background: Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multi-gene family. Although the function of the members of the PE_PGRS multi-gene family is not yet known, it is hypothesized that the PE_PGRS genes may be associated with genetic variability. Material and methods: Whole genome sequencing analysis was performed on (n= 37) extensively drug resistant (XDR) MTB strains from Pakistan which included Central Asian (n= 23), East African Indian (n= 2), X3 (n= 1), T group (n= 3) and Orphan (n= 8) MTB strains. Results: By analyzing 42 PE_PGRS genes, 111 SNPs were identified, of which 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in the PE_PGRS genes were as follows: 6, 9, 10 and 55 present in each of the CAS, EAI, Orphan, T1 and X3 XDR MTB strains studied. Deletions in PE_PGRS genes: 19, 21 and 23 were observed in 7 (35.0%) CAS1 and 3 (37.5%) in Orphan XDR MTB strains, while deletions in the PE_PGRS genes: 49 and 50 were observed in 36 (95.0%) CAS1 and all CAS, CAS2 and Orphan XDR MTB strains. An insertion in PE_PGRS6 gene was observed in all CAS, EAI3 and Orphan, while insertions in the PE_PGRS genes 19 and 33 were observed in 19 (95%) CAS1 and all CAS, CAS2, EAI3 and Orphan XDR MTB strains. Conclusion: Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs, Insertions and Deletions in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  1. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-01-21

    Background Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. Material and methods Whole genome sequencing analysis was performed on (n = 37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n = 2); Other lineage 1 (n = 3); Lineage 3 (Central Asian, n = 24); Other lineage 3 (n = 4); Lineage 4 (X3, n = 1) and T group (n = 3) MTB strains. Results There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes – 6, 9 and 10 – were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes – 3 and 19 – were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. Conclusion Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  2. SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome

    Directory of Open Access Journals (Sweden)

    Liu Bernard A

    2012-09-01

    Full Text Available Abstract Specific peptide ligand recognition by modular interaction domains is essential for the fidelity of information flow through the signal transduction networks that control cell behavior in response to extrinsic and intrinsic stimuli. Src homology 2 (SH2 domains recognize distinct phosphotyrosine peptide motifs, but the specific sites that are phosphorylated and the complement of available SH2 domains varies considerably in individual cell types. Such differences are the basis for a wide range of available protein interaction microstates from which signaling can evolve in highly divergent ways. This underlying complexity suggests the need to broadly map the signaling potential of systems as a prerequisite for understanding signaling in specific cell types as well as various pathologies that involve signal transduction such as cancer, developmental defects and metabolic disorders. This report describes interactions between SH2 domains and potential binding partners that comprise initial signaling downstream of activated fibroblast growth factor (FGF, insulin (Ins, and insulin-like growth factor-1 (IGF-1 receptors. A panel of 50 SH2 domains screened against a set of 192 phosphotyrosine peptides defines an extensive potential interactome while demonstrating the selectivity of individual SH2 domains. The interactions described confirm virtually all previously reported associations while describing a large set of potential novel interactions that imply additional complexity in the signaling networks initiated from activated receptors. This study of pTyr ligand binding by SH2 domains provides valuable insight into the selectivity that underpins complex signaling networks that are assembled using modular protein interaction domains.

  3. Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages

    Science.gov (United States)

    2014-01-01

    Background Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings. Results To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages. Conclusions We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration. PMID:24885550

  4. Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa

    Directory of Open Access Journals (Sweden)

    Keira A Cohen

    2015-01-01

    Full Text Available The largest global outbreak of extensively drug-resistant (XDR tuberculosis (TB was identified in Tugela Ferry, KwaZulu-Natal (KZN, South Africa in 2005. The antecedents and timing of the emergence of drug resistance in this fatal epidemic XDR outbreak are unknown, and it is unclear whether drug resistance in this region continues to be driven by clonal spread or by the development of de novo resistance. A whole genome sequencing and drug susceptibility testing (DST was performed on 337 clinical isolates of Mycobacterium tuberculosis (M.tb collected in KZN from 2008 to 2013, in addition to three historical isolates, one of which was isolated during the Tugela Ferry outbreak. Using a variety of whole genome comparative approaches, 11 drug-resistant clones of M.tb circulating from 2008 to 2013 were identified, including a 50-member clone of XDR M.tb that was highly related to the Tugela Ferry XDR outbreak strain. It was calculated that the evolutionary trajectory from first-line drug resistance to XDR in this clone spanned more than four decades and began at the start of the antibiotic era. It was also observed that frequent de novo evolution of MDR and XDR was present, with 56 and 9 independent evolutions, respectively. Thus, ongoing amplification of drug-resistance in KwaZulu-Natal is driven by both clonal spread and de novo acquisition of resistance. In drug-resistant TB, isoniazid resistance was overwhelmingly the initial resistance mutation to be acquired, which would not be detected by current rapid molecular diagnostics that assess only rifampicin resistance.

  5. Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites

    DEFF Research Database (Denmark)

    Boergesen, Michael; Pedersen, Thomas Åskov; Gross, Barbara

    2012-01-01

    The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs...... and correlate with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the roles of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligand-regulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily...... increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. Functional annotation of putative direct LXR target genes revealed a significant association with classical LXR-regulated pathways as well as peroxisome proliferator-activated receptor (PPAR...

  6. Deep-sequencing of Marburg virus genome during sequential mouse passaging and cell-culture adaptation reveals extensive changes over time.

    Science.gov (United States)

    Wei, Haiyan; Audet, Jonathan; Wong, Gary; He, Shihua; Huang, Xueyong; Cutts, Todd; Theriault, Steven; Xu, Bianli; Kobinger, Gary; Qiu, Xiangguo

    2017-06-13

    Marburg virus (MARV) has caused outbreaks of filoviral hemorrhagic fever since its discovery in 1967. The largest and deadliest outbreak occurred in Angola in 2005, with 252 cases and 227 deaths. In 2014, we developed a mouse-adapted MARV, Angola variant through serial passaging in mice. The mouse-adapted MARV exhibits many of the hallmarks of MARV disease in humans. By applying deep-sequencing to every passage of the virus, we are able to study virus evolution in this host with surprising precision. We show that two regions go through substantial changes: the intergenic region between NP and VP35, as well as the first 100 amino acids of the VP40 protein. Our results also reveal that there were profound changes during the production of the final virus stock in cell culture. Overall, our results show that a handful of regions carry most of the mutations acquired during the adaptation of the virus to a new host and that many mutations become fixed very early during the adaptation process.

  7. Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta).

    Science.gov (United States)

    Skaloud, Pavel; Peksa, Ondrej

    2010-01-01

    The genus Asterochloris is one of the most common lichen photobionts. We present a molecular investigation of 41 cultured strains, for which nuclear-encoded ITS rDNA and partial actin I sequences were determined. The loci studied revealed considerable differences in their evolutionary dynamics as well as sequence variation. As compared to ITS data, the actin sequences show much greater variation, and the phylogenies yield strong resolution and support of many internal branches. The partitioning of ITS dataset into several regions yielded better node resolution. We recognized 16 well-supported monophyletic lineages, of which one represents the type species of the genus (Asterochloris phycobiontica), and six correspond to species previously classified to the genus Trebouxia (T. erici, T. excentrica, T. glomerata, T. irregularis, T. italiana and T. magna). Only 15% of isolated photobionts considered in our study could be assigned with certainty to previously described species, emphasizing amazing cryptic variability in Asterochloris. Concurrently with the formal delimitation of the genus Asterochloris, we propose new combinations for the former Trebouxia species; furthermore, T. pyriformis is reduced to a synonym of A. glomerata. The present knowledge of global diversity of Asterochloris algae is discussed.

  8. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-01-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (FST = 0.01) and mitochondrial (ΦST = 0.47; FST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  9. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.

    Science.gov (United States)

    Cai, Lei; Tan, Dan; Aibaidula, Gulsimay; Dong, Xin-Ran; Chen, Jin-Chun; Tian, Wei-Dong; Chen, Guo-Qiang

    2011-11-01

    Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT) events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.

  10. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.

  11. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

    Science.gov (United States)

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A; Awosika, Joy; Briska, Adam; Ptashkin, Ryan N; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L; Mokashi, Vishwesh P; Chain, Patrick S G; Sozhamannan, Shanmuga

    2015-01-01

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.

  12. Comparative genomics study of polyhydroxyalkanoates (PHA and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships

    Directory of Open Access Journals (Sweden)

    Cai Lei

    2011-11-01

    Full Text Available Abstract Background Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. Results The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA, was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. Conclusions The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.

  13. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation.

    Science.gov (United States)

    Grober, Oli M V; Mutarelli, Margherita; Giurato, Giorgio; Ravo, Maria; Cicatiello, Luigi; De Filippo, Maria Rosaria; Ferraro, Lorenzo; Nassa, Giovanni; Papa, Maria Francesca; Paris, Ornella; Tarallo, Roberta; Luo, Shujun; Schroth, Gary P; Benes, Vladimir; Weisz, Alessandro

    2011-01-14

    Estrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Results indicate that the vast majority of the genomic targets of ERβ can bind

  14. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

    Directory of Open Access Journals (Sweden)

    Papa Maria

    2011-01-01

    Full Text Available Abstract Background Estrogen receptors alpha (ERα and beta (ERβ are transcription factors (TFs that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC. The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions Results indicate that the

  15. Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data

    Directory of Open Access Journals (Sweden)

    Xiao Sun

    2013-10-01

    Full Text Available Current technologies that are used for genome-wide microRNA (miRNA prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system.

  16. An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.

    Science.gov (United States)

    Bertioli, David J; Moretzsohn, Marcio C; Madsen, Lene H; Sandal, Niels; Leal-Bertioli, Soraya C M; Guimarães, Patricia M; Hougaard, Birgit K; Fredslund, Jakob; Schauser, Leif; Nielsen, Anna M; Sato, Shusei; Tabata, Satoshi; Cannon, Steven B; Stougaard, Jens

    2009-01-23

    Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes Lotus and Medicago (both with substantially sequenced genomes). In contrast, peanut (Arachis hypogaea) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of Arachis with Lotus and Medicago and improve our understanding of the Arachis genome and legume genomes in general. To do this we placed on the Arachis map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed. The Arachis genetic map was substantially aligned with Lotus and Medicago with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of Arachis from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The Arachis and model legume genomes comparison made here, together with a previously published comparison of Lotus and Medicago allowed all possible Arachis-Lotus-Medicago species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in Medicago and possibly also in Lotus, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more

  17. Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes.

    Science.gov (United States)

    Mahadevan, Padmanabhan; King, John F; Seto, Donald

    2009-01-01

    Sequence databases are growing exponentially due to 'next generation' DNA analysers and applications of these data. Databases include multiple sequences of previously sequenced organisms, particularly ones of consequence to human health. Applications are limited by tools available to mine them, particularly user-friendly tools that are useful for bench researchers. GeneOrder, CoreGenes and CGUG are web-based 'on-the-fly' tools that examine gene order and synteny, as well as proteomes for comparative genomics and for drug discovery and design targets. CoreGenes (CGUG) now allows analysis of genomes ranging up to 1.9 megabases. Many of these small genome bacteria have impacts on human health.

  18. A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome.

    Directory of Open Access Journals (Sweden)

    Patrícia Beldade

    2009-02-01

    Full Text Available Lepidopterans (butterflies and moths are a rich and diverse order of insects, which, despite their economic impact and unusual biological properties, are relatively underrepresented in terms of genomic resources. The genome of the silkworm Bombyx mori has been fully sequenced, but comparative lepidopteran genomics has been hampered by the scarcity of information for other species. This is especially striking for butterflies, even though they have diverse and derived phenotypes (such as color vision and wing color patterns and are considered prime models for the evolutionary and developmental analysis of ecologically relevant, complex traits. We focus on Bicyclus anynana butterflies, a laboratory system for studying the diversification of novelties and serially repeated traits. With a panel of 12 small families and a biphasic mapping approach, we first assigned 508 expressed genes to segregation groups and then ordered 297 of them within individual linkage groups. We also coarsely mapped seven color pattern loci. This is the richest gene-based map available for any butterfly species and allowed for a broad-coverage analysis of synteny with the lepidopteran reference genome. Based on 462 pairs of mapped orthologous markers in Bi. anynana and Bo. mori, we observed strong conservation of gene assignment to chromosomes, but also evidence for numerous large- and small-scale chromosomal rearrangements. With gene collections growing for a variety of target organisms, the ability to place those genes in their proper genomic context is paramount. Methods to map expressed genes and to compare maps with relevant model systems are crucial to extend genomic-level analysis outside classical model species. Maps with gene-based markers are useful for comparative genomics and to resolve mapped genomic regions to a tractable number of candidate genes, especially if there is synteny with related model species. This is discussed in relation to the identification of

  19. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

    Science.gov (United States)

    2010-01-01

    Background Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae. PMID:20626842

  20. A comparison of synteny and gene order on the homologue of chicken chromosome 7 between two passerine species and between passerines and chicken.

    Science.gov (United States)

    Hale, M C; Jensen, H; Birkhead, T R; Burke, T; Slate, J

    2008-01-01

    Wild populations of passerine birds have frequently been used in studies of ecology and evolution. However, the majority of species lack genetic linkage maps. The completion of a model avian genome sequence (the jungle fowl, Gallus gallus) has created an opportunity to advance genetic knowledge of other birds. Here we constructed genetic linkage maps of the homologue of chicken chromosome 7 for two passerine species, the zebra finch (Taeniopygia guttata) and the house sparrow (Passer domesticus). Linkage groups were constructed with a combination of SNP and microsatellite markers that were developed both in silico based on similarity to the chicken genome sequence, and de novo in the laboratory. Synteny was well conserved throughout the chromosome; however there were some gene rearrangements between chickens and passerines. This suggests that the transfer of map information from chicken to passerine and between different passerine species should not assume conserved gene order. The length of linkage maps of chromosome 7 were on average 60% that of chicken, consistent with the idea that passerines have a reduced recombination rate relative to chicken. Some evidence of heterochiasmy, i.e. a difference in the recombination rate between the sexes, was observed. (c) 2008 S. Karger AG, Basel

  1. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades.

    Science.gov (United States)

    Guyot, Romain; Lefebvre-Pautigny, Florent; Tranchant-Dubreuil, Christine; Rigoreau, Michel; Hamon, Perla; Leroy, Thierry; Hamon, Serge; Poncet, Valérie; Crouzillat, Dominique; de Kochko, Alexandre

    2012-03-20

    Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain

  2. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades

    Science.gov (United States)

    2012-01-01

    Background Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. Results Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. Conclusions These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time

  3. Journal of Agricultural Extension

    African Journals Online (AJOL)

    Mission Statement The mission of the "Journal of Agricultural Extension" is to publish conceptual papers and empirical research that tests, extends, or builds agricultural extension theory and contributes to the practice of extension worldwide. Scope of journal The Journal of Agricultural Extension" is devoted to the ...

  4. Polarization extension mechanism revealed through dynamic ferroelectric hysteresis and electric field driven structural distortions in lead free Na0.5Bi0.5TiO3 ceramic

    Science.gov (United States)

    Karthik, T.; Asthana, Saket

    2017-09-01

    The electric field amplitude (E o) dependent dynamic ferroelectric hysteresis and polarization current density curves measured at room temperature for Na0.5Bi0.5TiO3 (NBT), showed three different stages of polarization reversal mechanism. The scaling relationship confirmed the dominance of domain wall motion at Stage I (i.e. upto E o  <  35 kV cm-1), followed by domain switching at Stage II (35 kV cm-1  <  E o  <  60 kV cm-1). Interestingly, a unique behaviour with two sub stages was observed in Stage III (60 kV cm-1  <  E o  <  90 kV cm-1), with two distinct switching mechanisms viz., polarization rotation at Stage III-A and polarization extension at Stage III-B. X-ray diffraction analysis based on the Rietveld refined atomic positional co-ordinates, in electrically poled system strongly favors the polarization extension mechanism proposed at Stage III-B. The measured E o-dependent longitudinal piezoelectric response (d 33 and g33) values match closely with our proposed polarization reversal mechanism.

  5. Agricultural extension, research, and development for increased ...

    African Journals Online (AJOL)

    Analysis of the data collected revealed that the improvement of agricultural production, with the goal of sustainable food security, in South Africa, might not be achieved without an effective agricultural extension service that is strongly linked to research. It was also found that public sector extension work is a necessity for the ...

  6. Marketing Extension Needs for Sustainable Extension Practices ...

    African Journals Online (AJOL)

    The study investigated the marketing extension needs of cassava farmers in Surulere Local Government Area of Oyo State. Multistage sampling technique was used to select one hundred and five respondents from the list of contact farmers obtained from the state Agricultural Development Programme (ADP). Interview ...

  7. Less extensive surgery compared to extensive surgery

    DEFF Research Database (Denmark)

    Lauszus, Finn F; Petersen, Astrid C; Neumann, Gudrun

    2014-01-01

    OBJECTIVE: To describe the outcome of adult granulosa cell tumor (AGCT) with respect to initial clinical findings, methods of surgery, and perioperative treatment. STUDY DESIGN: Retrospective follow-up study. Setting: All hospitals in Jutland. Sample: 163 women diagnosed with AGCT. Methods: Follo...... with similar survival compared to extensive surgery, but with advancing age conservative surgery increased the risk of relapse and death....

  8. Comparative genomics reveals insights into avian genome evolution and adaptation

    Science.gov (United States)

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  9. Kentucky's Urban Extension Focus

    Science.gov (United States)

    Young, Jeffery; Vavrina, Charles

    2014-01-01

    Defining the success of Urban Extension units is sometimes challenging. For those Extension agents, specialists, administrators, and others who have worked to bring solid, research-based programming to urban communities, it is no surprise that working in these communities brings its own unique and sometimes difficult challenges. Kentucky's Urban…

  10. Priorities for Extension.

    Science.gov (United States)

    Hayward, J. A.

    Agricultural extension is one component in an array including research, training, education, marketing, international trade, etc. which develop together to bring about growth, and sustained growth determines the priorities for extension. These priorities depend inevitably on the stage of development of a country or region, and on the current…

  11. University Extension Before 1915

    Science.gov (United States)

    Eklund, Lowell R.

    1976-01-01

    The author traces university extension from its elite English roots to evolving forces toward democratization of educational opportunities and the simultaneous emergence of similar American programs such as library-related night schools, the Lyceum movement, Chataqua, the Philadelphia Society for Extension of University Teaching, and the…

  12. Algebraic extensions of fields

    CERN Document Server

    McCarthy, Paul J

    1991-01-01

    ""...clear, unsophisticated and direct..."" - MathThis textbook is intended to prepare graduate students for the further study of fields, especially algebraic number theory and class field theory. It presumes some familiarity with topology and a solid background in abstract algebra. Chapter 1 contains the basic results concerning algebraic extensions. In addition to separable and inseparable extensions and normal extensions, there are sections on finite fields, algebraically closed fields, primitive elements, and norms and traces. Chapter 2 is devoted to Galois theory. Besides the fundamenta

  13. Dettol: Managing Brand Extensions

    OpenAIRE

    Anand Kumar Jaiswal; Arpita Srivastav; Dhwani Kothari

    2009-01-01

    This case is about evolution of a parent brand and its subsequent extensions into different product categories. Dettol as a brand has immense trust and loyalty from the consumers. Since the 1930s when Dettol was introduced in India, it has occupied a distinct position in the mind of its consumers. To achieve fast growth and leverage the strong brand equity of Dettol, Reckitt Benckiser India Limited (RBIL) rolled out a number of brand extensions. Some of these extensions such as Dettol soap an...

  14. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

    KAUST Repository

    Gallego Llorente, M.

    2015-10-09

    Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5×coverage ancient genome of an Ethiopian male ("Mota") who lived approximately 4500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West, and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6 to 7% Eurasian ancestry.

  15. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts of at...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....

  16. Timed Extensions for SDL

    OpenAIRE

    Bozga, Marius; Graf, Susanne; Mounier, Laurent; Ober, Iulian; Roux, Jean-Luc; Vincent, Daniel

    2001-01-01

    International audience; In this paper we propose some extensions necessary to enable the specification and description language SDL to become an appropriate formalism for the design of real-time and embedded systems. The extensions we envisage concern both roles of SDL: First, in order to make SDL a real-time specification language, allowing to correctly simulate and verify real-time specifications, we propose a set of annotations to express in a flexible way assumptions and assertions on tim...

  17. Gamut extension for cinema

    OpenAIRE

    Zamir, Syed Waqas,; Vazquez-Corral, Javier; Bertalmío, Marcelo

    2017-01-01

    Emerging display technologies are able to produce images with a much wider color gamut than those of conventional distribution gamuts for cinema and TV, creating an opportunity for the development of gamut extension algorithms (GEAs) that exploit the full color potential of these new systems. In this paper, we present a novel GEA, implemented as a PDE-based optimization procedure related to visual perception models, that performs gamut extension (GE) by taking into account the analysis of dis...

  18. Analysis of the cat eye syndrome critical region in humans and the region of conserved synteny in mice: a search for candidate genes at or near the human chromosome 22 pericentromere.

    Science.gov (United States)

    Footz, T K; Brinkman-Mills, P; Banting, G S; Maier, S A; Riazi, M A; Bridgland, L; Hu, S; Birren, B; Minoshima, S; Shimizu, N; Pan, H; Nguyen, T; Fang, F; Fu, Y; Ray, L; Wu, H; Shaull, S; Phan, S; Yao, Z; Chen, F; Huan, A; Hu, P; Wang, Q; Loh, P; Qi, S; Roe, B A; McDermid, H E

    2001-06-01

    We have sequenced a 1.1-Mb region of human chromosome 22q containing the dosage-sensitive gene(s) responsible for cat eye syndrome (CES) as well as the 450-kb homologous region on mouse chromosome 6. Fourteen putative genes were identified within or adjacent to the human CES critical region (CESCR), including three known genes (IL-17R, ATP6E, and BID) and nine novel genes, based on EST identity. Two putative genes (CECR3 and CECR9) were identified, in the absence of EST hits, by comparing segments of human and mouse genomic sequence around two solitary amplified exons, thus showing the utility of comparative genomic sequence analysis in identifying transcripts. Of the 14 genes, 10 were confirmed to be present in the mouse genomic sequence in the same order and orientation as in human. Absent from the mouse region of conserved synteny are CECR1, a promising CES candidate gene from the center of the contig, neighboring CECR4, and CECR7 and CECR8, which are located in the gene-poor proximal 400 kb of the contig. This latter proximal region, located approximately 1 Mb from the centromere, shows abundant duplicated gene fragments typical of pericentromeric DNA. The margin of this region also delineates the boundary of conserved synteny between the CESCR and mouse chromosome 6. Because the proximal CESCR appears abundant in duplicated segments and, therefore, is likely to be gene poor, we consider the putative genes identified in the distal CESCR to represent the majority of candidate genes for involvement in CES.

  19. Constraints to agricultural extension work in Ethiopia: the insiders ...

    African Journals Online (AJOL)

    This paper examines principal obstacles to agricultural extension work in Ethiopia. The historical review reveals that extension programs and policies have been formulated without due consideration to the farmers' opinion, the various extension approaches have been biased against the livestock sub-sector, and research ...

  20. Android Access Control Extension

    Directory of Open Access Journals (Sweden)

    Anton Baláž

    2015-12-01

    Full Text Available The main objective of this work is to analyze and extend security model of mobile devices running on Android OS. Provided security extension is a Linux kernel security module that allows the system administrator to restrict program's capabilities with per-program profiles. Profiles can allow capabilities like network access, raw socket access, and the permission to read, write, or execute files on matching paths. Module supplements the traditional Android capability access control model by providing mandatory access control (MAC based on path. This extension increases security of access to system objects in a device and allows creating security sandboxes per application.

  1. Mobile Applications for Extension

    Science.gov (United States)

    Drill, Sabrina L.

    2012-01-01

    Mobile computing devices (smart phones, tablets, etc.) are rapidly becoming the dominant means of communication worldwide and are increasingly being used for scientific investigation. This technology can further our Extension mission by increasing our power for data collection, information dissemination, and informed decision-making. Mobile…

  2. Selecting Extensive Reading Materials

    Science.gov (United States)

    Jacobs, George M.

    2014-01-01

    This article offers guidance to teachers and students in selecting materials for extensive reading (ER). First, the article explains characteristics of ER and reviews some of the potential gains for students who do ER. Second, the article considers criteria for teachers to bear in mind when selecting ER materials. Third, the article then suggests…

  3. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements

    Directory of Open Access Journals (Sweden)

    Ocampo Daza Daniel

    2012-11-01

    Full Text Available Abstract Background Somatostatin and its related neuroendocrine peptides have a wide variety of physiological functions that are mediated by five somatostatin receptors with gene names SSTR1-5 in mammals. To resolve their evolution in vertebrates we have investigated the SSTR genes and a large number of adjacent gene families by phylogeny and conserved synteny analyses in a broad range of vertebrate species. Results We find that the SSTRs form two families that belong to distinct paralogons. We observe not only chromosomal similarities reflecting the paralogy relationships between the SSTR-bearing chromosome regions, but also extensive rearrangements between these regions in teleost fish genomes, including fusions and translocations followed by reshuffling through intrachromosomal rearrangements. These events obscure the paralogy relationships but are still tractable thanks to the many genomes now available. We have identified a previously unrecognized SSTR subtype, SSTR6, previously misidentified as either SSTR1 or SSTR4. Conclusions Two ancestral SSTR-bearing chromosome regions were duplicated in the two basal vertebrate tetraploidizations (2R. One of these ancestral SSTR genes generated SSTR2, -3 and -5, the other gave rise to SSTR1, -4 and -6. Subsequently SSTR6 was lost in tetrapods and SSTR4 in teleosts. Our study shows that extensive chromosomal rearrangements have taken place between related chromosome regions in teleosts, but that these events can be resolved by investigating several distantly related species.

  4. Gamut Extension for Cinema.

    Science.gov (United States)

    Zamir, Syed Waqas; Vazquez-Corral, Javier; Bertalmio, Marcelo

    2017-04-01

    Emerging display technologies are able to produce images with a much wider color gamut than those of conventional distribution gamuts for cinema and TV, creating an opportunity for the development of gamut extension algorithms (GEAs) that exploit the full color potential of these new systems. In this paper, we present a novel GEA, implemented as a PDE-based optimization procedure related to visual perception models, that performs gamut extension (GE) by taking into account the analysis of distortions in hue, chroma, and saturation. User studies performed using a digital cinema projector under cinematic (low ambient light, large screen) conditions show that the proposed algorithm outperforms the state of the art, producing gamut extended images that are perceptually more faithful to the wide-gamut ground truth, as well as free of color artifacts and hue shifts. We also show how currently available image quality metrics, when applied to the GE problem, provide results that do not correlate with users' choices.

  5. Need for Methamphetamine Programming in Extension Education

    Science.gov (United States)

    Beaudreault, Amy R.; Miller, Larry E.

    2011-01-01

    The study reported sought to identify the prevention education needs involving methamphetamine through survey methodology. The study focused on a random sample of U.S. states and the Extension Directors within each state, resulting in a 70% response rate (n = 134). Findings revealed that 11% reported they had received methamphetamine user…

  6. Newspapers' agricultural agenda setting and extension agents ...

    African Journals Online (AJOL)

    Newspapers content were analyzed from January to June 2002 for agricultural issues raised in them. Data were analyzed using frequencies, percentages, and Spearman rho correlation coefficient. The results revealed that extension agents ranked storage problems as most important (4.24) and investment in agriculture ...

  7. Rural Development And Agricultural Extension Administration In ...

    African Journals Online (AJOL)

    This paper reviewed the wide range of policies and approaches formulated and implemented to effect agricultural and rural development in Nigeria. The paper reveals that the common feature of all the strategies is the use of institutionalized agricultural extension service, devoted principally to augment smallholder ...

  8. attitude of extension personnel to training and visit extension system ...

    African Journals Online (AJOL)

    ISAAC E. ILEVBAOJE. ABSTRACT. This study was undertaken to find out the attitudes of extension workers to the training and visit (T&V) extension system as a complimentary step to specify if this extension approach is on course in Nigeria. Results obtained indicate that about 10. 8, 65.8 and 23.3% of the extension ...

  9. Selecting Extensive Reading Materials

    Directory of Open Access Journals (Sweden)

    George M Jacobs

    2014-05-01

    Full Text Available This article offers guidance to teachers and students in selecting materials for extensive reading (ER. First, the article explains characteristics of ER and reviews some of the potential gains for students who do ER. Second, the article considers criteria for teachers to bear in mind when selecting ER materials. Third, the article then suggests ways that teachers and students can find ER materials. Fourth, guidance is provided to students for when they select what to read from among the ER materials available to them. Finally, advice is given on integrating ER with course textbooks.

  10. Open Extension Topology

    Directory of Open Access Journals (Sweden)

    Вячеслав Бабич

    2015-10-01

    Full Text Available The paper contains the results which describe the properties of such general topological construction as open extension topology. In particular, we prove that this topology is not transitive. We find the base of the least cardinality for the topology and local one for the neighborhood system of every point. We calculate the interior, the closure, and the sets of isolated and limit points of any set. Also we prove that this space is path connected and is not metrizable, and investigate its cardinal invariants and separation axioms.

  11. Extensive air showers

    CERN Document Server

    Rao, M V S

    1997-01-01

    Ultrahigh energy cosmic rays carry information about their sources and the intervening medium apart from providing a beam of particles for studying certain features of high energy interactions currently inaccessible at man-made accelerators. They can at present be studied only via the extensive air showers (EAS's) they generate while passing through the Earth's atmosphere, since their fluxes are too low for the experiments of limited capability flown in balloons and satellites. The EAS is generated by a series of interactions of the primary cosmic ray and its progeny with the atmospheric nucle

  12. Logic regression and its extensions.

    Science.gov (United States)

    Schwender, Holger; Ruczinski, Ingo

    2010-01-01

    Logic regression is an adaptive classification and regression procedure, initially developed to reveal interacting single nucleotide polymorphisms (SNPs) in genetic association studies. In general, this approach can be used in any setting with binary predictors, when the interaction of these covariates is of primary interest. Logic regression searches for Boolean (logic) combinations of binary variables that best explain the variability in the outcome variable, and thus, reveals variables and interactions that are associated with the response and/or have predictive capabilities. The logic expressions are embedded in a generalized linear regression framework, and thus, logic regression can handle a variety of outcome types, such as binary responses in case-control studies, numeric responses, and time-to-event data. In this chapter, we provide an introduction to the logic regression methodology, list some applications in public health and medicine, and summarize some of the direct extensions and modifications of logic regression that have been proposed in the literature. Copyright © 2010 Elsevier Inc. All rights reserved.

  13. Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

    Science.gov (United States)

    Hill, Theresa; Ashrafi, Hamid; Chin-Wo, Sebastian Reyes; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard; Van Deynze, Allen

    2015-09-08

    Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper. Copyright © 2015 Hill et al.

  14. Attitude Of Extension Personnel To Training And Visit Extension ...

    African Journals Online (AJOL)

    In order to make the attitudes of extension workers more affirmative, the paper recommended, inter alia, staff motivation, minimizing political and administrative interference in staff work and a reasonable reduction in the work load of extension staff. Key words: attitude, extension personnel, training and visit. Journal of ...

  15. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements

    National Research Council Canada - National Science Library

    Ocampo Daza, Daniel; Sundström, Görel; Bergqvist, Christina A; Larhammar, Dan

    2012-01-01

    .... To resolve their evolution in vertebrates we have investigated the SSTR genes and a large number of adjacent gene families by phylogeny and conserved synteny analyses in a broad range of vertebrate species...

  16. Community health nursing and cooperative extension: a natural partnership.

    Science.gov (United States)

    Bigbee, Jeri L; Hampton, Carol; Blanford, Diane; Ketner, Paulette

    2009-10-01

    Community health nursing and cooperative extension represent two influential and respected disciplines in rural and frontier communities. The history and philosophy of the two disciplines reveal commonalities related to community-based health promotion and dissemination of research. A review of the extension and health sciences literature revealed some evidence of collaboration between extension and health science professionals, however very little documentation specifically of nurses' involvement with extension professionals. An exemplar of a highly effective ongoing cooperation between rural public health nurses and extension educators in one Idaho county is provided. This local interdisciplinary effort has resulted in enhanced community health promotion services, positive interprofessional relationships, and maximization of scarce resources. Nursing-extension collaboration presents creative opportunities for interdisciplinary practice, research, and educational innovations to enhance the health of rural and frontier communities.

  17. Extensive xanthogranulomatous cystitis mimicking bladder cancer

    Directory of Open Access Journals (Sweden)

    Amir M Ali

    2014-01-01

    Full Text Available Xanthogranulomatous cystitis (XC is a rare benign disease of unknown etiology. A 39-year-old female presented with 2 month history of urgency, dysuria, lower abdominal mass. On physical examination a hard hypogastric mass was present fixed to the rectus muscle. Computerized tomography (CT abdomen showed heterogeneous enhancing mass arising from the anterior bladder wall with infiltration of the overlying parietal wall. Cystoscopy revealed extensive growth involving the entire wall of the bladder. A biopsy showed cystitis with focal areas suggestive of urothelial neoplasia of unknown malignant potential. Suspecting bladder cancer, we proceeded with radical cystectomy with ileal conduit. Histopathology revealed cystitis cystica with XC of the entire bladder. This is, to our knowledge, the first time that a case has been found to be so extensive with infiltration of the parietal wall and second time that radical cystectomy has been performed for XC.

  18. Challenges of extension workers in reaching rural women farmers in ...

    African Journals Online (AJOL)

    Questionnaire was used to collect data from a sample size of 52 extension workers. Data were analyzed using percentage, mean statistic, chart and factor analysis. Results revealed that training and visit method (100%) and farmer group (98.1%) were the major extension approach used in reaching rural women farmers in ...

  19. Perceived Factors Affecting Performance Of Extension Workers In ...

    African Journals Online (AJOL)

    Data for the study was collected from 83 Extension agents from the Imo State Agricultural Development Programme (ADP). Results of the study revealed that the organizational factors that affect performance are mobility/logistic factors, job design and Administration. It is therefore recommended that Agricultural extension ...

  20. Research-Based Implications from Extensive Early Reading Interventions

    Science.gov (United States)

    Wanzek, Jeanne; Vaughn, Sharon

    2007-01-01

    A synthesis of the extant research on extensive early reading interventions for students with reading difficulties and disabilities is provided. Findings from 18 studies published between 1995 and 2005 revealed positive outcomes for students participating in extensive interventions. Results indicated higher effects for studies providing…

  1. The Impact Of Information And Communication In Extension ...

    African Journals Online (AJOL)

    The article examines the impact of information and communication in extension services to rural farmers in Niger- Delta. Questionnaire, interview and personal observation methods were employed to elicit information on the impact information and communication in extension services to rural farmers. The study reveals the ...

  2. Evolutionary history of the GABA transporter (GAT group revealed by marine invertebrate GAT-1.

    Directory of Open Access Journals (Sweden)

    Azusa Kinjo

    Full Text Available The GABA transporter (GAT group is one of the major subgroups in the solute career 6 (SLC6 family of transmembrane proteins. The GAT group, which has been well studied in mammals, has 6 known members, i.e., a taurine transporter (TAUT, four GABA transporters (GAT-1, -2, -3, - 4, and a creatine transporter (CT1, which have important roles in maintaining physiological homeostasis. However, the GAT group has not been extensively investigated in invertebrates; only TAUT has been reported in marine invertebrates such as bivalves and krills, and GAT-1 has been reported in several insect species and nematodes. Thus, it is unknown how transporters in the GAT group arose during the course of animal evolution. In this study, we cloned GAT-1 cDNAs from the deep-sea mussel, Bathymodiolus septemdierum, and the Antarctic krill, Euphausia superba, whose TAUT cDNA has already been cloned. To understand the evolutionary history of the GAT group, we conducted phylogenetic and synteny analyses on the GAT group transporters of vertebrates and invertebrates. Our findings suggest that transporters of the GAT group evolved through the following processes. First, GAT-1 and CT1 arose by tandem duplication of an ancestral transporter gene before the divergence of Deuterostomia and Protostomia; next, the TAUT gene arose and GAT-3 was formed by the tandem duplication of the TAUT gene; and finally, GAT-2 and GAT-4 evolved from a GAT-3 gene by chromosomal duplication in the ancestral vertebrates. Based on synteny and phylogenetic evidence, the present naming of the GAT group members does not accurately reflect the evolutionary relationships.

  3. Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

    Directory of Open Access Journals (Sweden)

    Fellers John P

    2013-01-01

    Full Text Available Abstract Background Wheat leaf rust (Puccinia triticina Eriks; Pt and stem rust fungi (P. graminis f.sp. tritici; Pgt are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion. Results A bacterial artificial chromosome (BAC library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt. Conclusions The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.

  4. Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.) using synteny between radish and Arabidopsis genomes.

    Science.gov (United States)

    Cho, Youngcho; Lee, Young-Pyo; Park, Beom-Seok; Han, Tae-Ho; Kim, Sunggil

    2012-08-01

    Cytoplasmic male sterility caused by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its nuclear restorer-of-fertility locus (Rfd1) with a linked molecular marker (A137) have been reported in radish (Raphanus sativus L.). To construct a linkage map of the Rfd1 locus, linked amplified fragment length polymorphism (AFLP) markers were screened using bulked segregant analysis. A 220-bp linked AFLP fragment sequence from radish showed homology with an Arabidopsis coding sequence. Using this Arabidopsis gene sequence, a simple PCR marker (A220) was developed. The A137 and A220 markers flanked the Rfd1 locus. Two homologous Arabidopsis genes with both marker sequences were positioned on Arabidopsis chromosome-3 with an interval of 2.4 Mb. To integrate the Rfd1 locus into a previously reported expressed sequence tag (EST)-simple sequence repeat (SSR) linkage map, the radish EST sequences located in three syntenic blocks within the 2.4-Mb interval were used to develop single nucleotide polymorphism (SNP) markers for tagging each block. The SNP marker in linkage group-2 co-segregated with male fertility in an F(2) population. Using radish ESTs positioned in linkage group-2, five intron length polymorphism (ILP) markers and one cleaved amplified polymorphic sequence (CAPS) marker were developed and used to construct a linkage map of the Rfd1 locus. Two closely linked markers delimited the Rfd1 locus within a 985-kb interval of Arabidopsis chromosome-3. Synteny between the radish and Arabidopsis genomes in the 985-kb interval were used to develop three ILP and three CAPS markers. Two ILP markers further delimited the Rfd1 locus to a 220-kb interval of Arabidopsis chromosome-3.

  5. attitude of extension personnel to training and visit extension system ...

    African Journals Online (AJOL)

    the training and visit (T&V) extension system as a complimentary step to specify if this extension approach is ... at 5 percent level of probability, the mean score for the project headquarters staff (106.25) was highest while ... which offered them the opportunity to use their knowledge and skills. Asiabiaka (1991) studied women ...

  6. Robotic hand with modular extensions

    Energy Technology Data Exchange (ETDEWEB)

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  7. Think - Baltic Extension / Kalle Kask

    Index Scriptorium Estoniae

    Kask, Kalle

    2002-01-01

    Tallinna TÜ Rehabilitatsiooni tehnoloogia keskus korraldas pressikonverentsi, kus tutvustati osalemist EL V raamprogrammis Think - Baltic Extension, mis on suunatud puuetega inimeste tööhõive tagamisele

  8. Extensive intestinal spirochaetosis in pigs challenged with Brachyspira pilosicoli

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Møller, Kristian

    2004-01-01

    of the study). Mild mucosal reddening and flecks of pus characterized the gross lesions, while diffuse, catarrhal colitis was revealed microscopically in all animals. Intestinal spirochaetosis with moderate to densely packed end-attached B. pilosicoli organisms was revealed extensively on the mucosal surface...

  9. Extensive Reading Coursebooks in China

    Science.gov (United States)

    Renandya, Willy A.; Hu, Guangwei; Xiang, Yu

    2015-01-01

    This article reports on a principle-based evaluation of eight dedicated extensive reading coursebooks published in mainland China and used in many universities across the country. The aim is to determine the extent to which these coursebooks reflect a core set of nine second language acquisition and extensive reading principles. Our analysis shows…

  10. Fuzzy extended preferences: fuzzified extension

    OpenAIRE

    Montero, Javier

    1988-01-01

    This paper deals with decision-making problems where a fuzzy preference relation with no unfuzzy nondominated alternatives has been defined. While in the first part randomized extension was considered in order to get a solution, in this second part an aggregative approach to fuzzified extension will be developed.

  11. Frames and extension problems I

    DEFF Research Database (Denmark)

    Christensen, Ole

    2014-01-01

    In this article we present a short survey of frame theory in Hilbert spaces. We discuss Gabor frames and wavelet frames and set the stage for a discussion of various extension principles; this will be presented in the article Frames and extension problems II (joint with H.O. Kim and R.Y. Kim)....

  12. Research-extension-farmer linkages

    African Journals Online (AJOL)

    charged with the role of articulating the most appropriate research and extension systems for Uganda. Following the recommendations of these working groups, national agricultural research and extension strategies and plans were adopted ..... meetings at institutes have been taking place regularly since 1994. These take ...

  13. Homomorphisms between C∗ -algebra extensions

    Indian Academy of Sciences (India)

    -algebra extensions. CHANGGUO WEI. School of Mathematical Sciences, Ocean University of China, Qingdao 266071, ... into the other in general, so we have to consider properties of extension homomorphisms before studying the ..... Theory (Dalhousie Univ., Halifax, N.S., 1973) Lecture Notes in Math. (Berlin: Springer).

  14. EXTENSION WORKERS' OPINIONS REGARDING THE ...

    African Journals Online (AJOL)

    The primary purpose of the study was to determine extension worker's opinions regarding the influence of the National Maize Competition (NAMCOM) on the farmers' agricultural practices and experiences in the Manzini region. A census population of front-line extension workers in charge of the participating areas in ...

  15. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  16. Journal of Agricultural Extension submitted to Agricultural Extension ...

    African Journals Online (AJOL)

    PROF. MADUKWE

    followed by lack of contact with extension agents (71.7%) and gender ... As women typically confront narrower range of labour markets than men, and lower wage ..... gap in accessibility to productive resources between male and female heads ...

  17. Extensions of the Poincare group

    CERN Document Server

    Antoniadis, Ignatios; Savvidy, George

    2011-01-01

    We construct an extension of the Poincare group which involves a mixture of internal and space-time supersymmetries. The resulting group is an extension of the superPoincare group with infinitely many generators which carry internal and space-time indices. It is a closed algebra since all Jacobi identities are satisfied and it has therefore explicit matrix representations. We investigate the massless case and construct the irreducible representations of the extended symmetry. They are divided into two sets, longitudinal and transversal representations. The transversal representations involve an infinite series of integer and half-integer helicities. Finally we suggest an extension of the conformal group along the same line.

  18. Programming Reactive Extensions and LINQ

    CERN Document Server

    Liberty, Jesse

    2011-01-01

    Pro Reactive Extensions and LINQ is a deep dive into the next important technology for .NET developers: Reactive Extensions. This in-depth tutorial goes beyond what is available anywhere else to teach how to write WPF, Silverlight, and Windows Phone applications using the Reactive Extensions (Rx) to handle events and asynchronous method calls. Reactive programming allows you to turn those aspects of your code that are currently imperative into something much more event-driven and flexible. For this reason, it's sometimes referred to as LINQ for Events. Reactive programming hinges on the concep

  19. Learning Joomla! 3 extension development

    CERN Document Server

    Plummer, Tim

    2013-01-01

    A practical guide with step-by-step examples that build on each other so you can learn by doing and get hands-on knowledge about creating your plugins, modules, and components in Joomla.""Learning Joomla! 3 Extension Development, Third Edition"" is for developers who want to create their own Joomla extensions. It is assumed you will have some basic PHP, HTML, and CSS knowledge, but you don't need any prior Joomla programming experience. This book will also be useful to people who just want to make minor customizations to existing Joomla extensions and build on the work of others in the open so

  20. Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

    Science.gov (United States)

    2008-01-01

    Background Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus. Results Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome. Conclusion These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency). PMID:18302785

  1. Chromosomal Locations of 5S and 45S rDNA in Gossypium Genus and Its Phylogenetic Implications Revealed by FISH.

    Science.gov (United States)

    Gan, Yimei; Liu, Fang; Chen, Dan; Wu, Qiong; Qin, Qin; Wang, Chunying; Li, Shaohui; Zhang, Xiangdi; Wang, Yuhong; Wang, Kunbo

    2013-01-01

    We investigated the locations of 5S and 45S rDNA in Gossypium diploid A, B, D, E, F, G genomes and tetraploid genome (AD) using multi-probe fluorescent in situ hybridization (FISH) for evolution analysis in Gossypium genus. The rDNA numbers and sizes, and synteny relationships between 5S and 45S were revealed using 5S and 45S as double-probe for all species, and the rDNA-bearing chromosomes were identified for A, D and AD genomes with one more probe that is single-chromosome-specific BAC clone from G. hirsutum (A1D1). Two to four 45S and one 5S loci were found in diploid-species except two 5S loci in G. incanum (E4), the same as that in tetraploid species. The 45S on the 7th and 9th chromosomes and the 5S on the 9th chromosomes seemed to be conserved in A, D and AD genomes. In the species of B, E, F and G genomes, the rDNA numbers, sizes, and synteny relationships were first reported in this paper. The rDNA pattern agrees with previously reported phylogenetic history with some disagreements. Combined with the whole-genome sequencing data from G. raimondii (D5) and the conserved cotton karyotype, it is suggested that the expansion, decrease and transposition of rDNA other than chromosome rearrangements might occur during the Gossypium evolution.

  2. Correlation between extension-block K-wire insertion angle and postoperative extension loss in mallet finger fracture.

    Science.gov (United States)

    Lee, S K; Kim, Y H; Moon, K H; Choy, W S

    2017-10-09

    Extension-block pinning represents a simple and reliable surgical technique. Although this procedure is commonly performed successfully, some patients develop postoperative extension loss. To date, the relationship between extension-block Kirschner wire (K-wire) insertion angle and postoperative extension loss in mallet finger fracture remains unclear. We aimed to clarify this relationship and further evaluate how various operative and non-operative factors affect postoperative extension loss after extension-block pinning for mallet finger fracture. A retrospective study was conducted to investigate a relationship between extension block K-wire insertion angle and postoperative extension loss. The inclusion criteria were: (1) a dorsal intra-articular fracture fragment involving 30% of the base of the distal phalanx with or without volar subluxation of the distal phalanx; and (2) angle and fixation angle of the distal interphalangeal (DIP) joint were assessed using lateral radiograph at immediate postoperative time. Postoperative extension loss was assessed by using lateral radiograph at latest follow-up. Extension-block K-wire insertion angle was defined as the acute angle between extension block K-wire and longitudinal axis of middle phalangeal head. DIP joint fixation angle was defined as the acute angle between the distal phalanx and middle phalanx longitudinal axes. Seventy-five patients were included. The correlation analysis revealed that extension-block K-wire insertion angle had a negative correlation with postoperative extension loss, whereas fracture size and time to operation had a positive correlation (correlation coefficient for extension block K-wire angle: -0.66, facture size: +0.67, time to operation: +0.60). When stratifying patients in terms of negative and positive fixation angle of the DIP joint, the independent t-test showed that mean postoperative extension loss is -3.67° and +4.54° (DIP joint fixation angles of angle (30°, 30°-40°, >40

  3. Horizontal Brand Extension and Customer perception

    OpenAIRE

    Khan, Khalid; Janthimapornkij, Rattanawilai

    2011-01-01

    Company use different method for extended their business to different market and to different segment. They use different method; brand extension is one of popular strategy for extension of business. Brand extension does not become successful for every brand, it is very risky. The purpose of this thesis is to study horizontal brand extension and customer perception. We will discuss horizontal brand extension and its two main types franchise brand extension and line extension. Brand extension ...

  4. Boiler-turbine life extension

    Energy Technology Data Exchange (ETDEWEB)

    Natzkov, S. [TOTEMA, Ltd., Sofia (Bulgaria); Nikolov, M. [CERB, Sofia (Bulgaria)

    1995-12-01

    The design life of the main power equipment-boilers and turbines is about 105 working hours. The possibilities for life extension are after normatively regulated control tests. The diagnostics and methodology for Boilers and Turbines Elements Remaining Life Assessment using up to date computer programs, destructive and nondestructive control of metal of key elements of units equipment, metal creep and low cycle fatigue calculations. As well as data for most common damages and some technical decisions for elements life extension are presented.

  5. Frames and extension problems II

    DEFF Research Database (Denmark)

    Christensen, Ole; Kim, Hong Oh; Kim, Rae Young

    2014-01-01

    This article is a follow-up on the article Frames and Extension Problems I. Here we will go into more recent progress on the topic and also present some open problems.......This article is a follow-up on the article Frames and Extension Problems I. Here we will go into more recent progress on the topic and also present some open problems....

  6. Agricultural extension and mass media.

    Science.gov (United States)

    Perraton, H

    1983-12-01

    To learn more about the use of the mass media for agricultural extension, the World Bank has considered the efforts of 2 units: INADES-formation in West Africa and the Extension Aids Branch of Malawi. The INADES-formation study focuses on Cameroon but also considers work in Rwanda and the Ivory Coast. Some general conclusions emerge from a comparison of the 2 organizations. Malawi operates an extension service which reaches farmers through extension agents, through farmer training centers, and through mass media. The Extension Aids Branch (EAB) has responsibility for its media work and broadcasts 4 1/2 hours of radio each week. Its 6 regular radio programs include a general program which interviews farmers, a music request program in which the music is interspersed with farming advice, a farming family serial, and a daily broadcast of agricultural news and information. The 17 cinema vans show some agricultural films, made by EAB, some entertainment films, and some government information films from departments other than the ministry of agriculture. EAB also has a well-developed program of research and evaluation of its own work. INADES-formation, the training section of INADES, works towards social and economic development of the population. It teaches peasant farmers and extension agents and does this through running face-to-face seminars, by publishing a magazine, "Agripromo," and through correspondence courses. In 1978-79 INADES-formation enrolled some 4500 farmers and extension agents as students. Both of these organizations work to teach farmers better agriculture techniques, and both were created in response to the fact that agricultural extension agents cannot meet all the farmers in their area. Despite the similarity of objective, there are differences in methods and philosophy. The EAB works in a single country and uses a variety of mass media, with print playing a minor role. INADES-formation is an international and nongovernmental organization and its

  7. Farmers' perception of agricultural extension service delivery in ...

    African Journals Online (AJOL)

    The study further revealed that extension activities had low impact on improving farm production yield and profitability (M=1.9, SD=±0.67) and enabling farmers to identify their own needs, problems and solve them (M=1.9, SD=±0.69). In conclusion it was found that extension is efficient, effective and visible in the study area.

  8. The Use of Extensive Reading in Teaching Reading

    OpenAIRE

    Ferdila, Raihani

    2014-01-01

    The study investigates benefits of using extensive reading in teaching reading and as well as students' attitudes toward it. A case study design as a part of qualitative research was employed in this study. The data were collected through classroom observation, questionnaire and interview. The participants of this study were a class of second graders in one of the public junior high schools in Bandung. The findings reveal that extensive reading was beneficial in teaching reading. There are fi...

  9. RURAL EXTENSION EPISTEMOLOGY AND THE TIME OF TOTAL EXTENSION

    Directory of Open Access Journals (Sweden)

    Silvio Calgaro Neto

    2016-09-01

    Full Text Available This article is dedicated to explore the field of knowledge related to rural extension. In general, a three complementary perspective is used as theoretical strategy to present this epistemological study. The first perspective, seeks to accomplish a brief archeology of rural extension, identifying the remarkable historical passages. At the second, we look to some theoretical models through the modern epistemological platform. Finally, the third perspective, aims to present a methodological proposal that contemplate this epistemic characteristics, relating with the contemporary transformations observed in the knowledge construction and technological transference for a rural development. Keywords: Total institutions. University.

  10. African Journal of Livestock Extension

    African Journals Online (AJOL)

    African Journal of Livestock Extension aims to bring to the fore the role and significance of livestock in maintaining rural, peri-urban and urban households, vis-à-vis its impact on poverty alleviation, household nutritional status, economic coping strategy and provision of employment. The focus of the journal relates to all ...

  11. Longest common extensions in trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2016-01-01

    The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE queries. In this paper we generalize the LCE problem to t...

  12. Dept. of Agricultural Economics & Extension

    African Journals Online (AJOL)

    duce poverty include education, credit, durable assets, living in the forest belt and in the south of the country. .... underscores the importance of education and extension services in the technology adoption/diffusion process. Poverty is a ...... Detwerminantes de la Pobreza de los hogares, México. Revista Mexicana de ...

  13. Extension Resources for International Trade

    Science.gov (United States)

    Seal, Susan D.

    2016-01-01

    With the opening of additional trade partnerships, the reduction of global transportation and communication costs, and the increase in demand for U.S. agricultural products and services, international trade is an area of great importance to more and more Extension clients and stakeholders. This article provides information about the primary…

  14. Symmetrical Extensions of Dirichlet Operators

    CERN Document Server

    Us, A G

    1997-01-01

    There is constructed and considered the extension of classical Diriclet operator corresponding to uniformly log-concave measure in the space of symmetric differential forms. Sufficient conditions for its essential self-adjointness in one-dimensional case as well as for the same of its "sypersymmetric" part in general situations are given.

  15. Extensiveness of Farmers' Buying Process

    NARCIS (Netherlands)

    Kool, M.; Meulenberg, M.T.G.; Broens, D.F.

    1997-01-01

    In this article we study farmers' buying processes, in particular the selection of a supplier for a given farm input. Extensiveness of farmers' buying processes is defined as the degree information acquisition and alternative evaluation effort carried out to prepare that selection. Hypotheses,

  16. A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae Population

    Directory of Open Access Journals (Sweden)

    Daniel Thorogood

    2017-08-01

    Full Text Available Self-incompatibility (SI is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L. possesses a well-documented two locus (S and Z gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3. These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with

  17. Poincare Algebra Extension with Tensor Generator

    OpenAIRE

    Soroka, Dmitrij V.; Soroka, Vyacheslav A.

    2005-01-01

    A tensor extension of the Poincar\\'e algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions $D=2,3,4$.

  18. Tensor extension of the Poincare algebra

    Energy Technology Data Exchange (ETDEWEB)

    Soroka, Dmitrij V. [Kharkov Institute of Physics and Technology, 61108 Kharkov (Ukraine)]. E-mail: dsoroka@kipt.kharkov.ua; Soroka, Vyacheslav A. [Kharkov Institute of Physics and Technology, 61108 Kharkov (Ukraine)]. E-mail: vsoroka@kipt.kharkov.ua

    2005-02-10

    A tensor extension of the Poincare algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions D=2,3,4.

  19. Linear programming foundations and extensions

    CERN Document Server

    Vanderbei, Robert J

    2001-01-01

    Linear Programming: Foundations and Extensions is an introduction to the field of optimization. The book emphasizes constrained optimization, beginning with a substantial treatment of linear programming, and proceeding to convex analysis, network flows, integer programming, quadratic programming, and convex optimization. The book is carefully written. Specific examples and concrete algorithms precede more abstract topics. Topics are clearly developed with a large number of numerical examples worked out in detail. Moreover, Linear Programming: Foundations and Extensions underscores the purpose of optimization: to solve practical problems on a computer. Accordingly, the book is coordinated with free efficient C programs that implement the major algorithms studied: -The two-phase simplex method; -The primal-dual simplex method; -The path-following interior-point method; -The homogeneous self-dual methods. In addition, there are online JAVA applets that illustrate various pivot rules and variants of the simplex m...

  20. Extension agents and conflict narratives

    DEFF Research Database (Denmark)

    Bond, Jennifer Lauren

    2016-01-01

    Purpose: This work investigated the narratives of development extensionists in relation to natural resource conflict, in order to understand the competing discourses surrounding the wicked problems of natural resource management in Laikipia County, Kenya. Methodology: Q methodology was used...... to elicit the conflict narratives present among extension professionals. A concourse of 221 statements were devised from interviews and group discussions with key informants and a final sample of 49 statements was used for the sorting. Thirteen Q-sorts were undertaken with among rural extension...... professionals from government, non-government, faith-based and private organizations. Findings: Four factors were elicited from the data, labelled—A: ‘Improved Leadership’; B: ‘Resource-centred conflict’; C: ‘Improved Governance’; and D: ‘Improved Management’. Practical Implications: Narratives of neo...

  1. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

    Directory of Open Access Journals (Sweden)

    Stephen B Goodwin

    2011-06-01

    Full Text Available The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic

  2. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish.

    Science.gov (United States)

    Amores, Angel; Catchen, Julian; Nanda, Indrajit; Warren, Wesley; Walter, Ron; Schartl, Manfred; Postlethwait, John H

    2014-06-01

    Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years. Copyright © 2014 by the Genetics Society of America.

  3. Rosacea with extensive extrafacial lesions

    OpenAIRE

    Pereira, TM; Vieira, AP; Sousa-Basto, A

    2008-01-01

    Rosacea is a very common skin disorder in the clinical practice that primarily affects the convex areas of the face. Extrafacial rosacea lesions have occasionally been described, but extensive involvement is exceptional. In the absence of its typical clinical or histological features, the diagnosis of extrafacial rosacea may be problematic. We describe an unusual case of rosacea with very exuberant extrafacial lesions, when compared with the limited involvement of the face.

  4. An Extension for ESO Headquarters

    Science.gov (United States)

    Fischer, Robert; Walsh, Jeremy

    2009-03-01

    The ESO Headquarters was completed in 1980, but is now too small to house all the ESO staff and currently only about 50% reside in the original building. A decision was taken to seek an extension to the Headquarters building in close proximity to the current one and a competition was launched for architectural designs. Three designs were shortlisted and the process of selection for the final design is described. Construction will begin in 2010 and is due for completion in 2012.

  5. Building the capacity of agricultural extension personnel for effective ...

    African Journals Online (AJOL)

    Findings reveal a tremendous shortage in the number and quality of extension personnel across the country as major reason for the poor performance of the ADPs thereby leaving no hope for the “beautiful” transformation agenda. This paper strongly recommends immediate recruitment of new hands as well as full ...

  6. Determinants Of Job Satisfaction Of Field Extension Workers In ...

    African Journals Online (AJOL)

    Three major factors were identified as strong determinants of job satisfaction of the field extension workers namely interpersonal relationship, organizational policies, and conditions of service. The study revealed that attainment of certain policy issues depends largely on interpersonal relationship in the organization.

  7. Factors Influencing Perceptions of Service Quality in Cooperative Extension Workers

    Science.gov (United States)

    Anaza, Nwamaka A.; Rutherford, Brian N.; Widdows, Richard

    2012-01-01

    The authors examined the direct and indirect impact of empowerment on service quality as perceived by Extension staff. Using a sample 283 respondents, the results revealed that along with empowerment, constructs such as job satisfaction and organizational identification positively affected service quality. Undoubtedly, each of these variables…

  8. Sources And Use Of Extension Information Among Maize Farmers In ...

    African Journals Online (AJOL)

    Furthermore, findings revealed that the respondents utilized extension information, to a great extent on the following technologies/recommendations; improved maize, seed rate, seed dressing, plant spacing, fertilizer application, post-harvest processing, and storage. Recommendations on herbicides and pesticides were ...

  9. Identifying Invasive Species Educational Needs in Florida: Opportunities for Extension

    Science.gov (United States)

    Huang, Pei-wen; Lamm, Alexa J.

    2016-01-01

    Florida's ecology has been adversely affected by invasive species. In Florida, a study was conducted to explore opportunities for Extension educators to contribute to combating the issue of invasive species. Florida residents' responses were captured through the use of an online public opinion survey. The findings revealed a need for invasive…

  10. Extensive Growth of an Anaplastic Meningioma

    Directory of Open Access Journals (Sweden)

    Hajrullah Ahmeti

    2013-01-01

    Full Text Available We present the case of a 30-year-old male patient with an almost complete destruction of the calvarial bone through an anaplastic meningioma diagnosed in line with dizziness. Neuroimaging revealed an extensive growing, contrast enhancing lesion expanding at the supra- and infratentorial convexity, infiltrating and destroying large parts of the skull, and infiltrating the skin. Due to progressive ataxia and dysarthria with proven tumor growth in the posterior fossa in the continuing course, parts of the tumor were resected. A surgical procedure with the aim of complete tumor resection in a curative manner was not possible. Six months after the first operation, due to a new tumor progression, most extensive tumor resection was performed. Due to the aggressive and destructive growth with a high rate of recurrence and tendency of metastases, anaplastic meningiomas can be termed as malignant tumors. The extrinsic growth masks the tumor until they reach a size, which makes these tumors almost unresectable. In the best case scenarios, the five-year survival is about 50%. With the presented case, we would like to show the aggressive behavior of anaplastic meningiomas in a very illustrative way. Chemotherapy, radiotherapy, and surgery reach their limits in this tumor entity.

  11. Parallel Extension Tectonics (PET): Early Cretaceous tectonic extension of the Eastern Eurasian continent

    Science.gov (United States)

    Liu, Junlai; Ji, Mo; Ni, Jinlong; Guan, Huimei; Shen, Liang

    2017-04-01

    The present study reports progress of our recent studies on the extensional structures in eastern North China craton and contiguous areas. We focus on characterizing and timing the formation/exhumation of the extensional structures, the Liaonan metamorphic core complex (mcc) and the Dayingzi basin from the Liaodong peninsula, the Queshan mcc, the Wulian mcc and the Zhucheng basin from the Jiaodong peninsula, and the Dashan magmatic dome within the Sulu orogenic belt. Magmatic rocks (either volcanic or plutonic) are ubiquitous in association with the tectonic extension (both syn- and post-kinematic). Evidence for crustal-mantle magma mixing are popular in many syn-kinematic intrusions. Geochemical analysis reveals that basaltic, andesitic to rhyolitic magmas were generated during the tectonic extension. Sr-Nd isotopes of the syn-kinematic magmatic rocks suggest that they were dominantly originated from ancient or juvenile crust partly with mantle signatures. Post-kinematic mafic intrusions with ages from ca. 121 Ma to Cenozoic, however, are of characteristic oceanic island basalts (OIB)-like trace element distribution patterns and relatively depleted radiogenic Sr-Nd isotope compositions. Integrated studies on the extensional structures, geochemical signatures of syn-kinematic magmatic rocks (mostly of granitic) and the tectono-magmatic relationships suggest that extension of the crust and the mantle lithosphere triggered the magmatisms from both the crust and the mantle. The Early Cretaceous tectono-magmatic evolution of the eastern Eurasian continent is governed by the PET in which the tectonic processes is subdivided into two stages, i.e. an early stage of tectonic extension, and a late stage of collapse of the extended lithosphere and transformation of lithospheric mantle. During the early stage, tectonic extension of the lithosphere led to detachment faulting in both the crust and mantle, resulted in the loss of some of the subcontinental roots, gave rise to

  12. Coal Combustion Products Extension Program

    Energy Technology Data Exchange (ETDEWEB)

    Tarunjit S. Butalia; William E. Wolfe

    2006-01-11

    This final project report presents the activities and accomplishments of the ''Coal Combustion Products Extension Program'' conducted at The Ohio State University from August 1, 2000 to June 30, 2005 to advance the beneficial uses of coal combustion products (CCPs) in highway and construction, mine reclamation, agricultural, and manufacturing sectors. The objective of this technology transfer/research program at The Ohio State University was to promote the increased use of Ohio CCPs (fly ash, FGD material, bottom ash, and boiler slag) in applications that are technically sound, environmentally benign, and commercially competitive. The project objective was accomplished by housing the CCP Extension Program within The Ohio State University College of Engineering with support from the university Extension Service and The Ohio State University Research Foundation. Dr. Tarunjit S. Butalia, an internationally reputed CCP expert and registered professional engineer, was the program coordinator. The program coordinator acted as liaison among CCP stakeholders in the state, produced information sheets, provided expertise in the field to those who desired it, sponsored and co-sponsored seminars, meetings, and speaking at these events, and generally worked to promote knowledge about the productive and proper application of CCPs as useful raw materials. The major accomplishments of the program were: (1) Increase in FGD material utilization rate from 8% in 1997 to more than 20% in 2005, and an increase in overall CCP utilization rate of 21% in 1997 to just under 30% in 2005 for the State of Ohio. (2) Recognition as a ''voice of trust'' among Ohio and national CCP stakeholders (particularly regulatory agencies). (3) Establishment of a national and international reputation, especially for the use of FGD materials and fly ash in construction applications. It is recommended that to increase Ohio's CCP utilization rate from 30% in 2005 to

  13. EXTENSION OPERATOR AND NEURON NETWORK

    OpenAIRE

    LUIZ CARLOS C PEDROZA

    1997-01-01

    Na tese se desenvolve a teoria do Operador de extensão (OPEX) e utiliza-se desta para compreender melhor algumas questões relativas a teoria de Redes Neurais(RN). A abordagem de Redes Neurais pela ótica do Operador de Extensão possibilita também um melhoramento no algoritmo de retropropagação de erro usado no treinamento supervisionado das Redes Neurais. In this thesis, theory of Extension Operator is developed and used to understand some questions related to ...

  14. Combined Dietotherapy after Extensive Hepatectomies

    Directory of Open Access Journals (Sweden)

    V. V. Kiselev

    2007-01-01

    Full Text Available Objective: to compare the time course of nutritional changes in relation to the components of nutritive support in the early postoperative period after extensive hepatectomies.Subjects and methods. Beginning with the 1st postoperative day, 12 patients had parenteral feeding comprising 20% glucose, fat emulsions, and specialized amino acid solutions (Group 1. Beginning with the same day, 14 patients were given the parenteral formula Oliclinomel (Group 2. Starting from the 2nd postoperative day, both groups additionally received a balanced feeding formula by sipping.Results. Postoperatively, first-to-second degree encephalopathy was recorded in both groups. Positive changes as consciousness recovery were found in both Group 1 in which the patients used branched-chain amino acid-enriched solutions and Group 2 (parenteral Oliclinomel feeding. The patients under examination were not given albumin solutions and fresh frozen plasma in the postoperative period. Moreover, by postoperative day 7, there were significant increases in the levels of albumin and total protein in Groups 1 and 2, in those of cholinesterase and the absolute count of lymphocytes, and a reduction in the concentration of C-reactive protein.Conclusion. Combined parenteral and enteral feedings are effective in patients after extensive hepatectomies. The parenteral feeding formula Oliclinomel may be used in this group of patients. 

  15. Karyotype evolution of giraffes (Giraffa camelopardalis) revealed by cross-species chromosome painting with Chinese muntjac (Muntiacus reevesi) and human (Homo sapiens) paints.

    Science.gov (United States)

    Huang, L; Nesterenko, A; Nie, W; Wang, J; Su, W; Graphodatsky, A S; Yang, F

    2008-01-01

    Considering the giraffe (Giraffa camelopardalis, GCA, 2n = 30) as a primitive species, its comparative genomic data are critical for our understanding of the karyotype evolution of pecorans. Here, we have established genome-wide chromosomal homologies between giraffe, Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and human (Homo sapiens, HSA, 2n = 46) with whole sets of chromosome-specific paints from Chinese muntjac and human, in addition to providing a high-resolution G-banding karyotype of giraffe. Chinese muntjac and human chromosome paints detected 32 and 45 autosomal homologs in the genome of giraffe, respectively. Our results suggest that it would require at least thirteen fissions, six fusions and three intrachromosomal rearrangements to 'transform' the 2n = 44 eutherian ancestral karyotype to the 2n = 58 pecoran ancestral karyotype. During giraffe evolution, some ancestral eutherian syntenies (i.e. association of HSA3/21, 4/8, 7/16, 14/15, 16/19 and two forms of 12/22) have been retained, while several derived syntenies (i.e. associations of human homologous segments 2/1, 2/9, 5/19, 4/12/22, 8/9, and 10/20) have been produced. The reduction of chromosome number in giraffe from the 2n = 58 pecoran ancestral karyotype could be primarily attributed to extensive Robertsonian translocations of ancestral chromosomal segments. More complex chromosomal rearrangements (including tandem fusion, centromere repositioning and pericentric inversion) have happened during the evolution of GCA2 and GCA8. Copyright 2008 S. Karger AG, Basel.

  16. An Expressive Extension of TLC

    DEFF Research Database (Denmark)

    Henriksen, Jesper Gulmann

    2002-01-01

    A temporal logic of causality (TLC) was introduced by Alur, Penczek and Peled in [1]. It is basically a linear time temporal logic interpreted over Mazurkiewicz traces which allows quantification over causal chains. Through this device one can directly formulate causality properties of distributed...... systems. In this paper we consider an extension of TLC by strengthening the chain quantification operators. We show that our logic TLC* adds to the expressive power of TLC. We do so by defining an Ehrenfeucht-Fraïssé game to capture the expressive power of TLC. We then exhibit a property and by means...... of this game prove that the chosen property is not definable in TLC. We then show that the same property is definable in TLC*. We prove in fact the stronger result that TLC* is expressively stronger than TLC exactly when the dependency relation associated with the underlying trace alphabet is not transitive....

  17. Fluorescein-related extensive jaundice.

    Science.gov (United States)

    Kalkan, Asim; Turedi, Suleyman; Aydin, Ibrahim

    2015-03-01

    Fluorescein is a chemical dye frequently used in eye diseases to assess blood flow in the retina, choroid tissue, and iris. Although it has many known adverse effects, it has not previously been reported to lead to jaundice. The purpose of this case report was to emphasize that for patients presenting at the emergency department with jaundice symptoms, it should not be forgotten by emergency physicians that jaundice can develop after fluorescein angiography. Case: A 65-year-old woman presented at the emergency department with extensive jaundice that had developed on her entire body a few hours after fluorescein angiography applied because of vision impairment. The test results for all the diseases considered to cause jaundice were normal,and fluorescein-related jaundice was diagnosed. Conclusion: A detailed anamnesis should be taken when jaundice is seen in patients who have undergone fluorescein angiography, and it should not be forgotten that fluorescein dye is a rare cause of jaundice.

  18. Competency Modeling in Extension Education: Integrating an Academic Extension Education Model with an Extension Human Resource Management Model

    Science.gov (United States)

    Scheer, Scott D.; Cochran, Graham R.; Harder, Amy; Place, Nick T.

    2011-01-01

    The purpose of this study was to compare and contrast an academic extension education model with an Extension human resource management model. The academic model of 19 competencies was similar across the 22 competencies of the Extension human resource management model. There were seven unique competencies for the human resource management model.…

  19. Extension contact and professional competencies needed by ...

    African Journals Online (AJOL)

    Extension contact and professional competencies needed by extension agents in the Central Region of Ghana for effective transfer of fish-processing technologies to small-scale women in fish processing - Provisional Communication.

  20. 7 CFR 15b.27 - Extension education.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Extension education. 15b.27 Section 15b.27 Agriculture... Education § 15b.27 Extension education. (a) General. A recipient to which this subpart applies that provides extension education may not, on the basis of handicap, exclude qualified handicapped persons. A recipient...

  1. Improving the Extension Facilities in C+

    Energy Technology Data Exchange (ETDEWEB)

    Dubois, P F; Scott, B A

    1999-09-24

    CXX is a facility for extending Python using C++. Recently, the authors have substantially revised and improved the way in which you create extension objects and extension modules in C++. The method is now much more natural and has much less overhead, both in the code generated and in the effort needed to create the objects and extensions.

  2. Effectiveness Of Communication Outreach Strategies Of Extension ...

    African Journals Online (AJOL)

    Communication is a major component of agricultural extension and extension agents utilize various methods to deliver messages to their clienteles. The paper focused on the effectiveness of communication outreach strategies of extension agents in Imo State, Nigeria. Data for the study was collected with the aid of ...

  3. Agricultural Extension training needs of the Nongovernment ...

    African Journals Online (AJOL)

    Extension practitioners from the private sector are highly trained in the Natural Science. Some shortfalls in their Extension Science training have been identified. Perceived training needs in the Extension Science within this sector have been privatised. A number of possible training inputs and options are suggested. Options ...

  4. Extensive Reading and the Effect of Shadowing

    Science.gov (United States)

    Nakanishi, Takayuki; Ueda, Atsuko

    2011-01-01

    The aim of this study is to investigate the effects of extensive reading (ER) and shadowing on performance on reading comprehension tests. This study addressed the following research questions: (a) Can extensive reading improve students' reading comprehension? and (b) can shadowing enhance the effects of extensive reading? The participants in the…

  5. Rural Extension Services. Policy Research Working Paper.

    Science.gov (United States)

    Anderson, Jock R.; Feder, Gershon

    This paper analyzes the considerations that lead policy makers to undertake extension investments as a key public responsibility, as well as the complex set of factors and intra-agency incentives that explain variations in performance between different extension systems. The goals of extension include transferring knowledge from researchers to…

  6. Extensions of cutting problems: setups

    Directory of Open Access Journals (Sweden)

    Sebastian Henn

    2013-08-01

    Full Text Available Even though the body of literature in the area of cutting and packing is growing rapidly, research seems to focus on standard problems in the first place, while practical aspects are less frequently dealt with. This is particularly true for setup processes which arise in industrial cutting processes whenever a new cutting pattern is started (i.e. a pattern is different from its predecessor and the cutting equipment has to be prepared in order to meet the technological requirements of the new pattern. Setups involve the consumption of resources and the loss of production time capacity. Therefore, consequences of this kind must explicitly be taken into account for the planning and control of industrial cutting processes. This results in extensions to traditional models which will be reviewed here. We show how setups can be represented in such models, and we report on the algorithms which have been suggested for the determination of solutions of the respective models. We discuss the value of these approaches and finally point out potential directions of future research.

  7. [Extensively drug-resistant tuberculosis].

    Science.gov (United States)

    Lange, C; Grobusch, M P; Wagner, D

    2008-02-01

    Recently an increasing number of antibiotic-resistant MYCOBACTERIUM TUBERCULOSIS (MTB) strains have been described worldwide. The term XDR- (extensively drug-resistant) tuberculosis (TB) has been introduced by the World Health Organisation (WHO) to characterize multi-drug-resistant MTB strains that are in vitro resistant against fluorochinolones and one of the injectible substances amikacin, capreomycin or kanamycin in addition to isoniazid and rifampin. Strains of XDR-MTB are currently increasingly seen in HIV-seropositive individuals with tuberculosis in southern Africa, where these strains are passed by person-to person contact. XDR-TB has become a serious problem for the health administrations in this region. In contrast, cases of XDR-TB are only rarely seen in Germany so far, mainly among the population of pre-treated migrants from eastern Europe. The development of rapid diagnostic tests for resistance testing and new drugs for the treatment of tuberculosis has lacked support for several decades. The sudden emergence of XDR-MTB strains now warrants immediate action for the development of such tests and new classes of antibiotics to give all patients with TB a chance for a successful treatment.

  8. XPL the Extensible Presentation Language

    Directory of Open Access Journals (Sweden)

    A. Santangelo

    2009-01-01

    Full Text Available The last decade has witnessed a growing interest in the development of web interfaces enabling both multiple ways to access contents and, at the same time, fruition by multiple modalities of interaction (point-and-click, contents reading, voice commands, gestures, etc.. In this paper we describe a framework aimed at streamlining the design process of multi-channel, multimodal interfaces enabling full reuse of software components. This framework is called the eXtensible Presentation architecture and Language (XPL, a presentation language based on design pattern paradigm that keeps separated the presentation layer from the underlying programming logic. The language supplies a methodology to expedite multimodal interface development and to reduce the effort to implement interfaces for multiple access devices, by means of using the same code. This paper describes a methodology approach based on Visual Design Pattern (ViDP and Verbal Design Pattern (VeDP, offering examples of multimodal and multichannel interfaces created with the XPL Editor.

  9. Anaesthetic management of a case of schwannoma with intraoral extension

    Directory of Open Access Journals (Sweden)

    Mamta Bhardwaj

    2015-04-01

    Full Text Available Schwannoma is a benign nerve sheath tumour. This benign lesion frequently occurs in the soft tissues of head and neck region and has various complicated growth patterns. These patients can present a challenge to the anaesthesiologist due to intraoral extension, leading to difficult mask ventilation and intubation. We report a 16 year old male with mandibular nerve schwannoma with intraoral extension. Intraoral examination revealed a diffuse swelling in the left side of soft palate with deviation of uvula to right side. He was advised gargles with 4 ml of 2% xylocaine viscous and 2–3 puffs of 10% xylocaine spray done in oral cavity and oropharynx. Check laryngoscopy revealed Cormack and Lehane grade 1 view. Patient was intubated using standard induction technique and successfully managed

  10. Extensive Reading in the EFL Classroom: Benefits of a Face-to-Face Collaboration Activity

    Science.gov (United States)

    Kirchhoff, Cheryl

    2015-01-01

    Extensive reading is an approach to language education that has shown great promise for foreign language learners to acquire language; however, implementation reveals difficulty in maintaining student motivation to read over long periods of time. This study investigates students' experience of face-to-face talk about books in an extensive reading…

  11. Two endogenous proteins that induce cell wall extension in plants

    Science.gov (United States)

    McQueen-Mason, S.; Durachko, D. M.; Cosgrove, D. J.

    1992-01-01

    Plant cell enlargement is regulated by wall relaxation and yielding, which is thought to be catalyzed by elusive "wall-loosening" enzymes. By employing a reconstitution approach, we found that a crude protein extract from the cell walls of growing cucumber seedlings possessed the ability to induce the extension of isolated cell walls. This activity was restricted to the growing region of the stem and could induce the extension of isolated cell walls from various dicot stems and the leaves of amaryllidaceous monocots, but was less effective on grass coleoptile walls. Endogenous and reconstituted wall extension activities showed similar sensitivities to pH, metal ions, thiol reducing agents, proteases, and boiling in methanol or water. Sequential HPLC fractionation of the active wall extract revealed two proteins with molecular masses of 29 and 30 kD associated with the activity. Each protein, by itself, could induce wall extension without detectable hydrolytic breakdown of the wall. These proteins appear to mediate "acid growth" responses of isolated walls and may catalyze plant cell wall extension by a novel biochemical mechanism.

  12. Extension of platelet concentrate storage.

    Science.gov (United States)

    Simon, T L; Nelson, E J; Carmen, R; Murphy, S

    1983-01-01

    Extension of the storage time of platelet concentrates in a satellite bag which is part of a new blood bag system was studied by reinfusing autologous 51Cr-labeled platelets into normal volunteers, and measuring postinfusion platelet counts and bleeding times in patients requiring platelet transfusions. This satellite bag, made of polyvinylchloride plasticized with a new agent, was found to protect platelet concentrates against fall of pH better than other containers studied. This protection was felt to be due to the greater gas permeability of the new plastic. Mean in vivo recovery and half-life (greater than 31% and 3.3 days, respectively) of autologous reinfused platelets were satisfactory following 5 days of storage. Following 7 days of storage, mean recovery was 41 percent and half-life was 2.8 days. Peripheral platelet count increments in patients following platelet transfusions with concentrates stored 4 to 7 days in the new plastic were comparable to increments following transfusion of platelets stored 2 to 3 days in the other plastics studied. Bleeding times shortened in three of four patients receiving platelet concentrates stored from 4 to 6 days in the new plastic. Platelet concentrates stored in the new bag at 20 to 24 degrees C with flat-bed or elliptical agitation could be transfused for up to 5 days following phlebotomy with acceptable clinical results. The new plastic container is promising for storage of platelet concentrates for up to 7 days. Due to the higher pH of 50-ml platelet concentrates stored in bags made with the new plastic, the concentrates were superior at any storage interval to those stored in bags made of the other plastics studied.

  13. Extension Large Colon Resection in 12 Horses

    Science.gov (United States)

    Arighi, Mimi; Ducharme, Norman G.; Horney, F. Donald.; Livesey, Michael A.

    1987-01-01

    Extensive resection (50-75%) of the large colon was performed in 12 horses. Indications for resection were: loss of viability due to large colon volvulus (seven), thromboembolic episode (three), impairment of flow of ingesta due to adhesions (one), or congenital abnormalities (one). The time required to correct the primary cause of abdominal pain and complete the resection ranged from 2.5 to 4.75 hours. Three horses had severe musculoskeletal problems postoperatively and were euthanized in the recovery stall. Four other horses were euthanized early in the postoperative period because of: further large colon infarction (two), ileus (one), or small intestinal problems (one). Five horses survived with no apparent nutritional or metabolic problems during two to three weeks of hospitalization. Clinical data were obtained from these horses from nine months to eighteen months postoperatively and revealed no clinical or clinicopathological abnormalities in four of them; the fifth horse exhibited diarrhea and weight loss four months postoperatively but responded to diet change. PMID:17422768

  14. Knowledge and perception of extension workers towards ict utilization in agricultural extension service delivery in Gazipur district of Bangladesh

    Directory of Open Access Journals (Sweden)

    F.A. Prodhan

    2014-12-01

    Full Text Available The primary purpose of the study was to assess the extent of knowledge and perception of extension workers towards ICT utilization and to determine the relationship between the selected characteristics of the respondents and knowledge and perception of extension workers towards ICT utilization in extension service delivery. The study was conducted in Gazipur district and comprised proportionate random sample of 90 extension workers from five upazila of Gazipur district. A pre-tested interview schedule was used to collect data from the respondents. To measure the knowledge on ICT utilization 35 statements were selected regarding 7 ICT with five possible answer of each tools and a score of one was given to the right answer and zero to the wrong answer alternatively to measure the perception of the respondents rated each of 10 statements ICT utilization in agriculture on a 5-point Likert type scale and the total of these ratings formed perception index. The result of the study showed that out of seven ICT tools the knowledge of extension workers was highest in case of MS Word this was followed by internet/ web service and the lowest knowledge was found in case of Geographical Information System. It is observed that an overwhelming majority (88.9% of agricultural extension workers in the study area had low to medium knowledge towards ICT utilization. Findings reveal that the respondents had top most perception on the ICT utilization in respect of ‘Extension work can be greatly enhanced by ICT’ followed by on ‘The benefits of ICT use outweigh the financial burden involved’. The result also indicated that more than fourth-fifth (84.4% of the respondents had medium to high perception towards ICT utilization. There were significant relationship between service experience and use of the information sources of the respondents with their knowledge towards ICT utilization conversely innovativeness, cosmopoliteness and job satisfaction of the

  15. Extension systems in Southern African countries: A review | Oladele ...

    African Journals Online (AJOL)

    Global Approaches to Extension Practice: A Journal of Agricultural Extension ... programmes to improve rural areas, extensive grassroots coverage, use of ICT, high involvement of farmers in extension planning, potential for effective programme implementation, and effective setting of extension administration units.

  16. The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species

    OpenAIRE

    Byrne, Kevin P.; Wolfe, Kenneth H

    2005-01-01

    We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome du...

  17. Extension of Mittag-Leffler function

    OpenAIRE

    Rahman, G.; K.S. Nisar; Mubeen, S; Arshad, M.

    2017-01-01

    In this paper, we present an extension of Mittag-Leffler function by using the extension of beta functions (\\"{O}zergin et al. in J. Comput. Appl. Math. 235 (2011), 4601-4610) and obtain some integral representation of this newly defined function. Also, we present the Mellin transform of this function in terms of Wright hypergeometric function. Furthermore, we show that the extended fractional derivative of the usual Mittag-Leffler function gives the extension of Mittag-Leffler function.

  18. Revealing the 1 nm/s Extensibility of Nanoscale Amorphous Carbon in a Scanning Electron Microscope

    DEFF Research Database (Denmark)

    Zhang, Wei

    2013-01-01

    In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformati...... positive implications to explore some amorphous carbon as electron field emission device. SCANNING 35: 261-264, 2013. © 2012 Wiley Periodicals, Inc.......In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformation...... promoted by the electric field, which resulted from an inner secondary electron potential difference from the main trunk of carbon film to the tip end of branches under electron beam. This result demonstrates importance of applying electrical effects to modify properties of carbon materials. It may have...

  19. Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis

    Science.gov (United States)

    2009-08-27

    DNA chip . One of four destination colonies that matched the expected insert size was selected and rearrayed into deep well plates with 2 yeast extract...Jagels, K., Karlyshev, A. V., Leather , S., Moule, S., Oyston, P. C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S...Snyder, M. (2001) Global analysis of protein activities using proteome chips . Science 293, 2101–2105 18. Schmid, K. E., Keasey, S. L., Pittman, P

  20. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

    Science.gov (United States)

    Bredeson, Jessen V; Lyons, Jessica B; Prochnik, Simon E; Wu, G Albert; Ha, Cindy M; Edsinger-Gonzales, Eric; Grimwood, Jane; Schmutz, Jeremy; Rabbi, Ismail Y; Egesi, Chiedozie; Nauluvula, Poasa; Lebot, Vincent; Ndunguru, Joseph; Mkamilo, Geoffrey; Bart, Rebecca S; Setter, Tim L; Gleadow, Roslyn M; Kulakow, Peter; Ferguson, Morag E; Rounsley, Steve; Rokhsar, Daniel S

    2016-05-01

    Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

  1. Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization.

    Science.gov (United States)

    He, Zhesi; Wang, Lihong; Harper, Andrea L; Havlickova, Lenka; Pradhan, Akshay K; Parkin, Isobel A P; Bancroft, Ian

    2017-05-01

    Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait-controlling dosage effects. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  2. Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae), a genus that has undergone rapid radiation

    National Research Council Canada - National Science Library

    Wan, Dongshi; Sun, Yongshuai; Zhang, Xu; Bai, Xiaotao; Wang, Jun; Wang, Ailan; Milne, Richard

    2014-01-01

    During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character...

  3. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages.

    Science.gov (United States)

    Bidon, Tobias; Janke, Axel; Fain, Steven R; Eiken, Hans Geir; Hagen, Snorre B; Saarma, Urmas; Hallström, Björn M; Lecomte, Nicolas; Hailer, Frank

    2014-06-01

    Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Analysis of patterns of bushmeat consumption reveals extensive exploitation of protected species in eastern Madagascar.

    Directory of Open Access Journals (Sweden)

    Richard K B Jenkins

    Full Text Available Understanding the patterns of wild meat consumption from tropical forests is important for designing approaches to address this major threat to biodiversity and mitigate potential pathways for transmission of emerging diseases. Bushmeat consumption has been particularly poorly studied in Madagascar, one of the world's hottest biodiversity hotspots. Studying bushmeat consumption is challenging as many species are protected and researchers must consider the incentives faced by informants. Using interviews with 1154 households in 12 communes in eastern Madagascar, as well as local monitoring data, we investigated the importance of socio-economic variables, taste preference and traditional taboos on consumption of 50 wild and domestic species. The majority of meals contain no animal protein. However, respondents consume a wide range of wild species and 95% of respondents have eaten at least one protected species (and nearly 45% have eaten more than 10. The rural/urban divide and wealth are important predictors of bushmeat consumption, but the magnitude and direction of the effect varies between species. Bushmeat species are not preferred and are considered inferior to fish and domestic animals. Taboos have provided protection to some species, particularly the Endangered Indri, but we present evidence that this taboo is rapidly eroding. By considering a variety of potential influences on consumption in a single study we have improved understanding of who is eating bushmeat and why. Evidence that bushmeat species are not generally preferred meats suggest that projects which increase the availability of domestic meat and fish may have success at reducing demand. We also suggest that enforcement of existing wildlife and firearm laws should be a priority, particularly in areas undergoing rapid social change. The issue of hunting as an important threat to biodiversity in Madagascar is only now being fully recognised. Urgent action is required to ensure that heavily hunted species are adequately protected.

  5. The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy.

    Directory of Open Access Journals (Sweden)

    Daniel R Beniac

    Full Text Available BACKGROUND: Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. CONCLUSIONS: The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope.

  6. The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy.

    Science.gov (United States)

    Beniac, Daniel R; Melito, Pasquale L; Devarennes, Shauna L; Hiebert, Shannon L; Rabb, Melissa J; Lamboo, Lindsey L; Jones, Steven M; Booth, Timothy F

    2012-01-01

    Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope.

  7. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...

  8. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

    Science.gov (United States)

    van de Guchte, M; Penaud, S; Grimaldi, C; Barbe, V; Bryson, K; Nicolas, P; Robert, C; Oztas, S; Mangenot, S; Couloux, A; Loux, V; Dervyn, R; Bossy, R; Bolotin, A; Batto, J-M; Walunas, T; Gibrat, J-F; Bessières, P; Weissenbach, J; Ehrlich, S D; Maguin, E

    2006-06-13

    Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

  9. Analysis of infantile fibrosarcoma reveals extensive T-cell responses within tumors: Implications for immunotherapy.

    Science.gov (United States)

    Zhu, Hua; Gu, Song; Yin, Minzhi; Shi, Min; Xin, Chao; Zhu, Jianmin; Wang, Jing; Huang, Siqi; Xie, Chenjie; Ma, Jing; Pan, Ci; Tang, Jingyan; Xu, Min; Bai, Xue-Feng

    2018-02-01

    Infantile fibrosarcoma (IFS) is a rare pediatric malignancy with relatively good prognosis, but the risk of progression or recurrence after therapy exists. To understand the immune microenvironment of IFS and determine if immunotherapy is a potential treatment, we analyzed T-cell responses in IFS tumors. IFS tumors were analyzed by immunohistochemistry and multicolor flow cytometry to characterize immune cell infiltration and function. Tumor infiltrating lymphocytes (TILs) were expanded in vitro and evaluated for recognition of autologous tumor cells. Real-time PCR was applied to evaluate tumor expression of chemokines/cytokines and tumor antigens. Significant infiltration of both CD4+ and CD8+ T cells was found in seven of 10 IFS but rarely found in age- and sex-matched rhabdomyosarcoma tumors. The TILs from recurrent IFS tumors expressed high levels of costimulatory molecules such as CD28, 4-1BB, and OX40, but little or no coinhibitory molecules such as PD-1 and CTLA4, Tim3, Lag3, and CD39. Upon activation, large portions of TILs produced IFN-γ and TNF-α. Eighteen out of 40 T cell lines generated from surgically removed tumors could recognize autologous tumor cells. Moreover, we found that IFS tumors expressed high levels of T-cell chemokines such as CXCL10 and CXCL16, and also classic tumor antigens such as CTAG2, GAGE, and NY-ESO-1, whose expression could be further enhanced by treatment with epigenetic modulator decitabine. IFS tumors are highly immunogenic and expansion of TILs followed by adoptive cell transfer could be a potential immunotherapy for IFS patients undergoing tumor recurrence. © 2017 Wiley Periodicals, Inc.

  10. Replication history of B lymphocytes reveals homeostatic proliferation and extensive antigen-induced B cell expansion

    NARCIS (Netherlands)

    M.C. van Zelm (Menno); T. Szczepanski (Tomasz); M. van der Burg (Mirjam); J.J.M. van Dongen (Jacques)

    2007-01-01

    textabstractThe contribution of proliferation to B lymphocyte homeostasis and antigen responses is largely unknown. We quantified the replication history of mouse and human B lymphocyte subsets by calculating the ratio between genomic coding joints and signal joints on kappa-deleting recombination

  11. Expanded target-chemical analysis reveals extensive mixed-organic-contaminant exposure in USA streams

    Science.gov (United States)

    Bradley, Paul M.; Journey, Celeste A.; Romanok, Kristin; Barber, Larry B.; Buxton, Herbert T.; Foreman, William; Furlong, Edward T.; Glassmeyer, Susan T.; Hladik, Michelle L.; Iwanowicz, Luke R.; Jones, Daniel K.; Kolpin, Dana W.; Kuivila, Kathryn M.; Loftin, Keith A.; Mills, Marc A.; Meyer, Michael T.; Orlando, James L.; Reilly, Timothy J.; Smalling, Kelly L.; Villeneuve, Daniel L.

    2017-01-01

    Surface water from 38 streams nationwide was assessed using 14 target-organic methods (719 compounds). Designed-bioactive anthropogenic contaminants (biocides, pharmaceuticals) comprised 57% of 406 organics detected at least once. The 10 most-frequently detected anthropogenic-organics included eight pesticides (desulfinylfipronil, AMPA, chlorpyrifos, dieldrin, metolachlor, atrazine, CIAT, glyphosate) and two pharmaceuticals (caffeine, metformin) with detection frequencies ranging 66–84% of all sites. Detected contaminant concentrations varied from less than 1 ng L–1 to greater than 10 μg L–1, with 77 and 278 having median detected concentrations greater than 100 ng L–1 and 10 ng L–1, respectively. Cumulative detections and concentrations ranged 4–161 compounds (median 70) and 8.5–102 847 ng L–1, respectively, and correlated significantly with wastewater discharge, watershed development, and toxic release inventory metrics. Log10 concentrations of widely monitored HHCB, triclosan, and carbamazepine explained 71–82% of the variability in the total number of compounds detected (linear regression; p-values: environment application (pesticides), designed-bioactive organics (median 41 per site at μg L–1 cumulative concentrations) in developed watersheds present aquatic health concerns, given their acknowledged potential for sublethal effects to sensitive species and lifecycle stages at low ng L–1.

  12. Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism

    DEFF Research Database (Denmark)

    Hao, Qin; Yadav, Rachita; Basse, Astrid L.

    2015-01-01

    We applied digital gene expression profiling to determine the transcriptome of brown and white adipose tissues (BAT and WAT, respectively) during cold exposure. Male C57BL/6J mice were exposed to cold for 2 or 4 days. A notable induction of genes related to glucose uptake, glycolysis, glycogen...... exposure, we propose a model for the intermediary glucose metabolism in activated BAT: 1) fluxes through glycolysis and the pentose phosphate pathway are induced, the latter providing reducing equivalents for de novo fatty acid synthesis; 2) glycerol synthesis from glucose is increased, facilitating...

  13. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

    DEFF Research Database (Denmark)

    Bowl, Michael R.; Simon, Michelle M.; Ingham, Neil J.

    2017-01-01

    The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. O...

  14. Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer

    DEFF Research Database (Denmark)

    Su, Ying; Subedee, Ashim; Bloushtain-Qimron, Noga

    2015-01-01

    genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but a high degree...

  15. Biocytin Filling of Adult Gonadotropin-Releasing Hormone Neurons in Situ Reveals Extensive, Spiny, Dendritic Processes

    National Research Council Canada - National Science Library

    Campbell, Rebecca E; Han, Seong-Kyu; Herbison, Allan E

    2005-01-01

    .... Using acute brain slices prepared from transgenic GnRH-green fluorescent protein mice, individual fluorescing GnRH neurons were identified, patched, and filled with the small-molecular-weight dye biocytin...

  16. A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

    DEFF Research Database (Denmark)

    Grove, C.; De Masi, Federico; Newburger, Daniel

    2009-01-01

    parameters remain undetermined. We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs, and model these data into an integrated network. This network displays both specificity and promiscuity, as some b...

  17. Phosphoproteome analysis of streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation

    DEFF Research Database (Denmark)

    Manteca, Angel; Ye, Juanying; Sánchez, Jesús

    2011-01-01

    Streptomycetes are bacterial species that undergo a complex developmental cycle that includes programmed cell death (PCD) events and sporulation. They are widely used in biotechnology because they produce most clinically relevant secondary metabolites. Although Streptomyces coelicolor is one...... events were detected during the presporulation and sporulation stages (80%). Most of these phosphorylations were not reported before in Streptomyces, and included sporulation factors, transcriptional regulators, protein kinases and other regulatory proteins. Several of the identified phosphorylated...

  18. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a comput......RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...

  19. Seeing the Whole Elephant: Imaging Flow Cytometry Reveals Extensive Morphological Diversity within Blastocystis Isolates

    Science.gov (United States)

    Yason, John Anthony; Tan, Kevin Shyong Wei

    2015-01-01

    Blastocystis is a common protist isolated in humans and many animals. The parasite is a species complex composed of 19 subtypes, 9 of which have been found in humans. There are biological and molecular differences between Blastocystis subtypes although microscopy alone is unable to distinguish between these subtypes. Blastocystis isolates also display various morphological forms. Several of these forms, however, have not been properly evaluated on whether or not these play significant functions in the organism's biology. In this study, we used imaging flow cytometry to analyze morphological features of Blastocystis isolates representing 3 subtypes (ST1, ST4 and ST7). We also employed fluorescence dyes to discover new cellular features. The profiles from each of the subtypes exhibit considerable differences with the others in terms of shape, size and granularity. We confirmed that the classical vacuolar form comprises the majority in all three subtypes. We have also evaluated other morphotypes on whether these represent distinct life stages in the parasite. Irregularly-shaped cells were identified but all of them were found to be dying cells in one isolate. Granular forms were present as a continuum in both viable and non-viable populations, with non-viable forms displaying higher granularity. By analyzing the images, rare morphotypes such as multinucleated cells could be easily observed and quantified. These cells had low granularity and lower DNA content. Small structures containing nucleic acid were also identified. We discuss the possible biological implications of these unusual forms. PMID:26618361

  20. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

    Directory of Open Access Journals (Sweden)

    Marie Foulongne-Oriol

    2016-05-01

    Full Text Available Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG, and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens.

  1. Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins.

    Science.gov (United States)

    Khater, Shradha; Mohanty, Debasisa

    2014-07-24

    Bacterial phosphothreonine lyases catalyze a novel posttranslational modification involving formation of dehydrobutyrine/dehyroalanine by β elimination of the phosphate group of phosphothreonine or phosphoserine residues in their substrate proteins. Though there is experimental evidence for presence of dehydro amino acids in human proteins, no eukaryotic homologs of these lyases have been identified as of today. A comprehensive genome-wide search for identifying phosphothreonine lyase homologs in eukaryotes was carried out. Our fold-based search revealed structural and catalytic site similarity between bacterial phosphothreonine lyases and BLES03 (basophilic leukemia-expressed protein 03), a human protein with unknown function. Ligand induced conformational changes similar to bacterial phosphothreonine lyases, and movement of crucial arginines in the loop region to the catalytic pocket upon binding of phosphothreonine-containing peptides was seen during docking and molecular dynamics studies. Genome-wide search for BLES03 homologs using sensitive profile-based methods revealed their presence not only in eukaryotic classes such as chordata and fungi but also in bacterial and archaebacterial classes. The synteny of these archaebacterial BLES03-like proteins was remarkably similar to that of type IV lantibiotic synthetases which harbor LanL-like phosphothreonine lyase domains. Hence, context-based analysis reinforced our earlier sequence/structure-based prediction of phosphothreonine lyase catalytic function for BLES03. Our in silico analysis has revealed that BLES03-like proteins with previously unknown function are novel eukaryotic phosphothreonine lyases involved in biosynthesis of dehydro amino acids, whereas their bacterial and archaebacterial counterparts might be involved in biosynthesis of natural products similar to lantibiotics. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Tsallis non-extensive statistics and solar wind plasma complexity

    Science.gov (United States)

    Pavlos, G. P.; Iliopoulos, A. C.; Zastenker, G. N.; Zelenyi, L. M.; Karakatsanis, L. P.; Riazantseva, M. O.; Xenakis, M. N.; Pavlos, E. G.

    2015-03-01

    This article presents novel results revealing non-equilibrium phase transition processes in the solar wind plasma during a strong shock event, which took place on 26th September 2011. Solar wind plasma is a typical case of stochastic spatiotemporal distribution of physical state variables such as force fields (B → , E →) and matter fields (particle and current densities or bulk plasma distributions). This study shows clearly the non-extensive and non-Gaussian character of the solar wind plasma and the existence of multi-scale strong correlations from the microscopic to the macroscopic level. It also underlines the inefficiency of classical magneto-hydro-dynamic (MHD) or plasma statistical theories, based on the classical central limit theorem (CLT), to explain the complexity of the solar wind dynamics, since these theories include smooth and differentiable spatial-temporal functions (MHD theory) or Gaussian statistics (Boltzmann-Maxwell statistical mechanics). On the contrary, the results of this study indicate the presence of non-Gaussian non-extensive statistics with heavy tails probability distribution functions, which are related to the q-extension of CLT. Finally, the results of this study can be understood in the framework of modern theoretical concepts such as non-extensive statistical mechanics (Tsallis, 2009), fractal topology (Zelenyi and Milovanov, 2004), turbulence theory (Frisch, 1996), strange dynamics (Zaslavsky, 2002), percolation theory (Milovanov, 1997), anomalous diffusion theory and anomalous transport theory (Milovanov, 2001), fractional dynamics (Tarasov, 2013) and non-equilibrium phase transition theory (Chang, 1992).

  3. A lyapunov-based extension to particle swarm dynamics for continuous function optimization.

    Science.gov (United States)

    Bhattacharya, Sayantani; Konar, Amit; Das, Swagatam; Han, Sang Yong

    2009-01-01

    The paper proposes three alternative extensions to the classical global-best particle swarm optimization dynamics, and compares their relative performance with the standard particle swarm algorithm. The first extension, which readily follows from the well-known Lyapunov's stability theorem, provides a mathematical basis of the particle dynamics with a guaranteed convergence at an optimum. The inclusion of local and global attractors to this dynamics leads to faster convergence speed and better accuracy than the classical one. The second extension augments the velocity adaptation equation by a negative randomly weighted positional term of individual particle, while the third extension considers the negative positional term in place of the inertial term. Computer simulations further reveal that the last two extensions outperform both the classical and the first extension in terms of convergence speed and accuracy.

  4. A Giant Guteal Schwannoma with extension into the Pelvis: A case ...

    African Journals Online (AJOL)

    RESULTS: Clinical examination revealed a 40cm by 60cm mass in the right gluteal region and continuous with a 25 cm by 15 cm pelvic mass. The ultrasound scan revealed a very complex (mixed solid and fluid containing) gluteal mass with extension to the pelvis. The CT scan showed a very large, well defined lobulated ...

  5. Towards professionalism in agricultural extension: The professional ...

    African Journals Online (AJOL)

    Towards professionalism in agricultural extension: The professional registration of Extensionists in South Africa – A dream or a reality? The role of the South African Society of Extensionists in South Africa – A dream or a reality? The role of the South African Society of Agricultural Extension (SASAE)

  6. Effective Use of Facebook for Extension Professionals

    Science.gov (United States)

    Mains, Mark; Jenkins-Howard, Brooke; Stephenson, Laura

    2013-01-01

    As the use of social media increases, Extension is challenged to stay relevant with cliental by using digital tools. This article illustrates how Facebook can be part of Extension's repertoire of methods for communication, program implementation, education, and marketing. This allows professionals to build social networking capacity with…

  7. Job satisfaction of extension agents towards innovation ...

    African Journals Online (AJOL)

    The study assessed job satisfaction of extension agents towards innovation dissemination to fish farmers in Lagos State, Nigeria. A simple random sampling technique was used to select 44 extension officers from which data were collected. A structured questionnaire consisting of 6 personal characteristics, 23 management ...

  8. Plagiarism within Extension: Origin and Current Effects

    Science.gov (United States)

    Rollins, Dora

    2011-01-01

    Extension publication editors from around the United States are finding cases of plagiarism within manuscripts that Extension educators submit as new public education materials. When editors confront such educators with the problem, some don't understand it as such, rationalizing that reproducing published information for a new purpose qualifies…

  9. Extension Sustainability Camp: Design, Implementation, and Evaluation

    Science.gov (United States)

    Brain, Roslynn; Upton, Sally; Tingey, Brett

    2015-01-01

    Sustainability Camps provide an opportunity for Extension educators to be in the forefront of sustainability outreach and to meet the growing demand for sustainability education. This article shares development, implementation, and evaluation of an Extension Sustainability Camp for youth, grades 4-6. Camp impact was measured via daily pre-and…

  10. Sound Type-Dependent Syntactic Language Extension

    NARCIS (Netherlands)

    Lorenzen, Florian; Erdweg, S.T.

    2016-01-01

    Syntactic language extensions can introduce new facilities into a programming language while requiring little implementation effort and modest changes to the compiler. It is typical to desugar language extensions in a distinguished compiler phase after parsing or type checking, not affecting any of

  11. Implementing socially responsive forestry extension programmes ...

    African Journals Online (AJOL)

    Following a literature review which pays particular attention to southern African references, a socially responsive forestry extension model is outlined. It is contended that the initial establishment of sustainable extension programmes rest upon the nature of the relations between the central-level office, the extensionist and ...

  12. Agricultural extension officers' perceptions of integrated pest ...

    African Journals Online (AJOL)

    The extension officers further believed that IPM has the potential to contribute effectively in pest management by the majority of small scale farmers in Kenya. The extension officers viewed crop rotation, a cultural practice, to be of priority use in pest management. Most of the other IPM practices were considered practical in ...

  13. Communication for Strengthening Agricultural Extension and Rural ...

    African Journals Online (AJOL)

    chrischisoni

    communication theories, methods, technologies and strategies. Yet they feel inadequately trained in these areas. Extension workers' views on decentralization. The government's policies on decentralization and pluralistic and demand-driven extension were introduced in 2000. This study was conducted almost a decade ...

  14. Farmer Experience of Pluralistic Agricultural Extension, Malawi

    Science.gov (United States)

    Chowa, Clodina; Garforth, Chris; Cardey, Sarah

    2013-01-01

    Purpose: Malawi's current extension policy supports pluralism and advocates responsiveness to farmer demand. We investigate whether smallholder farmers' experience supports the assumption that access to multiple service providers leads to extension and advisory services that respond to the needs of farmers. Design/methodology/approach: Within a…

  15. Subintegrality, invertible modules and Laurent polynomial extensions

    Indian Academy of Sciences (India)

    Let ⊆ be a commutative ring extension. Let I(, ) be the multiplicative group of invertible -submodules of . In this article, we extend a result of Sadhu and Singh by finding a necessary and sufficient condition on an integral birational extension ⊆ of integral domains with dim ≤ 1, so that the natural map I(, ...

  16. Perception of Commercialization of Agricultural Extension Service ...

    African Journals Online (AJOL)

    Public extension service delivery system has been unable to satisfactorily respond to the challenges of agricultural development, poverty eradication and rural transformation in Nigeria, resulting in continued calls for alternative systems, including commercialization of extension service. Because of their strategically ...

  17. Extension Learners' Use of Electronic Technology

    Science.gov (United States)

    Guenthner, Joseph F.; Swan, Benjamin G.

    2011-01-01

    Extension clientele use electronic technology for entertainment, communication, and business. Educational programs that use electronic technology can enhance learning. To learn more about use of electronic technology among Extension clientele, we surveyed 80 university students and 135 potato farmers. We found that the farmers were likely to use…

  18. Livestock extension practice and competency among agricultural ...

    African Journals Online (AJOL)

    The challenge of meeting the ever-increasing demand for animal products in Nigeria has become keen over the years. A major factor is low technology input by the bulk of animal producers. Because Extension has a crucial role to play, the purpose of this study was to investigate livestock extension (LE) activities and ...

  19. Job satisfaction amongst agricultural extension personnel in ...

    African Journals Online (AJOL)

    Job satisfaction broadly is considered to be as attitude of a person reflecting the degree to which his/her important needs are satisfied by this job. To study the job satisfaction level and factors associated with job satisfaction of Extension personnel, a sample of 74 extension personnel from Kurdistan province of Iran were ...

  20. Declarative language extensions for Prolog courses

    NARCIS (Netherlands)

    Neumerkel, U.; Triska, M.; Wielemaker, J.

    2008-01-01

    In this paper we present several extensions to support a more declarative view of programming in Prolog. These extensions enable introductory Prolog courses to concentrate on the pure parts of Prolog for longer periods than without. Even quite complex programs can now be written free of any

  1. Extensive Reading in Enhancing Lexical Chunks Acquisition

    Science.gov (United States)

    Pereyra, Nilsa

    2015-01-01

    The purpose of this action research was to investigate the effect of extensive reading and related activities on the acquisition of lexical chunks in EFL students. Seven adult EFL learners with an Intermediate level volunteered to take part in the 16 week project following Extensive Reading principles combined with tasks based on the Lexical…

  2. Extensive Reading Materials Produced by Learning Communities

    Science.gov (United States)

    Jacobs, G. M.

    2013-01-01

    This article advocates that students and teachers create some of their own extensive reading materials. Learning communities act as a means of motivating and sustaining student and teacher production of extensive reading materials. The article begins by explaining learning communities. The bulk of the article has two parts. The first part focuses…

  3. Extensive Reading: Students' Performance and Perception

    Science.gov (United States)

    Fernandez de Morgado, Nelly

    2009-01-01

    Reading is thought to be a crucial skill in the EFL learning process, and Extensive Reading a very useful strategy. However, very few teachers implement it on a regular basis. The process of introducing Extensive Reading (ER) is considered far too expensive, complicated, and time-consuming. One way to encourage its use would be to more deeply…

  4. Creating Teams Increases Extension Educator Productivity

    Science.gov (United States)

    Chalker-Scott, Linda; Daniels, Catherine H.; Martini, Nicole

    2016-01-01

    The Garden Team at Washington State University is a transdisciplinary group of faculty, staff, and students with expertise in applied plant and soil sciences and an interest in Extension education. The team's primary mission is to create current, relevant, and peer-reviewed materials as Extension publications for home gardeners. The average yearly…

  5. 77 FR 16022 - Agency Information Collection Extension

    Science.gov (United States)

    2012-03-19

    ... 1995. The information collection requests a three-year extension of its Better Buildings, Better Plants... and Regulatory Affairs, Office of Management and Budget, New Executive Office Building, Room 10102... of Energy Efficiency and Renewable Energy Agency Information Collection Extension AGENCY: Office of...

  6. User contributions and public extension delivery modes ...

    African Journals Online (AJOL)

    This study examined a number of extension communication channels through which farmers received farm management services/information from the public extension agent. The idea was, first, to find out the dominant channel(s) through which information/services were received and, second, to assess the willingness of ...

  7. Bilateral Wilms Tumor With Ureteral Extension.

    Science.gov (United States)

    Lockwood, Gina; Ferrer, Fernando; Makari, John

    2017-04-01

    Wilms tumor is the most common renal tumor in children. However, tumor extension into the ureter is exceedingly rare. We present a case of bilateral Wilms tumor with unilateral ureteral extension into the bladder. This case illustrates the importance of thoughtful diagnostic evaluation and surgical planning to obtain a good oncologic outcome while preserving renal function. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. assessment of extension agents' communication methods

    African Journals Online (AJOL)

    USER

    ABSTRACT. The need to improve aquaculture production through enhanced technology transfer necessitated this study to assess extension agents' use of communication methods and its impact on linkage. A structured questionnaire was administered to 44 extension agents who were randomly selected from Lagos State ...

  9. Revitalizing Agricultural Extension Curriculum for Effective ...

    African Journals Online (AJOL)

    The authors argue that African agricultural universities and colleges must strengthen their capacities to develop and deliver responsive extension training programs in order to train extension staff to become critical thinkers and reflective practitioners. A framework is proposed to guide universities and colleges interested in ...

  10. Extension Service Delivery Of Agricultural Development ...

    African Journals Online (AJOL)

    The study was conducted to assess the extension service delivery within the Agricultural Development Programmes of Southwest Nigeria after the cessation of the World Bank funding between 1996 and 2013. Primary data were collected from 201 extension agents across 50% of the states in the area of study using ...

  11. Controleum - an independently extensible control system

    DEFF Research Database (Denmark)

    Jensen, Martin Lykke Rytter

    2014-01-01

    challenging kind of system to design for independent extension. This thesis presents two new software technologies that improve the extensibility of control systems: First, the concept of dynamic links is introduced and Decouplink – an implementation of dynamic links for Java - is presented. Dynamic links......While the extensibility of many software systems has been greatly improved during the past two decades, nontrivial control systems remain to be a category of software systems that are remarkably difficult for independent parties to extend. Support for independent extension is the ability...... is introduced, and an implementation is presented. The extensible controller is a component framework designed to automatically resolve conflicts among mutually unaware components in a control system. The solution is based on the idea that independent components implement different kinds of control concerns...

  12. Impact of invasive extranodal extension on the prognosis of patients with papillary thyroid carcinoma.

    Science.gov (United States)

    Moritani, Sueyoshi

    2014-12-01

    Although 20-50% of papillary thyroid carcinoma (PTC) patients initially present with lymph node metastases, prognosis is excellent. Thus, the significance of lymph node metastasis in PTC remains controversial. In this study, we examined the impact of extranodal extension to surrounding organs (invasive extranodal extension) on the prognosis for PTC patients. Medical records of PTC patients who underwent surgery as their initial treatment at our institution between 1981 and 2008 were retrospectively reviewed. Patients with or without invasive extranodal extension were selected. Our therapeutic strategy for PTC with invasive extranodal extension included complete resection and functional reconstruction. Intergroup comparison was performed using Student's t-test or the chi-square test as appropriate. Survival curves determined by the Kaplan-Meier method were compared for statistical significance using the log-rank test. A Cox-hazard regression model with the forward stepwise method was used for multivariate analysis. The study cohort included 60 (12.3%) patients with and 428 (87.7%) without invasive extranodal extension. The most common site of invasive extranodal extension in the central neck compartment was the recurrent laryngeal nerve, whereas the internal jugular vein was the most frequently invaded site in the lateral neck compartment. The locoregional recurrence rate did not differ significantly between patients with and without invasive extranodal extension, but the distant recurrence rate was higher for those with invasive extranodal extension. The 10-year disease-specific survival rate was significantly lower for patients with invasive extranodal extension than for those without invasive extranodal extension. Furthermore, multivariate analysis revealed that being aged ≥45 years, poor differentiation, and extrathyroidal extension were independent predictive factors for disease-specific death in PTC. Invasive extranodal extension had no effect on the

  13. Mixed periapical lesion: an atypical radicular cyst with extensive calcifications.

    Science.gov (United States)

    Ramos-Perez, Flávia Maria de Moraes; Pontual, Andréa dos Anjos; França, Talita Ribeiro Tenório de; Pontual, Maria Luiza dos Anjos; Beltrão, Ricardo Villar; Perez, Danyel Elias da Cruz

    2014-01-01

    The radicular cyst is an inflammatory odontogenic cyst of endodontic origin. Radiographically, the lesion appears as a periapical radiolucent image. This report describes a very rare case of a mixed periapical radiographic image diagnosed as a radicular cyst. A 37-year-old female patient presented a mixed, well-circumscribed image located in the periapical region of the left maxillary central incisor, which presented unsatisfactory endodontic treatment. Microscopic examination revealed a cavity lined by non-keratinized squamous epithelium and extensive calcifications in the cystic lumen and lining epithelium. Diagnosis of radicular cyst with extensive calcifications was established. Endodontic retreatment was performed and no radiographic signs of recurrence were observed 18 months after treatment. Although very rare, a radicular cyst should be considered in the differential diagnosis of a mixed periapical image associated to teeth with pulp necrosis.

  14. Identification of Current Proficiency Level of Extension Competencies and the Competencies Needed for Extension Agents to Be Successful in the 21st Century

    Directory of Open Access Journals (Sweden)

    Dona Lakai

    2014-02-01

    Full Text Available In this era of globalization, competency is an issue of concern to any field of professionals and their clients. Competency is an integrated set of skills, knowledge, and attitudes that allow one to effectively carry out the activities of a given work to the standards expected in the employment context. The purpose of this descriptive survey study was to determine the current proficiency level of North Carolina Cooperative Extension agents’ competencies and the other competencies they need to develop to be successful in Cooperative Extension. Findings indicate that the current proficiency level of competency for Extension agents in North Carolina Cooperative Extension varies from moderate to high in all 42 items listed in the survey. Multiple regression analysis confirmed that Extension agents’ years of Extension experience and age were major determinants of their overall proficiency level. Extension agents’ proficiency levels did not vary with gender, level of education, professional association affiliation, job position, or area of job responsibility. The research revealed that emotional intelligence, interpersonal skills, flexibility for adapting to changing environments, and ability to manage resources were the most significant other competencies needed for Extension agents to be successful in current context.

  15. A New Extension Model: The Memorial Middle School Agricultural Extension and Education Center

    Science.gov (United States)

    Skelton, Peter; Seevers, Brenda

    2010-01-01

    The Memorial Middle School Agricultural Extension and Education Center is a new model for Extension. The center applies the Cooperative Extension Service System philosophy and mission to developing public education-based programs. Programming primarily serves middle school students and teachers through agricultural and natural resource science…

  16. Extension Approach for an Effective Fisheries and Aquaculture Extension Service in India

    Science.gov (United States)

    Kumaran, M.; Vimala, D. Deboral; Chandrasekaran, V. S.; Alagappan, M.; Raja, S.

    2012-01-01

    Purpose: Public-funded fisheries extension services have been blamed as poor and responsible for the slow pace of aquaculture development in India. The present investigation aimed to find concrete interventions to streamline the extension service by understanding the research-extension-farmer linkage indirectly in terms of information sources of…

  17. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    Science.gov (United States)

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  18. Synthetic cannabinoids revealing adrenoleukodystrophy.

    Science.gov (United States)

    Fellner, Avi; Benninger, Felix; Djaldetti, Ruth

    2016-02-01

    We report a 41-year-old man who presented with a first generalized tonic-clonic seizure after recent consumption of a synthetic cannabinoid. MRI showed extensive bilateral, mainly frontal, white matter lesions. Blood analysis for very long chain fatty acids was compatible with adrenoleukodystrophy, and a missense mutation in the ABCD1 gene confirmed the diagnosis. We hypothesize that cannabinoid use might have contributed to metabolic decompensation with subacute worsening of the underlying condition. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Extension versus Bending for Continuum Robots

    Directory of Open Access Journals (Sweden)

    George Grimes

    2008-11-01

    Full Text Available In this paper, we analyze the capabilities of a novel class of continuous-backbone ("continuum" robots. These robots are inspired by biological "trunks, and tentacles". However, the capabilities of established continuum robot designs, which feature controlled bending but not extension, fall short of those of their biological counterparts. In this paper, we argue that the addition of controlled extension provides dual and complementary functionality, and correspondingly enhanced performance, in continuum robots. We present an interval-based analysis to show how the inclusion of controllable extension significantly enhances the workspace and capabilities of continuum robots.

  20. abc: An Extensible AspectJ Compiler

    DEFF Research Database (Denmark)

    Avgustinov, Pavel; Christensen, Aske Simon; Hendren, Laurie J.

    2006-01-01

    checking and code generation, as well as data flow and control flow analyses. The AspectBench Compiler (abc) is an implementation of such a workbench. The base version of abc implements the full AspectJ language. Its front end is built using the Polyglot framework, as a modular extension of the Java...... overview of how to use abc to implement an extension. We illustrate the extension mechanisms of abc through a number of small, but nontrivial, examples. We then proceed to contrast the design goals of abc with those of the original AspectJ compiler, and how these different goals have led to different...

  1. Generalized extensions and blocking factors for FITS

    Science.gov (United States)

    Grosbol, P.; Harten, R. H.; Greisen, E. W.; Wells, D. C.

    1988-06-01

    A general design for extending the Flexible Image Transport System (FITS) tape format is proposed. The present design is shown to preserve compatibility with existing FITS tapes and software (including the 'random groups'), while being general enough to permit a wide variety of new extension files to be designed in the future. Rules are given for the blocking of FITS logical records. The rules for the generalized extension of FITS ensure that extensions can be located and decoded by standard routines without interfering with each other.

  2. Comparative evolutionary histories of kisspeptins and kisspeptin receptors in vertebrates reveal both parallel and divergent features

    Directory of Open Access Journals (Sweden)

    Jérémy ePasquier

    2012-12-01

    Full Text Available During the past decade, the kisspeptin system has been identified in various vertebrates, leading to the discovery of multiple genes encoding both peptides (Kiss and receptors (Kissr. The investigation of recently published genomes from species of phylogenetic interest, such as a chondrichthyan, the elephant shark, an early sarcopterygian, the coelacanth, a non-teleost actinopterygian, the spotted gar, and an early teleost, the European eel, allowed us to get new insights into the molecular diversity and evolution of both Kiss and Kissr families. We identified four Kissr in the spotted gar and coelacanth genomes, providing the first evidence of four Kissr genes in vertebrates. We also found three Kiss in the coelacanth and elephant shark genomes revealing two new species, in addition to Xenopus, presenting three Kiss genes. Considering the increasing diversity of kisspeptin system, phylogenetic and synteny analyses enabled us to clarify both Kiss and Kissr classifications. We also could trace back the evolution of both gene families from the early steps of vertebrate history. Four Kissr and four Kiss paralogs may have arisen via the two whole genome duplication rounds (1R & 2R in early vertebrates. This would have been followed by multiple independent Kiss and Kissr gene losses in the sarcopterygian and actinopterygian lineages. In particular, no impact of the teleost-specific 3R could be recorded on the numbers of teleost Kissr or Kiss paralogs. The origin of their diversity via 1R & 2R, as well as the subsequent occurrence of multiple gene losses, represent common features of the evolutionary histories of Kiss and Kissr families in vertebrates. In contrast, comparisons also revealed un-matching numbers of Kiss and Kissr genes in some species, as well as a large variability of Kiss/Kissr couples according to species. These discrepancies support independent features of the Kiss and Kissr evolutionary histories across vertebrate radiation.

  3. 77 FR 58364 - Agency Information Collection Extension

    Science.gov (United States)

    2012-09-20

    ... Information Administration Agency Information Collection Extension AGENCY: Energy Information Administration... sent to Colleen Blessing, EI-40, Energy Information Administration, Department of Energy, 1000.... Both quantitative and qualitative studies are developed by EIA. Quantitative studies classify and count...

  4. Veld management: a challenge to agricultural extension ...

    African Journals Online (AJOL)

    Keywords: Adaptive research; Agricultural extension; agriculture; communication; Farmers; Knowledge diffusion; Knowledge generation; management; National Grazing Strategy; On-farm adaptive research; research; south africa; strategies; technology; Veld management. Journal of the Grassland Society of Southern Africa.

  5. Youth Development Agents' Needs: Challenges for Extension ...

    African Journals Online (AJOL)

    ... the areas of competencies. Regular training was therefore recommended for youth development agents to enable them update, improve and learn new strategies in the application of their competencies for extension service delivery. Keywords: Youth, Development, Agents' needs, Volunteer management, Competencies.

  6. Offshore extension of Gomati river, Dwarka

    Digital Repository Service at National Institute of Oceanography (India)

    Vora, K.H.; Naik, D.K.; Ganesan, P.; Moraes, C.

    information. Attempts have been made to identify the submerged extension of Gomati River by diving inspection and based on the results obtained such as findings like stone and iron anchors, circular bastions, etc. While many features reported earlier...

  7. ERP extension - Supply Chain Management (SCM

    Directory of Open Access Journals (Sweden)

    Vasile LUPSE

    2006-01-01

    Full Text Available This article presents an extension of a ERP (Enterprise Resource Planning, more precisely the Supply Chain Management (SCM, together with some personal considerations and contributions of the authors, regarding the presented concepts.

  8. Integrated Composite Rocket Nozzle Extension Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ORBITEC proposes to develop and demonstrate an Integrated Composite Rocket Nozzle Extension (ICRNE) for use in rocket thrust chambers. The ICRNE will utilize an...

  9. 78 FR 13333 - Agency Information Collection Extension

    Science.gov (United States)

    2013-02-27

    ... energy resource reserves, production, demand, technology, and related economic and statistical... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY U.S. Energy Information Administration Agency Information Collection Extension AGENCY: U.S. Energy Information...

  10. Bandwidth extension of speech using perceptual criteria

    CERN Document Server

    Berisha, Visar; Liss, Julie

    2013-01-01

    Bandwidth extension of speech is used in the International Telecommunication Union G.729.1 standard in which the narrowband bitstream is combined with quantized high-band parameters. Although this system produces high-quality wideband speech, the additional bits used to represent the high band can be further reduced. In addition to the algorithm used in the G.729.1 standard, bandwidth extension methods based on spectrum prediction have also been proposed. Although these algorithms do not require additional bits, they perform poorly when the correlation between the low and the high band is weak. In this book, two wideband speech coding algorithms that rely on bandwidth extension are developed. The algorithms operate as wrappers around existing narrowband compression schemes. More specifically, in these algorithms, the low band is encoded using an existing toll-quality narrowband system, whereas the high band is generated using the proposed extension techniques. The first method relies only on transmitted high-...

  11. 77 FR 46750 - Agency Information Collection Extension

    Science.gov (United States)

    2012-08-06

    ... information collection, EIA-882T, ``Generic Clearance for Questionnaire Testing, Evaluation, and Research...: Generic Clearance for Questionnaire Testing, Evaluation, and Research; (3) Type of Request: Extension... questionnaires and validate EIA survey forms data quality, including conducting pretest ] surveys, pilot surveys...

  12. Generalized module extension Banach algebras: Derivations and ...

    African Journals Online (AJOL)

    Let A and X be Banach algebras and let X be an algebraic Banach A-module. Then the ℓ-1direct sum A x X equipped with the multiplication (a; x)(b; y) = (ab; ay + xb + xy) (a; b ∈ A; x; y ∈ X) is a Banach algebra, denoted by A ⋈ X, which will be called "a generalized module extension Banach algebra". Module extension ...

  13. Cooperative Extension as a Framework for Health Extension: The Michigan State University Model.

    Science.gov (United States)

    Dwyer, Jeffrey W; Contreras, Dawn; Eschbach, Cheryl L; Tiret, Holly; Newkirk, Cathy; Carter, Erin; Cronk, Linda

    2017-10-01

    The Affordable Care Act charged the Agency for Healthcare Research and Quality to create the Primary Care Extension Program, but did not fund this effort. The idea to work through health extension agents to support health care delivery systems was based on the nationally known Cooperative Extension System (CES). Instead of creating new infrastructure in health care, the CES is an ideal vehicle for increasing health-related research and primary care delivery. The CES, a long-standing component of the land-grant university system, features a sustained infrastructure for providing education to communities. The Michigan State University (MSU) Model of Health Extension offers another means of developing a National Primary Care Extension Program that is replicable in part because of the presence of the CES throughout the United States. A partnership between the MSU College of Human Medicine and MSU Extension formed in 2014, emphasizing the promotion and support of human health research. The MSU Model of Health Extension includes the following strategies: building partnerships, preparing MSU Extension educators for participation in research, increasing primary care patient referrals and enrollment in health programs, and exploring innovative funding. Since the formation of the MSU Model of Health Extension, researchers and extension professionals have made 200+ connections, and grants have afforded savings in salary costs. The MSU College of Human Medicine and MSU Extension partnership can serve as a model to promote health partnerships nationwide between CES services within land-grant universities and academic health centers or community-based medical schools.

  14. Initiation of diapirism by regional extension

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, M.P.A.; Vendeville, B.C. (Univ. of Texas, Austin, TX (United States). Bureau of Economic Geology)

    1992-01-01

    Initiation of diapirism is one of the least understood aspects of salt tectonics. Sedimentary differential loading is a favorite explanation, but special conditions such as focused sedimentation are needed to trigger diapirism by differential loading. Compilation of published data from 18 of the world's salt-diapir provinces shows that salt upwelling is consistently linked in time with regional extension, whether thin-skinned or thick-skinned. Extended salt basins typically develop salt structures, whereas nonextended basins typically do not. In some basins containing thick salt (SW Iran), diapirism was delayed as long as 400 Ma until the basin was regionally extended. In other salt provinces (Maritime Alps), episodic growth of salt diapirs correlates with episodic regional extension during opening of the Neo-Tethys and Atlantic Oceans. Once initiated, salt diapirism can continue after regional extension is succeeded by contraction or quiescence. Thus even in salt basins overprinted by inversion or orogenic contraction (Morocco, Lusitania, Basque-Cantabrian, North Sea), the diapirs were initiated during extension on divergent continental margins or in intracontinental rifts. This observed temporal link between extension and diapirism is consistent with physical and numerical modeling, which demonstrates that extensional faulting of the overburden directly causes diapirism whether the salt was deposited before, during, or after rifting. Where the overburden is thinned by extension, pressurized salt wells up in response to the shifting positions of fault blocks.

  15. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  16. Pituitary adenoma with extensive calcaficcations mimicking crainopharyngioma: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Sung Chan; Lee, Seoung Ro; Kwon, Bae Ju; Moon, Won Jin; Jeon, Eui Yong [Hanyang Univ. College of Medicine, Seoul (Korea, Republic of)

    2001-01-01

    A 27-year-old man presented with complaints of headache and visual disturbance, first noted six months earlier. Simple radiographs of skull sellar widening and calcification. Brian CT revealed a 3 x 3 x 4 cm-sized sellar suprasellar mass with heavy calcification. T1-weighted MR images showed that the signal intencity of the mass was slightly lower than that of the gray matter, while T2-weighted images showed heterogeneous high signal intensity with centrl low-signal-intensity foci, suggesting calcification After contrast infusion, enancement was irregular. Surgery revealed a 4 x 5 cm sized, well-demarcated, lobulated mass adhering to the meninges. Papillary-type pituitary adenoma was histologically confirmed. We report the CT and MR findings of atypical pituitary adenoma with extensive internal calcification mimicking craniopharyngioma.

  17. Negative extensibility metamaterials: Occurrence and design-space topology

    Science.gov (United States)

    Karpov, Eduard G.; Danso, Larry A.; Klein, John T.

    2017-08-01

    A negative extensibility material structure pulls back and contracts when the external tensile load reaches a certain critical level. In this paper, we reveal basic mathematical features of the nonlinear strain energy function responsible for this unusual mechanical property. A systematic discussion leads to a comprehensive phase diagram in terms of design parameters for a simple unit cell structure that provides a panoramic view of all possible nonlinear mechanical behaviors. A negative extensibility region clearly is identified in the diagram. The sought property is seen to be rare, occurring only for a very narrow range of the design parameters. Nonetheless, due to the simplicity of the studied structure we suggest that the negative extensibility should be a more common phenomenon than previously thought. It can appear in simple bistable cells made of only several linearly elastic links, although at some peculiar combinations of their properties. These bistable unit cells can be used to design periodic mechanical metamaterials whose examples are shown as well as innovative architectural metastructures.

  18. An Educational Extension Service in India

    Science.gov (United States)

    Krichevsky, M. I.

    2001-12-01

    A strength of US education is interaction with the public under the Land Grant University program. The public benefits from outreach through extension services which evolved for communication with end users, e.g., farmers, homemakers, public health providers, schoolchildren and entrepreneurs i.e., the public with problems and the extension agents who advise on solutions. Further, the agents can seek specialized advice from university faculty. No such system exists in India. The University of Pune (UP), Bionomics International (BI), and WorldSpace Foundation (WSF) will use digital radio broadcasts to facilitate educational extension services. The UP (350,000 students, 250 campuses, among dispersed communities) is a useful institutional setting to demonstrate the value of an outreach system in India. The UP will coordinate development of the broadcast content and the teaching faculty. The campuses will be focal points for outreach. BI will consult on development of the extension structure. WSF will provide the facilities and technical expertise for use of the digital system under the terms of an agreement with Bionomics International. Digital radios (&$slash75-150 each) and PCs will be at each campus and community. The major components of the Extension Service are broadcast of 1) University lecture and examination material in many disciplines; 2) outreach to the general population with of "canned" presentations and talks, skits, songs, games. The steps are: 1) Enhance communication among the campuses by use of satellite digital audio and multimedia broadcasts with feedback by telephone, mail, fax, etc. 2) Develop course material for training of extension personnel. 3) Train extension personnel to interface between the faculty of the University and the local population. 4) Extend digital radio services to population centers for communication of locally useful information. 5) Utilize extension personnel for system maintenance, motivating use of the broadcast

  19. Metadata to Support Next-Generation Library Resource Discovery: Lessons from the eXtensible Catalog, Phase 1

    National Research Council Canada - National Science Library

    Jennifer Bowen

    2008-01-01

      The eXtensible Catalog (XC) Project at the University of Rochester will design and develop a set of open-source applications to provide libraries with an alternative way to reveal their collections to library users...

  20. Coral Cores for selected locations in the Pacific Ocean obtained to determine calcification and extension rates of Porites spp. corals

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Laboratory experiments reveal calcification and extension rates of corals are strongly correlated to seawater aragonite saturation state. Predictions of reduced...

  1. Timeability in Extensive-Form Games

    DEFF Research Database (Denmark)

    Jakobsen, Sune K.; Sørensen, Troels Bjerre; Conitzer, Vincent

    2016-01-01

    Extensive-form games constitute the standard representation scheme for games with a temporal component. But do all extensive-form games correspond to protocols that we can implement in the real world? We often rule out games with imperfect recall, which prescribe that an agent forget something...... that she knew before. In this paper, we show that even some games with perfect recall can be problematic to implement. Specifically, we show that if the agents have a sense of time passing (say, access to a clock), then some extensive-form games can no longer be implemented; no matter how we attempt...... to time the game, some information will leak to the agents that they are not supposed to have. We say such a game is not exactly timeable. We provide easy-to-check necessary and sufficient conditions for a game to be exactly timeable. Most of the technical depth of the paper concerns how to approximately...

  2. Mathematics for common entrance three (extension) answers

    CERN Document Server

    Alexander, Serena

    2015-01-01

    This book contains answers to all exercises featured in the accompanying textbook Mathematics for Common Entrance Three (Extension) , which provides essential preparation for Level 3 of the ISEB 13+ Mathematics exam, as well as for CASE and other scholarship exams. - Clean, clear layout for easy marking. - Includes examples of high-scoring answers with diagrams and workings. Also available to purchase from the Galore Park website www.galorepark.co.uk :. - Mathematics for Common Entrance Three (Extension). - Mathematics for Common Entrance One. - Mathematics for Common Entrance One Answers. - M

  3. Graded junction termination extensions for electronic devices

    Science.gov (United States)

    Merrett, J. Neil (Inventor); Isaacs-Smith, Tamara (Inventor); Sheridan, David C. (Inventor); Williams, John R. (Inventor)

    2007-01-01

    A graded junction termination extension in a silicon carbide (SiC) semiconductor device and method of its fabrication using ion implementation techniques is provided for high power devices. The properties of silicon carbide (SiC) make this wide band gap semiconductor a promising material for high power devices. This potential is demonstrated in various devices such as p-n diodes, Schottky diodes, bipolar junction transistors, thyristors, etc. These devices require adequate and affordable termination techniques to reduce leakage current and increase breakdown voltage in order to maximize power handling capabilities. The graded junction termination extension disclosed is effective, self-aligned, and simplifies the implementation process.

  4. Extensive keloidal healing of pemphigus vulgaris

    Directory of Open Access Journals (Sweden)

    Khanna Neena

    1997-01-01

    Full Text Available Bullae of pemphigus vulgaris heal without scarring. We here report a patient of pemphigus vulgaris whose lesions healed with a one-month history of extensive flaccid bullae and uninfected erosions on the trunk and extremities along with superficial erosions in the oral mucosa. The clinical suspicion of pemphigus vulgaris was confirmed by histopathological and immunohistological examination. Pulse therapy with monthly parenteral dexamethasone and cyclophosphamide pulse was instituted. The cutaneous lesions on healing formed extensive keloidal scars despite high dose of monthly corticosteroid therapy.

  5. Switchings, extensions, and reductions in central digraphs

    DEFF Research Database (Denmark)

    Kündgen, André; Leander, Gregor; Thomassen, Carsten

    2011-01-01

    A directed graph is called central if its adjacency matrix A satisfies the equation A2=J, where J is the matrix with a 1 in each entry. It has been conjectured that every central directed graph can be obtained from a standard example by a sequence of simple operations called switchings, and also ...... that it can be obtained from a smaller one by an extension. We disprove these conjectures and present a general extension result which, in particular, shows that each counterexample extends to an infinite family....

  6. Algomaster Platform Extension for Improved Usability

    Directory of Open Access Journals (Sweden)

    BENEJ Martin

    2017-05-01

    Full Text Available Visualizations of algorithms and data structures can be effectively used for supporting the teaching process. However, such visualization must be comprehensive for students and still semantically correct. Algomaster visualization platform offers effective visualization and simple extensibility. In this paper we describe major platform extensions we have implemented, including support for visualization of complex algorithms, features for real-time student testing and the tool for simplified development of new Algomaster plugins. These complex algorithms comprise visualization of operations with self-balancing trees and hashing algorithm. To enable the real-time student testing we have created a database and a separate tool for its management.

  7. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  8. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  9. Characteristics of Human Brain Activity during the Evaluation of Service-to-Service Brand Extension.

    Science.gov (United States)

    Yang, Taeyang; Lee, Seungji; Seomoon, Eunbi; Kim, Sung-Phil

    2018-01-01

    Brand extension is a marketing strategy to apply the previously established brand name into new goods or service. A number of studies have reported the characteristics of human event-related potentials (ERPs) in response to the evaluation of goods-to-goods brand extension. In contrast, human brain responses to the evaluation of service extension are relatively unexplored. The aim of this study was investigating cognitive processes underlying the evaluation of service-to-service brand extension with electroencephalography (EEG). A total of 56 text stimuli composed of service brand name (S1) followed by extended service name (S2) were presented to participants. The EEG of participants was recorded while participants were asked to evaluate whether a given brand extension was acceptable or not. The behavioral results revealed that participants could evaluate brand extension though they had little knowledge about the extended services, indicating the role of brand in the evaluation of the services. Additionally, we developed a method of grouping brand extension stimuli according to the fit levels obtained from behavioral responses, instead of grouping of stimuli a priori . The ERP analysis identified three components during the evaluation of brand extension: N2, P300, and N400. No difference in the N2 amplitude was found among the different levels of a fit between S1 and S2. The P300 amplitude for the low level of fit was greater than those for higher levels ( p < 0.05). The N400 amplitude was more negative for the mid- and high-level fits than the low level. The ERP results of P300 and N400 indicate that the early stage of brain extension evaluation might first detect low-fit brand extension as an improbable target followed by the late stage of the integration of S2 into S1. Along with previous findings, our results demonstrate different cognitive evaluation of service-to-service brand extension from goods-to-goods.

  10. Characteristics of Human Brain Activity during the Evaluation of Service-to-Service Brand Extension

    Directory of Open Access Journals (Sweden)

    Taeyang Yang

    2018-02-01

    Full Text Available Brand extension is a marketing strategy to apply the previously established brand name into new goods or service. A number of studies have reported the characteristics of human event-related potentials (ERPs in response to the evaluation of goods-to-goods brand extension. In contrast, human brain responses to the evaluation of service extension are relatively unexplored. The aim of this study was investigating cognitive processes underlying the evaluation of service-to-service brand extension with electroencephalography (EEG. A total of 56 text stimuli composed of service brand name (S1 followed by extended service name (S2 were presented to participants. The EEG of participants was recorded while participants were asked to evaluate whether a given brand extension was acceptable or not. The behavioral results revealed that participants could evaluate brand extension though they had little knowledge about the extended services, indicating the role of brand in the evaluation of the services. Additionally, we developed a method of grouping brand extension stimuli according to the fit levels obtained from behavioral responses, instead of grouping of stimuli a priori. The ERP analysis identified three components during the evaluation of brand extension: N2, P300, and N400. No difference in the N2 amplitude was found among the different levels of a fit between S1 and S2. The P300 amplitude for the low level of fit was greater than those for higher levels (p < 0.05. The N400 amplitude was more negative for the mid- and high-level fits than the low level. The ERP results of P300 and N400 indicate that the early stage of brain extension evaluation might first detect low-fit brand extension as an improbable target followed by the late stage of the integration of S2 into S1. Along with previous findings, our results demonstrate different cognitive evaluation of service-to-service brand extension from goods-to-goods.

  11. Mysterious Blob Galaxies Revealed

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2Figure 3 This image composite shows a giant galactic blob (red, figure 2) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow, figure 3). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images like the one shown in figure 2, reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together (figure 3). Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile.

  12. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein.

    Science.gov (United States)

    Kankainen, Matti; Paulin, Lars; Tynkkynen, Soile; von Ossowski, Ingemar; Reunanen, Justus; Partanen, Pasi; Satokari, Reetta; Vesterlund, Satu; Hendrickx, Antoni P A; Lebeer, Sarah; De Keersmaecker, Sigrid C J; Vanderleyden, Jos; Hämäläinen, Tuula; Laukkanen, Suvi; Salovuori, Noora; Ritari, Jarmo; Alatalo, Edward; Korpela, Riitta; Mattila-Sandholm, Tiina; Lassig, Anna; Hatakka, Katja; Kinnunen, Katri T; Karjalainen, Heli; Saxelin, Maija; Laakso, Kati; Surakka, Anu; Palva, Airi; Salusjärvi, Tuomas; Auvinen, Petri; de Vos, Willem M

    2009-10-06

    To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated the colinearity. A significant number of strain-specific genes were predicted in these islands (80 in GG and 72 in LC705). The GG-specific islands included genes coding for bacteriophage components, sugar metabolism and transport, and exopolysaccharide biosynthesis. One island only found in L. rhamnosus GG contained genes for 3 secreted LPXTG-like pilins (spaCBA) and a pilin-dedicated sortase. Using anti-SpaC antibodies, the physical presence of cell wall-bound pili was confirmed by immunoblotting. Immunogold electron microscopy showed that the SpaC pilin is located at the pilus tip but also sporadically throughout the structure. Moreover, the adherence of strain GG to human intestinal mucus was blocked by SpaC antiserum and abolished in a mutant carrying an inactivated spaC gene. Similarly, binding to mucus was demonstrated for the purified SpaC protein. We conclude that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial. The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues.

  13. Characterization of the biocontrol activity of pseudomonas fluorescens strain X reveals novel genes regulated by glucose.

    Directory of Open Access Journals (Sweden)

    Gerasimos F Kremmydas

    Full Text Available Pseudomonas fluorescens strain X, a bacterial isolate from the rhizosphere of bean seedlings, has the ability to suppress damping-off caused by the oomycete Pythium ultimum. To determine the genes controlling the biocontrol activity of strain X, transposon mutagenesis, sequencing and complementation was performed. Results indicate that, biocontrol ability of this isolate is attributed to gcd gene encoding glucose dehydrogenase, genes encoding its co-enzyme pyrroloquinoline quinone (PQQ, and two genes (sup5 and sup6 which seem to be organized in a putative operon. This operon (named supX consists of five genes, one of which encodes a non-ribosomal peptide synthase. A unique binding site for a GntR-type transcriptional factor is localized upstream of the supX putative operon. Synteny comparison of the genes in supX revealed that they are common in the genus Pseudomonas, but with a low degree of similarity. supX shows high similarity only to the mangotoxin operon of Ps. syringae pv. syringae UMAF0158. Quantitative real-time PCR analysis indicated that transcription of supX is strongly reduced in the gcd and PQQ-minus mutants of Ps. fluorescens strain X. On the contrary, transcription of supX in the wild type is enhanced by glucose and transcription levels that appear to be higher during the stationary phase. Gcd, which uses PQQ as a cofactor, catalyses the oxidation of glucose to gluconic acid, which controls the activity of the GntR family of transcriptional factors. The genes in the supX putative operon have not been implicated before in the biocontrol of plant pathogens by pseudomonads. They are involved in the biosynthesis of an antimicrobial compound by Ps. fluorescens strain X and their transcription is controlled by glucose, possibly through the activity of a GntR-type transcriptional factor binding upstream of this putative operon.

  14. Confidence of Extension Staff in Akwa Ibom State Agricultural ...

    African Journals Online (AJOL)

    the extension agents (EAs), block extension agents (BEAs), block extension supervisors (BESs), and zonal extension officers (ZEOs) were sometimes satisfied with AKADEP as their organization. Age, household size, and years of extension experience of EAs were strong indicators of organizational confidence. Age, level of ...

  15. Expanding Agricultural and Rural Extension Roles for Sustainable ...

    African Journals Online (AJOL)

    Expanding Agricultural and Rural Extension Roles for Sustainable Extension Practice in Nigeria. ... The expanded scope could include marketing extension, non-farm rural micro enterprise development, service to farmers' associations, technical extension service and urban extension. These services should be provided at ...

  16. Global Approaches to Extension Practice: A Journal of Agricultural ...

    African Journals Online (AJOL)

    Global Approaches to Extension Practice (GAEP), A publication of the Department of Agricultural Extension, Federal University of Technology, Owerri, Imo State, Nigeria is an international journal which considers articles from all areas of Agricultural Extension: rural sociology, environmental extension, extension ...

  17. Particle Swarm Optimisation with Spatial Particle Extension

    DEFF Research Database (Denmark)

    Krink, Thiemo; Vesterstrøm, Jakob Svaneborg; Riget, Jacques

    2002-01-01

    In this paper, we introduce spatial extension to particles in the PSO model in order to overcome premature convergence in iterative optimisation. The standard PSO and the new model (SEPSO) are compared w.r.t. performance on well-studied benchmark problems. We show that the SEPSO indeed managed...... to keep diversity in the search space and yielded superior results....

  18. Longest Common Extensions in Sublinear Space

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Knudsen, Mathias Bæk Tejs

    2015-01-01

    The longest common extension problem (LCE problem) is to construct a data structure for an input string T of length n that supports LCE(i,j) queries. Such a query returns the length of the longest common prefix of the suffixes starting at positions i and j in T. This classic problem has a well...

  19. ANTLR Tree Grammar Generator and Extensions

    Science.gov (United States)

    Craymer, Loring

    2005-01-01

    A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

  20. Communication for Rural Innovation : rethinking agricultural extension

    NARCIS (Netherlands)

    Leeuwis, C.; Ban, van den A.W.

    2004-01-01

    This important book is the re-titled third edition of the extremely well received and widely used Agricultural Extension (van den Ban & Hawkins, 1988, 1996). Building on the previous editions, Communication for Rural Innovation maintains and adapts the insights and conceptual models of value

  1. Banana Algebra: Compositional Syntactic Language Extension

    DEFF Research Database (Denmark)

    Andersen, Jacob; Brabrand, Claus; Christiansen, David Raymond

    2013-01-01

    We propose an algebra of languages and transformations as a means of compositional syntactic language extension. The algebra provides a layer of high-level abstractions built on top of languages (captured by context-free grammars) and transformations (captured by constructive catamorphisms). The ...

  2. Equivalence relations of AF-algebra extensions

    Indian Academy of Sciences (India)

    In this paper, we consider equivalence relations of *-algebra extensions and describe the relationship between the isomorphism equivalence and the unitary equivalence. We also show that a certain group homomorphism is the obstruction for these equivalence relations to be the same.

  3. 78 FR 31885 - Patent Term Extension

    Science.gov (United States)

    2013-05-28

    ... Intellectual Property and Communications Omnibus Reform Act of 1999, require the USPTO to notify the applicant... 1995, Public Law 104-13 (44 U.S.C. 3506(c)(2)(A)). DATES: Written comments must be submitted on or... the extension provisions of 35 U.S.C. 156, the USPTO may in some cases extend the term of an original...

  4. Semi extensive methods - two main systems are

    African Journals Online (AJOL)

    next litter readily within a few days after weaning. It has long been ... terms of early growth and overall efficiency of conversion of ... 21-day Weaning. Semi extensive methods - two main systems are adopted, the first using arks with outside runs on pasture and the second using similar arks but fitted with slatted or weld mesh ...

  5. Seroprevalence Study Of Bovine Brucellosis In Extensive ...

    African Journals Online (AJOL)

    The prevalence of bovine brucellosis was measured in cross sectional study in Jimma zone, Western Ethiopia using Rose Bengal Plate Test (RBT) and CFT from October 2003 to April 2004. The study animals consisted of 1305 local breed found in extensive system in five districts of in the zone. The overall individual animal ...

  6. Stress: Professional Development Needs of Extension Faculty.

    Science.gov (United States)

    Place, Nick T.; Jacob, Steve

    2001-01-01

    Responses from 314 of 422 extension faculty showed a variety of levels of job stress, primarily from time pressures and overcommitment. Those who used formal planning and time management techniques had lower stress scores. Time with family was a common coping mechanism. (Contains 19 references.) (SK)

  7. Tools for Creating Mobile Applications for Extension

    Science.gov (United States)

    Drill, Sabrina L.

    2012-01-01

    Considerations and tools for developing mobile applications for Extension include evaluating the topic, purpose, and audience. Different computing platforms may be used, and apps designed as modified Web pages or implicitly programmed for a particular platform. User privacy is another important consideration, especially for data collection apps.…

  8. South African Journal of Agricultural Extension

    African Journals Online (AJOL)

    The South African Journal of Agricultural Extensionaims to: * advance and apply the science of extension and of rural development as scientific discipline by stimulating thought, study, research, discussion and the publication and exchange of knowledge both nationally and internationally. * promote the professionalism ...

  9. A Graph Library Extension of SVG

    DEFF Research Database (Denmark)

    Nørmark, Kurt

    2007-01-01

    be aggregated as a single node, and an entire graph can be embedded in a single node. In addition, a number of different graph animations are described. The starting point of the SVG extension is a library that provides an exact of mirror of SVG 1.1 in the functional programming language Scheme. Each element...

  10. On Touchard's continued fraction and extensions: combinatorices ...

    African Journals Online (AJOL)

    We give a direct and simple proof of Touchard's continued fraction, provide an extension of it, and transform it into similar expansions related to Motzkin and Schroder numbers. Another proof is then given that uses only induction. We use this machinery on two examples that appear in recent papers of Josuat-Verges; with an ...

  11. Emergency Food Programs: Untapped Opportunities for Extension?

    Science.gov (United States)

    Mobley, Amy R.

    2012-01-01

    This article reports results from a questionnaire that assessed the frequency and type of nutrition questions asked at emergency food programs to determine if Extension professionals need to increase direct outreach efforts. Emergency food program workers (n = 460) were recruited via mail to complete a self-administered survey. More than one-third…

  12. Equivalence relations of AF-algebra extensions

    Indian Academy of Sciences (India)

    Introduction. Brown, Douglas and Fillmore [3] gave the famous BDF theory to study essentially normal operators on an infinite dimensional Hilbert space and extensions of C∗. -algebra C(X) by. K in the 1970's, where X is a compact metric space and K is the C*-algebra of compact operators on an infinite dimensional ...

  13. Measuring Florida Extension Faculty's Agricultural Paradigmatic Preferences

    Science.gov (United States)

    Warner, Laura A.; Murphrey, Theresa Pesl; Lawver, David E.; Baker, Matt; Lindner, James R.

    2014-01-01

    The demand for sustainable agriculture has increased, and many institutions, including the University of Florida, have adopted agricultural sustainability as a major goal. Extension has been identified as a critical information source, important in disseminating sustainable agricultural growing techniques. However, research has demonstrated that…

  14. Assessment Of Shell Petroleum Development Company Extension ...

    African Journals Online (AJOL)

    The study assessed Shell Petroleum Development Company Extension Services in Etche Local Government Area of Rivers State, Nigeria. Data were gathered form four categories of respondents drawn from the Company\\'s staff and the communities. A total of 180 respondents participated in the study. means scores and ...

  15. assessment of shell petroleum development company extension ...

    African Journals Online (AJOL)

    ABSTRACT. The study assessed Shell Petroleum DeVelopment Company Extension. Services in Etche Local Government Area of Rivers State, Nigeria. Data were gathered form four categories of respondents drawn from the. Company's staff and the communities. A total of 180 respondents participated in the study. means ...

  16. Effectively Communicating Science to Extension Audiences

    Science.gov (United States)

    Robinson, Patrick

    2013-01-01

    This article discusses the concept of "framing" within the context of relevant communication and psychological research and considers its potential applicability to Extension science communication. Examples of research-based support for the framing of scientific issues are presented, along with a literature-based discussion of the…

  17. Matching Extension Service With Farmers' Needs: Towards ...

    African Journals Online (AJOL)

    of the farming family and the farm can better target its programs to meet farmers' needs. In this study 305 farm households, from two districts of northcentral Ethiopia are used as a case study, to examine key socio-economic and ecological indicators that affect effective use of extension services. Data was collected using the ...

  18. Improving Generation Y Volunteerism in Extension Programs

    Science.gov (United States)

    Andrews, Kevin B.; Lockett, Landry L.

    2013-01-01

    Members of Generation Y have many positive attributes that make them attractive to Extension volunteer administrators as a potential source of labor. However, they think differently, have unique needs, require new management styles, and have less tolerance for unpleasant working conditions than previous generations. Additionally, they are engaged…

  19. Integrating Reading and Writing through Extensive Reading

    Science.gov (United States)

    Park, Jeongyeon

    2016-01-01

    This study explores whether an extensive reading (ER) approach can enhance L2 learners' writing performance in an English for Academic Purposes context. Two classes were compared in terms of writing improvement after one semester: a 'traditional' writing class primarily focused on writing practice and grammar instruction, and an ER class in which…

  20. Does Extensive Reading Promote Reading Speed?

    Science.gov (United States)

    He, Mu

    2014-01-01

    Research has shown a wide range of learning benefits accruing from extensive reading. Not only is there improvement in reading, but also in a wide range of language uses and areas of language knowledge. However, few research studies have examined reading speed. The existing literature on reading speed focused on students' reading speed without…

  1. Definable maximal discrete sets in forcing extensions

    DEFF Research Database (Denmark)

    Törnquist, Asger Dag; Schrittesser, David

    2017-01-01

    that in the Sacks and Miller extensions there is a Π11 maximal orthogonal family ("mof") of Borel probability measures on Cantor space. A similar result is also obtained for Π11 mad families. By contrast, we show that if there is a Mathias real over L then there are no Σ12 mofs....

  2. 75 FR 9403 - Agency Information Collection Extension

    Science.gov (United States)

    2010-03-02

    ... Management and Budget (OMB) review; comment request. SUMMARY: The Department of Energy (DOE) has submitted an... 1995. The information collection requests a three-year extension of its Exchange/Sale Report, Excess... and Budget. DATES: Comments regarding this collection must be received on or before April 1, 2010. If...

  3. 78 FR 38305 - Agency Information Collection Extension

    Science.gov (United States)

    2013-06-26

    ... Budget (OMB) review; comment request. SUMMARY: The Department of Energy (DOE) has submitted an... 1995. The information collection requests a three-year extension of its Exchange/Sale Report, Excess... Management and Budget. DATES: Comments regarding this collection must be received on or before July 26, 2013...

  4. Catastrophic failure of polymer melts during extension

    DEFF Research Database (Denmark)

    Rasmussen, Henrik K.

    2013-01-01

    Numerical flow modeling has been applied to study the break of monodisperse polymer melts during extension. These continuum mechanical based computations are within the ideas of the microstructural ’interchain pressure’ theory. Calculated breaks, a result of small initial sample imperfections, ag...

  5. On an extension of a combinatorial identity

    Indian Academy of Sciences (India)

    On an extension of a combinatorial identity. M RANA and A K AGARWAL. Center for Advanced Study in Mathematics, Panjab University, Chandigarh 160 014,. India. E-mail: aka@pu.ac.in. MS received 22 August 2007. Abstract. Using Frobenius partitions we extend the main results of [4]. This leads to an infinite family of ...

  6. Entrepreneurial Extension Conducted via Social Media

    Science.gov (United States)

    Cornelisse, Sarah; Hyde, Jeffrey; Raines, Christopher; Kelley, Kathleen; Ollendyke, Dana; Remcheck, James

    2011-01-01

    The widespread availability of and access to the Internet have led to the development of new forms of communication. Collectively termed "social media," these new communication tools have created vast opportunities for Extension professionals in how they perform their work and how businesses interact with consumers. This article outlines currently…

  7. Extension of a theorem due to Ramanujan

    Directory of Open Access Journals (Sweden)

    Medhat A. Rakha

    2014-12-01

    Full Text Available The aim of this research paper is to establish an extension of a theorem due to Ramanujan. The result is obtained with the help of two terminating results for the series $_3F_{2}$ very recently obtained by Rakha et al. A few interesting special cases are also given.

  8. Livestock extension programmes participation and impact on ...

    African Journals Online (AJOL)

    In rural South Africa, the sustainability of cattle-based livelihoods is threatened by the competition for natural resources such as land and water. The central and provincial governments continue to invest funds in agricultural extension in order to uplift the productivity and safeguard the multifunctionality of cattle farming.

  9. Trials and Triumphs of Expanded Extension Programs.

    Science.gov (United States)

    Leavengood, Scott; Love, Bob

    1998-01-01

    Oregon extension faced challenges in presenting programs in the wood products industry. Several traditional tactics, revised to suit a new audience, have proved successful: personal coaching, building partnerships, and providing a high level of service. Newer methods, such as database marketing and distance learning, are also proving to be…

  10. Forestry Extension: An Indispensable Service for Sustainable ...

    African Journals Online (AJOL)

    Unfortunately human activities have depleted the forest through, uncontrolled lumbering, bush burning, charcoal production just to mention a few. ... is the premise on which the challenges facing effective forestry extension delivery in Nigeria and suggested solutions to the highlighted challenges is the focus of this write up.

  11. Developing Students' Reading Ability through Extensive Reading

    Science.gov (United States)

    Meng, Fanshao

    2009-01-01

    A good reading competence is a necessity for those studying English for academic and occupational purposes. Based on the results of previous research, theory and practice on L2 Extensive Reading, this paper analyses current situation for teaching and learning reading in our Chinese universities and proposes practical applications of extensive…

  12. Making Extensive Reading Even More Student Centered

    Science.gov (United States)

    Jacobs, George M.; Renandya, Willy A.

    2015-01-01

    This article begins by explaining the student centered learning paradigm. Next, the article explains various features of a student centered approach to education and how extensive reading (ER), as it is most often practiced, fits with those features. The bulk of the article suggests how ER might be implemented to make it even more learner centered.

  13. MAKING EXTENSIVE READING EVEN MORE STUDENT CENTERED

    Directory of Open Access Journals (Sweden)

    George Jacobs

    2015-01-01

    Full Text Available Abstract: This article begins by explaining the student centered learning paradigm.  Next, the article explains various features of a student centered approach to education and how extensive reading (ER, as it is most often practiced, fits with those features.  The bulk of the article suggests how ER might be implemented to make it even more learner centered.

  14. Some extensions and applications of Eisenstein Irreducibility ...

    Indian Academy of Sciences (India)

    Some extensions and applications of Eisenstein Irreducibility. Criterion. Sudesh Kaur Khanduja. Department of ... Suppose that there exists a prime number p such that. • a0 is not divisible by p,. • ai is divisible by p for .... + fn(xn) with complex coefficients is ir- reducible provided the degrees of f1. (x1. ), ..., fn(xn) have greatest ...

  15. Rhinoscleroma with orbital extension: CT and MRI

    Energy Technology Data Exchange (ETDEWEB)

    Le Hir, P. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Marsot-Dupuch, K. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Bigel, P. [Department of Pathology, CHU Saint-Antoine, Paris (France); Elbigourmie, T.M. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Jacquier, I. [ENT Department, CHU Saint-Antoine, Paris (France); Brunereau, L. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Tubiana, J.M. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France)

    1996-02-01

    We describe the MRI features of a rhinoscleroma with orbital extension. This benign bacterial and granulomatous lesion of the paranasal sinuses gave homogeneous low intensity on T2-weighted images and enhanced with gadolinium. It could simulate a malignant sinonasal tumour or a fungal sinusitis; the diagnosis must be considered in patients from endemic areas. (orig.). With 3 figs.

  16. 75 FR 20561 - Patent Term Extension

    Science.gov (United States)

    2010-04-20

    ... Patent and Trademark Office Patent Term Extension ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its continuing effort to reduce... the Chief Information Officer, United States Patent and Trademark Office, P.O. Box 1450, Alexandria...

  17. Transforming agriculture through contracted extension service ...

    African Journals Online (AJOL)

    Transformation of small holder agriculture from subsistence farming to agribusiness focused systems, is paramount towards attainment of Kenya's vision 2030 and the Millennium Development Goals. This requires extension service delivery systems that focus on addressing challenges within agricultural product value ...

  18. Extensive Actinomyces naeslundii infection in a child.

    OpenAIRE

    Dobson, S R; Edwards, M. S.

    1987-01-01

    A case of extensive Actinomyces naeslundii infection in a globally retarded patient is reported. To our knowledge, this uncommon Actinomyces species has not previously been described as a cause of widespread disease. Mental retardation and thoracic scoliosis were identified as features predisposing to infection.

  19. abc: An extensible AspectJ compiler

    DEFF Research Database (Denmark)

    Avgustinov, Pavel; Christensen, Aske Simon; Hendren, Laurie

    2005-01-01

    checking and code generation, as well as data flow and control flow analyses. The AspectBench Compiler (abc) is an implementation of such a workbench. The base version of abc implements the full AspectJ language. Its frontend is built, using the Polyglot framework, as a modular extension of the Java...

  20. Transmural intrathoracic lipoma with intraspinal extension.

    Science.gov (United States)

    Jain, Vishesh; Singal, Arbinder K; Gupta, Arun K; Bhatnagar, Veereshwar

    2007-12-01

    A rare case of transmural dumbbell intrathoracic lipoma with intraspinal extension is reported. Preoperative diagnosis was possible with a computed tomographic scan and fine-needle aspiration cytology. Complete excision was curative. The chest wall defect was repaired with Prolene mesh. Only one similar case has been previously reported in the English literature.

  1. Professional extension support: A prerequisite for sustainable ...

    African Journals Online (AJOL)

    professionalism and reflects on the general perceptions for professional extension support in irrigation management perceived by small- scale and commercial irrigation farmers. It also portrays the findings on the assessment of the technical competence and knowledge of irrigation extensionists. Possible barriers why ...

  2. An Effective Aquaculture Extension System from Farmers ...

    African Journals Online (AJOL)

    Regionally, government extension system and reading materials also played a significant role in the diffusion of aquaculture information to peri-urban farmers, and were considered to be of high quality and very accessible. This study recommends that the aquaculture division should identify the institutional mechanism ...

  3. Communication for strengthening agricultural extension and rural ...

    African Journals Online (AJOL)

    This paper argues that extension workers need training in Communication for Development (C4D), an emerging body of knowledge for addressing problems, such as participation, integration and capacity building for them to relate more effectively with development partners. Thus, this paper proposes a C4D framework for ...

  4. Extension Procedures for Confirmatory Factor Analysis

    Science.gov (United States)

    Nagy, Gabriel; Brunner, Martin; Lüdtke, Oliver; Greiff, Samuel

    2017-01-01

    We present factor extension procedures for confirmatory factor analysis that provide estimates of the relations of common and unique factors with external variables that do not undergo factor analysis. We present identification strategies that build upon restrictions of the pattern of correlations between unique factors and external variables. The…

  5. Dialogic Reading Aloud to Promote Extensive Reading

    Science.gov (United States)

    Jacobs, George M.

    2016-01-01

    How can teachers motivate students to read extensively in a second language? One strategy is for teachers to read aloud to students to promote the joys of reading generally, to build students' language skills and to introduce students to specific authors, book series, genres, websites, etc. This article begins by discussing why teachers might want…

  6. Testing Extension Services through AKAP Models

    Science.gov (United States)

    De Rosa, Marcello; Bartoli, Luca; La Rocca, Giuseppe

    2014-01-01

    Purpose: The aim of the paper is to analyse the attitude of Italian farms in gaining access to agricultural extension services (AES). Design/methodology/approach: The ways Italian farms use AES are described through the AKAP (Awareness, Knowledge, Adoption, Product) sequence. This article investigated the AKAP sequence by submitting a…

  7. Journal of Environmental Extension: Editorial Policies

    African Journals Online (AJOL)

    Focus and Scope. Journal of Environmental Extension is to be published annually to generate ideas on formulation, packaging, dissemination and consequential impacts of ideas/policies relating to the quality and sustainability of the environment. Focus of the Journal is on: Health Agriculture Technology Waste ...

  8. Women Empowerment And Agricultural Extension Policy: The ...

    African Journals Online (AJOL)

    This paper examined the role and challenges of extension agents in empowering women in a bid to revamp the agricultural sector. The activities of women in agricultural production are reviewed against the backdrop of global shift to gender sensitivity, particularly the emphasis on the role of women in agriculture. The paper ...

  9. Ethics and morals in the extension work

    Directory of Open Access Journals (Sweden)

    Fátima Lourdes Morales Intriago

    2017-05-01

    Full Text Available One of the main discussions about agents that provide rural extension is the lack of adequate proposals for the reality of farmers. The exyensionists work according to ethics and morals. Was carried out a theoretical search by made analyzing concepts about these terms and that are applied by extension agents. In This paper discusses how agents act with respect to the aforementioned notions and the conflicts they can cause with rural communities. It was found that the extensionist’s behavior is based on its values, norms and sanctions formation that can be object, which determines the changes that occur in the communities served. On the other hand, farmers do not receive appropriate attention by organisms that facilitate the Rural Extension, ignoring their interests and priorities. In addition, agents, as servants of institutions that provide assistance and extension, lose autonomy during the contact with communities. It was concluded that agents act correctly according to morality, as well as what concerns to ethics, since lowing the rules of the institution to which they belong, which does not always match with what rural people pursued.

  10. Home Food Preservation Training for Extension Educators

    Science.gov (United States)

    Goard, Linnette Mizer; Hill, Melinda; Shumaker, Katharine; Warrix, Marisa

    2013-01-01

    During times of economic downturn, there has been an increased interest in home food preservation. As the primary resource for current research-based recommendations, a team of Extension Family and Consumer Sciences educators with specialization in food safety and food preservation responded to this demand by developing a standardized food…

  11. FISHERIES EXTENSION SERVICES IN OGUN STATE | Olopade ...

    African Journals Online (AJOL)

    The study attempts to assess the current trends, impact and constraints of fisheries extension services to artisanal fishers in Ogun Waterside Local Government Area of Ogun State. The survey approach was used to generate the needed data using 120 structured questionnaires. Simple statistical techniques such as means ...

  12. Tampa Bay Extension Agents’ Views of Urban Extension: Philosophy and Program Strategies

    Directory of Open Access Journals (Sweden)

    Amy Harder

    2017-06-01

    Full Text Available The purpose of this article was to explore the concept of urban Extension as perceived by Extension agents within the Tampa Bay area, one of Florida’s fastest growing metropolitan areas. From a theoretical perspective, it is critical to understand Extension agents’ beliefs about urban Extension because behaviors are directly related to attitudes (Ajzen, 2012. In 2016, a qualitative investigation was undertaken to explore the perspectives of 23 agents working within the Tampa Bay area. Results showed the majority of agents believed that context and client needs are unique for urban Extension, and that to a lesser extent, unique agent expertise is required. Further, these beliefs impacted how agents reported their approach to programming, with an emphasis on providing convenience and seeking partnerships. Difficulties were identified related to identifying the role of Extension in a resource-rich environment of service providers, which contributed to the existence of a perceived disconnect between urban audiences and Extension. Opportunities exist for Extension leadership to provide strategic organizational support that will enhance agents’ abilities to succeed in the metropolitan environment.

  13. Extension Study Group Members View Their Clubs and Extension Home Economists. ANREI Publication No. 28.

    Science.gov (United States)

    Miller, Mason E.

    The data presented in this report were selected from a 1972 study of Michigan Extension Study Group (ESG) members. Included are data descriptive of the women themselves and their situation (area and type of home, age, income, ESG experience, and especially their attitudes toward their ESG and their Extension Home Economists). Selected findings are…

  14. 78 FR 65242 - Occupational Exposure to Crystalline Silica; Extension of Comment Period; Extension of Period To...

    Science.gov (United States)

    2013-10-31

    ... Exposure to Crystalline Silica; Extension of Comment Period; Extension of Period To Submit Notices of... Notice of Proposed Rulemaking (NPRM) on Occupational Exposure to Crystalline Silica for an additional 47... occupational exposure to respirable crystalline silica (78 FR 56274). This notice requested written comments by...

  15. Tensor extension of the Poincar\\'e algebra

    OpenAIRE

    Soroka, Dmitrij V.; Soroka, Vyacheslav A.

    2004-01-01

    A tensor extension of the Poincar\\'e algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions $D=2,3,4$.

  16. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

    Directory of Open Access Journals (Sweden)

    Walter J. Müller

    2016-09-01

    Full Text Available Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.

  17. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01.

    Science.gov (United States)

    Müller, Walter J; Tlalajoe, Nokuthula; Cason, Errol D; Litthauer, Derek; Reva, Oleg; Brzuszkiewicz, Elzbieta; van Heerden, Esta

    2016-09-08

    Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain's genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin-Benson-Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3 (-) rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01. Copyright © 2016 Müller et al.

  18. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principal Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

    Science.gov (United States)

    Müller, Walter J.; Tlalajoe, Nokuthula; Cason, Errol D.; Litthauer, Derek; Reva, Oleg; Brzuszkiewicz, Elzbieta; van Heerden, Esta

    2016-01-01

    Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01. PMID:27412985

  19. Structured RNAs and synteny regions in the pig genome

    DEFF Research Database (Denmark)

    Anthon, Christian; Tafer, Hakim; Havgaard, Jakob Hull

    2014-01-01

    , a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. RESULTS: We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure...... similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58......, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated...

  20. Structured RNAs and synteny regions in the pig genome

    DEFF Research Database (Denmark)

    Anthon, Christian; Tafer, Hakim; Havgaard, Jakob H

    2014-01-01

    , a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. RESULTS: We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure...... for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). CONCLUSIONS: We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70......BACKGROUND: Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However...

  1. Genetic linkage maps, synteny and map based cloning

    DEFF Research Database (Denmark)

    Sandal, Niels Nørgaard; Sato, Shusei

    2014-01-01

    Nitrogen fixation is a very important trait in agriculture and nature. It is made possible through symbiosis between plants, mainly legumes, and microorganisms such as rhizobia. Like most plants, legumes have symbiosis with mycorrhizal fungi. In order to isolate the plant genes that are important...... for symbiosis with nitrogen-fixing organisms and mycorrhizal symbiosis, Lotus japonicus was suggested as a model legume by Handberg and Stougaard (1992)...

  2. Traumatic knee extension deficit (the locked knee)

    DEFF Research Database (Denmark)

    Helmark, I C; Neergaard, K; Krogsgaard, M R

    2007-01-01

    In the present study we investigated the validity of magnetic resonance imaging (MRI) and arthroscopy in knees with acute, traumatic extension deficit (the "locked knee"), and evaluated whether arthroscopy of knees with no mechanical pathology could be avoided by MRI evaluation. The study consisted...... of 50 patients who had an acute, traumatic extension deficit of the knee. All patients were submitted to MRI prior to arthroscopy. Following MRI and surgery, standardized forms were filled out, attempting to objectify the findings. The orthopaedic surgeon was not aware of the MRI result prior to surgery......, the following results were calculated for the overall appearance of a lesion able to cause locking: Positive predictive value = 0.85, negative predictive value = 0.77, sensitivity = 0.95, specificity = 0.53. Two knees were erroneously evaluated with no mechanical locking at MRI (one bucket-handle lesion and one...

  3. Army European Tour Extension: An Interdisciplinary Approach

    Science.gov (United States)

    1985-02-01

    Rollgleu Job -Family Enlisted Spousal Wellbeing Facilities Fit P.rceptin PerceptionCommunity of Familyr’. , Support Satisfacion Attend Religious...Extens+om Logit i model , . Family life -IFactor analysis) SIMOS .. . .% Economics Regressions, Job satisfaction."" ,. ,,~., ,l ’ .; " -C. 20. AUS ACT...amounts of the proposed extension bonuses as well as with increase in satis- Lam faction with job and family life. Smaller lump sum bonuses were (Continued

  4. Mathematical model of subscriber extension line

    OpenAIRE

    Petříková, Iva; Diviš, Zdeněk; Tesař, Zdeněk

    2012-01-01

    The paper focuses on measurement properties of metallic subscriber extension lines to build regression mathematical model for a symmetric pair cable. The regression model is compared with an analytical model based on a theoretical description of transfer parameters for this type of line. The output of the paper should demonstrate the impact of electromagnetic interference on the symmetric pair. The paper also describes the method to identify the interference sources and ...

  5. Extensions and degeneration of spectral triples

    DEFF Research Database (Denmark)

    Christensen, Erik; Ivan, Cristina

    2009-01-01

    To a compact non commutative metric space associated to a C*-algebra A and an extension E of A, we construct 2-parameter family of compact non commutative metric spaces associated to E. It is shown that under certain limits along paths in the parameter space the corresponding spaces converge...... in the quantum Gromov-Hausdorff metric towards either the given non commutative metric space or towards a compact non commutative metric space associated to the compact operators....

  6. Cauchy-Davenport theorem in group extensions

    CERN Document Server

    Karolyi, G

    2005-01-01

    Let A and B be nonempty subsets of a finite group G in which the order of the smallest nontrivial subgroup is not smaller than d=|A|+|B|-1. Then the product set AB has at least d elements. This extends a classical theorem of Cauchy and Davenport to noncommutative groups. We also generalize Vosper's inverse theorem in the same spirit, giving a complete description of the critical pairs. The proofs depend on the structure of group extensions.

  7. Stable Extensions with(out) Gravity

    DEFF Research Database (Denmark)

    Antipin, Oleg; Krog, Jens; Mojaza, Matin

    2014-01-01

    We investigate the vacuum stability as well as the gravitational corrections in extensions of the Standard Model featuring a new complex scalar, and two Dirac fermions for different choices of the hypercharge of the scalar and one of the two fermions. The neutral fermion acquires loop-induced mag...... and discover that the models can be compatible with the asymptotically safe gravity scenario at the price of a heavier Higgs and lighter top mass...

  8. Learning PrimeFaces extensions development

    CERN Document Server

    Jonna, Sudheer

    2014-01-01

    This book provides a step by step approach that explains the most important extension components and their features. All the major features are explained by using the JobHub application with supporting screenshots.If you are an intermediate to advanced level user (or developer) who already has a basic working knowledge of PrimeFaces, then this book is for you.The only thing you need to know is Java Server Faces(JSF).

  9. Deformed Fredkin spin chain with extensive entanglement

    Science.gov (United States)

    Salberger, Olof; Udagawa, Takuma; Zhang, Zhao; Katsura, Hosho; Klich, Israel; Korepin, Vladimir

    2017-06-01

    We introduce a new spin chain which is a deformation of the Fredkin spin chain and has a phase transition between bounded and extensive entanglement entropy scaling. In this chain, spins have a local interaction of three nearest neighbors. The Hamiltonian is frustration-free and its ground state can be described analytically as a weighted superposition of Dyck paths that depends on a deformation parameter t. In the purely spin 1/2 case, whenever t\

  10. Emergence of Extensively Drug Resistant Tuberculosis

    Centers for Disease Control (CDC) Podcasts

    2007-03-01

    Extensively drug-resistant tuberculosis (XDR TB) outbreaks have been reported in South Africa, and strains have been identified on 6 continents. Dr. Peter Cegielski, team leader for drug-resistant TB with the Division of Tuberculosis Elimination at CDC, comments on a multinational team's report on this emerging global public health threat.  Created: 3/1/2007 by Emerging Infectious Diseases.   Date Released: 3/26/2007.

  11. Extensive air showers in the classroom

    Science.gov (United States)

    Badalà, A.; Blanco, F.; La Rocca, P.; Pappalardo, G. S.; Pulvirenti, A.; Riggi, F.

    2007-09-01

    The basic properties of extensive air showers of particles produced in the interaction of a high-energy primary cosmic ray in the Earth's atmosphere are discussed in the context of educational cosmic ray projects involving undergraduate students and high-school teams. Simulation results produced by an air shower development code were made available on the Web by the use of ASCII files and EXCEL spreadsheets to allow people to carry out graphical and numerical analyses in cosmic ray physics.

  12. Identity between space-time and physical substance’s extension

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2015-06-01

    Full Text Available This paper argues the identity between space-time and physical substance’s extension following Descartes and Einstein. Field and particles’ distinct spatiotemporal attributes are derived from their different extension types. Through elucidating the continuous space-time of the field world, we can supersede the genesis of the universe by the beginning of the particle world. Given two proposals: (i any fundamental particle is finite but unbounded, (ii a singularity is the only site for transformations of two extension types of physical substance, and then by the general theory of relativity, we determine the flexible intertwined structure of the cosmological time and its irreversibility. The thermodynamic entropy can only be applied in the particle world, which indicates that the thermodynamic time is a constituent part of the cosmological time. The indestructibility of physical substance reveals that the reciprocal transformations of two extension types of physical substance enable a self-sufficient universe.

  13. Wegener's granulomatosis with unusual cavernous sinus and sella turcica extension

    Energy Technology Data Exchange (ETDEWEB)

    Hermann, M.; Bobek-Billewicz, B. [Dept. of Radiology, Medical University of Gdansk (Poland); Bullo, B.; Hermann, A.; Rutkowski, B. [Dept. of Nephrology, Medical University of Gdansk (Poland)

    1999-07-01

    Intracerebral extension of Wegener's granulomatosis (WG) is rare. We present a patient with oculomotor and trochlear nerve palsy with histologically proved WG. An MR examination revealed granulomatous tissue in nasal cavity, paranasal sinuses with meningeal infiltration, and uncommon penetration into cavernous sinus and sella turcica. The MR images before and during pharmacological therapy are presented. (orig.)

  14. Unravelling the secret of successful brand extensions: a case study to explore consumer response

    NARCIS (Netherlands)

    Mulder-Nijkamp, Maaike; Eggink, Wouter; Bohemia, Erik; Rieple, Alison; Liedtka, Jeanne; Cooper, Rachel

    2014-01-01

    In this paper we try to disentangle the design of successful brand extensions and test this with two case studies. Earlier research revealed that typicality and novelty are related to the aesthetic preference of products. Despite the fact these two predictors are also each other’s suppressors, the

  15. Leadership Characteristics and Work Ethic of Extension Family and Consumer Science Educators.

    Science.gov (United States)

    Hollingsworth, Connie; Brewer, Ernest W.; Petty, Gregory C.

    2002-01-01

    Instruments completed by 166 Tennessee extension educators revealed a significant relationship between leadership orientation and work ethic. Their preferred leadership orientation was human relations; work ethic preferences included dependability and interpersonal skills. Higher work ethic scores predicted leadership effectiveness. (Contains 23…

  16. Frontal mucocele with intracranial extension causing frontal lobe syndrome.

    Science.gov (United States)

    Weidmayer, Sara

    2015-06-01

    Mucoceles are mucus-containing cysts that form in paranasal sinuses; although mucoceles themselves are benign, this case report highlights the extensive damage they can cause as their expansion may lead to bony erosion and extension of the mucocele into the orbit and cranium; it also presents a rarely reported instance of frontal sinus mucocele leading to frontal lobe syndrome. A thorough discussion and review of mucoceles is included. A 68-year-old white man presented with intermittent diplopia and a pressure sensation in the right eye. He had a history of chronic sinusitis and had had endoscopic sinus surgery 5 years prior. A maxillofacial computed tomography scan revealed a large right frontal sinus mucocele, which had caused erosion along the medial wall of the right orbit and the outer and inner tables of the right frontal sinus. The mucocele had protruded both into the right orbit and intracranially, causing mass effect on the frontal lobe, which led to frontal lobe syndrome. The patient was successfully treated with endoscopic right ethmoidectomy, radial frontal sinusotomy, marsupialization of the mucocele, and transcutaneous irrigation. Paranasal sinus mucoceles may expand and lead to bony erosion and can become very invasive in surrounding structures such as the orbit and cranium. This case not only exhibits a very rare presentation of frontal sinus mucocele with intracranial extension and frontal lobe mass effect causing a frontal lobe syndrome but also demonstrates many of the ocular and visual complications commonly associated with paranasal sinus mucoceles. Early identification and surgical intervention is vital for preventing and reducing morbidity associated with invasive mucoceles, and the patient must be followed regularly to monitor for recurrence.

  17. Conservative Intensional Extension of Tarski's Semantics

    Directory of Open Access Journals (Sweden)

    Zoran Majkić

    2013-01-01

    Full Text Available We considered an extension of the first-order logic (FOL by Bealer's intensional abstraction operator. Contemporary use of the term “intension” derives from the traditional logical Frege-Russell doctrine that an idea (logic formula has both an extension and an intension. Although there is divergence in formulation, it is accepted that the “extension” of an idea consists of the subjects to which the idea applies, and the “intension” consists of the attributes implied by the idea. From the Montague's point of view, the meaning of an idea can be considered as particular extensions in different possible worlds. In the case of standard FOL, we obtain a commutative homomorphic diagram, which is valid in each given possible world of an intensional FOL: from a free algebra of the FOL syntax, into its intensional algebra of concepts, and, successively, into an extensional relational algebra (different from Cylindric algebras. Then we show that this composition corresponds to the Tarski's interpretation of the standard extensional FOL in this possible world.

  18. LIMB Demonstration Project Extension and Coolside Demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Goots, T.R.; DePero, M.J.; Nolan, P.S.

    1992-11-10

    This report presents results from the limestone Injection Multistage Burner (LIMB) Demonstration Project Extension. LIMB is a furnace sorbent injection technology designed for the reduction of sulfur dioxide (SO[sub 2]) and nitrogen oxides (NO[sub x]) emissions from coal-fired utility boilers. The testing was conducted on the 105 Mwe, coal-fired, Unit 4 boiler at Ohio Edison's Edgewater Station in Lorain, Ohio. In addition to the LIMB Extension activities, the overall project included demonstration of the Coolside process for S0[sub 2] removal for which a separate report has been issued. The primary purpose of the DOE LIMB Extension testing, was to demonstrate the generic applicability of LIMB technology. The program sought to characterize the S0[sub 2] emissions that result when various calcium-based sorbents are injected into the furnace, while burning coals having sulfur content ranging from 1.6 to 3.8 weight percent. The four sorbents used included calcitic limestone, dolomitic hydrated lime, calcitic hydrated lime, and calcitic hydrated lime with a small amount of added calcium lignosulfonate. The results include those obtained for the various coal/sorbent combinations and the effects of the LIMB process on boiler and plant operations.

  19. Two Extension Block Kirschner Wires’ Technique for Bony Mallet Thumb

    Directory of Open Access Journals (Sweden)

    Yutaka Mifune

    2016-01-01

    Full Text Available Mallet fingers with an avulsion fracture of the distal phalanx or rupture of the terminal tendon of the extensor mechanism is known as a common injury, while mallet thumb is very rare. In this paper, the case of a 19-year-old woman with a sprained left thumb sustained while playing basketball is presented. Plain radiographs and computed tomography revealed an avulsion fracture involving more than half of the articular surface at the base of the distal phalanx. Closed reduction and percutaneous fixation were performed using the two extension block Kirschner wires’ technique under digital block anesthesia. At 4 months postoperatively, the patient had achieved excellent results according to Crawford’s evaluation criteria and had no difficulties in working or playing basketball. Various conservative and operative treatment strategies have been reported for management of mallet thumb. We chose the two extension block Kirschner wires’ technique to minimize invasion of the extensor mechanism and nail bed and to stabilize the large fracture fragment.

  20. EXTENSION EDUCATION SYMPOSIUM: Getting the most out of your extension appointment and still having a life.

    Science.gov (United States)

    Powers, W; Cockett, N; Lardy, G

    2017-04-01

    Managing the demands of an academic appointment in extension can be a challenging task. Demands from constituent groups, expectations of supervisors, and rigors of promotion and tenure processes can create pressures that young faculty did not expect. Throw in spousal and family duties and you have created a situation that many will find hard to navigate. However, there are ways to cope and, even better news, there are ways to excel in meeting the demands of an academic appointment and enjoying life. Because many new extension faculty members do not have prior experience in extension, best practices in documenting programs and extension scholarship over the pretenure period are provided in this paper. Appointments that include both research and extension are quite common at many land grant universities. The advantages of joint appointments are numerous and include the fact that more and more grant agencies are seeking integrated research, teaching, and/or extension projects. However, the time demands of joint appointments can be challenging. Joint appointments can be designed to help faculty members conduct important translational research and have it be applied in a production setting. By seeking commonalities in research and extension efforts, joint appointments can be very synergistic. Development of highly successful programs requires planning on the front end with an emphasis on an in-depth needs assessment to determine stakeholder needs for both research and extension. Impact assessment should be part of this planning effort. Performing as a successful extension faculty member while maintaining relationships outside of work is challenging and requires deliberate effort on the part of employees and supervisors to realize there is more to life than work. Some authors have referred to this as work-life balance, but it may be more helpful to think of it as work-life effectiveness. To do this, one needs to 1) define what success looks like, 2) set boundaries and

  1. Supervisory skills of extension managers in Sekhukhune District of ...

    African Journals Online (AJOL)

    ... namely at the supervisory level (Sub-District Extension Coordinators) and the top extension management level (Extension Heads). These are the two management levels that can potentially have the biggest influence on the efficiency of extension delivery. Keywords: management, leadership skills, differential perception, ...

  2. Constraints in the implementation of crop protection extension ...

    African Journals Online (AJOL)

    ... management of research information; basing distribution of needed inputs on full time farming criterion, involving more crop protectionists in extension work, removal of non-extension function from extension, provision of logistic supports and periodic staff training on crop protection extension methodology, communication, ...

  3. Private Agricultural Extension System in Kenya: Practice and Policy Lessons

    Science.gov (United States)

    Muyanga, Milu; Jayne, T. S.

    2008-01-01

    Private extension system has been at the centre of a debate triggered by inefficient public agricultural extension. The debate is anchored on the premise that the private sector is more efficient in extension service delivery. This study evaluates the private extension system in Kenya. It employs qualitative and quantitative methods. The results…

  4. Journal of Agricultural Extension Vol.17 (2) December, 2013 ISSN ...

    African Journals Online (AJOL)

    ONIKOYI

    Turkey and offers a model for mainstreaming it in extension programming. Keywords. Agricultural extension in Turkey, Communication for extension Development. Introduction. Agricultural extension in Turkey started in 1931 .... Use social networking web sites a. Facebook b. Twitter c. LinkedIn d. Orkut. 90.8. 70.4. 3.1. 2.0.

  5. A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms.

    Science.gov (United States)

    Mathew, Lisa S; Spannagl, Manuel; Al-Malki, Ameena; George, Binu; Torres, Maria F; Al-Dous, Eman K; Al-Azwani, Eman K; Hussein, Emad; Mathew, Sweety; Mayer, Klaus F X; Mohamoud, Yasmin Ali; Suhre, Karsten; Malek, Joel A

    2014-04-15

    The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified. Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome. Based on a modified genotyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

  6. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.

    Science.gov (United States)

    Byrne, Kevin P; Wolfe, Kenneth H

    2005-10-01

    We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404).

  7. CT of perineural tumor extension: pterygopalatine fossa

    Energy Technology Data Exchange (ETDEWEB)

    Curtin, H.D.; Williams, R.; Johnson, J.

    1985-01-01

    Tumors of the oral cavity and paranasal sinuses can spread along nerves to areas apparently removed from the primary tumor. In tumors of the palate, sinuses, and face, this perineural spread usually involves the maxillary division of the trigeminal nerve. The pterygopalatine fossa is a pathway of the maxillary nerve and becomes a key landmark in the detection of neural metastasis by computed tomography (CT). Obliteration of the fat in the fossa suggests pathology. Case material illustrating neural extension is presented and the CT findings are described.

  8. Subintegrality, invertible modules and Laurent polynomial extensions

    Indian Academy of Sciences (India)

    N그(A,B): kernel of the map 그(A[X],B[X]) → 그(A,B) (Here the map is induced by the B-algebra homomorphism B[X] → B given by X ↦→ 0). Recall from §2 of [4] that for any commutative ring extension A ⊆ B, we have the exact sequence. 1 → U(A) → U(B) → 그(A,B) → Pic A → Pic B. Applying M, K we obtain the chain ...

  9. Analytic extension of the nuclear algebraic potential

    Energy Technology Data Exchange (ETDEWEB)

    Lichtenthaeler, R. (Departamento de Fisica Nuclear, Laboratorio do Pelletron, Universidade de Sao Paulo, Caixa Postal 20516, 01452-990 Sao Paulo, Sao Paulo (Brazil)); Gomes, L.C. (Grupo de Fisica Nuclear Teorica e Fenomenologia de Particulas Elementares Instituto de Fisica Universidade de Sao Paulo, Caixa Postal 20516, 01498-970 Sao Paulo, Sao Paulo (Brazil))

    1994-12-01

    An analytic extension of the nuclear algebraic potential in the complex energy and angular momentum planes is discussed and an approximation for the algebraic potential in agreement with the known analytic properties of the [ital S]-matrix is proposed. The invariance of the energy spectrum of the Coulomb part of the interaction is established. The results are applied to the Regge pole analysis of the [sup 12]C+[sup 24]Mg elastic collision at [ital E][sub [ital l][ital a][ital b

  10. A CART extension using Quadratic Decision Borders

    DEFF Research Database (Denmark)

    Hartelius, Karsten

    1999-01-01

    -space into subsets which are successively more class-homogeneous. Guided by the fact that class-distributions in feature-space are very often hyper-elliptical shaped, we give an extension to the original CART which also uses quadratic shaped decision borders which can be modelled by a mean-vector and a dispersion......In this article we put forward an extention to the hierarchical CART classification method which uses quadratic decision borders. The original CART applies univariate splits on individual variables as well as splits on combinations of variables to recursively partition the feature...

  11. Software extension and integration with type classes

    DEFF Research Database (Denmark)

    Lämmel, Ralf; Ostermann, Klaus

    2006-01-01

    expressiveness, by using the language concept of \\emph{type classes}, as it is available in the functional programming language Haskell. A detailed comparison with related work shows that type classes provide a powerful framework in which solutions to known software extension and integration problems can......The abilities to extend a software module and to integrate a software module into an existing software system without changing existing source code are fundamental challenges in software engineering and programming-language design. We reconsider these challenges at the level of language...... be provided. We also pinpoint several limitations of type classes in this context....

  12. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  13. On Shor's Channel Extension and Constrained Channels

    Science.gov (United States)

    Holevo, A. S.; Shirokov, M. E.

    Several equivalent formulations of the additivity conjecture for constrained channels, which formally is substantially stronger than the unconstrained additivity, are given. To this end a characteristic property of the optimal ensemble for such a channel is derived, generalizing the maximal distance property. It is shown that the additivity conjecture for constrained channels holds true for certain nontrivial classes of channels. After giving an algebraic formulation for Shor's channel extension, its main asymptotic property is proved. It is then used to show that additivity for two constrained channels can be reduced to the same problem for unconstrained channels, and hence, ``global'' additivity for channels with arbitrary constraints is equivalent to additivity without constraints.

  14. Emergency Anaesthetic Management of Extensive Thoracic Trauma

    Directory of Open Access Journals (Sweden)

    H C Chandola

    2007-01-01

    Full Text Available High speed vehicles, drug abuse, alcohol and easy availability of handguns are the main reasons of increasing number of trauma especially thoracic trauma. Anaesthesiologist plays an important role in the management of extensive thoracic trauma. Thoracic trauma, penetrating or blunt, may cause damage to organs suspended in thorax viz. pleura, lungs, heart, great vessels, trachea and oesophagus. It may lead to pneumothorax, cardiac tamponade or life threatening haemorrhage. With aggressive care and management of these factors, majority of patients can survive and return to normal life.

  15. Radar reflection off extensive air showers

    Directory of Open Access Journals (Sweden)

    Werner F.

    2013-06-01

    Full Text Available We investigate the possibility of detecting extensive air showers by the radar technique. Considering a bistatic radar system and different shower geometries, we simulate reflection of radio waves off the static plasma produced by the shower in the air. Using the Thomson cross-section for radio wave reflection, we obtain the time evolution of the signal received by the antennas. The frequency upshift of the radar echo and the power received are studied to verify the feasibility of the radar detection technique.

  16. Brand Extension: a Case Study of Starbucks

    OpenAIRE

    Bokii, Artem

    2017-01-01

    The thesis investigates the topic of brand extension and its importance in the business practice of companies. The theoretical part of the research outlines the key theoretical aspects related to brand and brand extension. The practical part investigates the case study of Starbucks brand extension and compares it with other famous brand extension cases. The paper illustrates how Starbucks brand extension from coffee onto the ice cream market had been successful on the initial stage, and how i...

  17. A Case of Extensive polyostotic fibrous dysplasia

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Byung Do [Dept. of Oral and Maxillofacial Radiology, School of Dentistry, Wonkwang University, Iksan (Korea, Republic of); Hwang, Eui Hwan; Lee, Sang Rae [Dept. of Oral and Maxillofacial Radiology, School of Dentistry, Kyunghee University, Seoul (Korea, Republic of)

    2000-06-15

    Fibrous dysplasia is a benign disorder of bone consisting of intramedullary proliferation of fibrous tissue and irregularly distributed, poorly developed bone. The disease manifests itself in the monostotic form in which only one bone is involved and the polyostotic form in which multiple bones at different sites are affected. We reported a extensive case of polyostotic fibrous dysplasia with involvement of craniofacial bones, mandible, ribs, extremities. A 18-year-old man showed remarkable right facial swelling who had been treated on right femur 3 years ago with a bone graft for pathologic fracture and he recognized facial swelling 5 years ago. Extraoral radiograms and computed tomogram showed diffuse sclerosis with a ground glass appearance of the most calvarial bones, facial bones. The right mandibular lesion showed very expansible lesion with mottled appearance. Bone scans showed multifocal increased uptakes in craniofacial bones, right mandible, bilaterally in ribs, humerus, femur, tibia and characteristic various deformity of right femur (shepherd's crook deformity). This case showed exceptionally bilateral, extensive nature of bone lesion and didn't show any features of skin pigmentation and endocrine disturbances.

  18. Cmapanalysis: an extensible concept map analysis tool

    Directory of Open Access Journals (Sweden)

    Alberto J. Cañas

    2013-03-01

    Full Text Available Concept maps are used extensively as an assessment tool, and the literature is abundant with studies on the use of concept maps for assessment and on the assessment of concept maps. The assessment of concept maps can be an arduous process, in particular when assessing a large number of maps. CmapAnalysis is a software tool that facilitates performing various analysis measures on a collection of concept maps. A set of measures that consider size, quality and structure properties of the maps are included. The program is designed to be extensible, allowing users to add their own measures. The program is not intended to replace the individual evaluation of concept maps by teachers and instructors, as it does not capable of “understanding” the content of the maps. It is aimed at researchers who are looking for more general trends and measures across a large number of maps, and who can extend it with their own measures. The output of CmapAnalysis is an Excel spreadsheet that can be further analyzed.

  19. Sampling approaches for extensive surveys in nematology.

    Science.gov (United States)

    Prot, J C; Ferris, H

    1992-12-01

    Extensive surveys of the frequency and abundance of plant-parasitic nematodes over large geographic areas provide useful data of unknown reliability. Time, cost, and logistical constraints may limit the sampling intensity that can be invested at any survey site. We developed a computer program to evaluate the probability of detection and the reliability of population estimates obtained by different strategies for collecting one sample of 10 cores from a field. We used data from two fields that had been sampled systematically and extensively as the basis for our analyses. Our analyses indicate that, at least for those two fields, it is possible to have a high probability of detecting the presence of nematode species and to reliably estimate abundance, with a single 10-core soil sample from a field. When species were rare or not uniformly distributed in a field, the probability of detection and reliability of the population estimate were correlated with the distance between core removal sites. Increasing the prescribed distance between cores resulted in the composite sample representing a wider range of microenvironments in the field.

  20. Life extension by calorie restriction in humans.

    Science.gov (United States)

    Everitt, Arthur V; Le Couteur, David G

    2007-10-01

    Long-term reduction in energy intake in the diet (calorie restriction [CR]) extends the life of the laboratory rat by about 25%. However, in humans there are no life-long studies of CR, but only short-term trials which indicate that 20% CR acting over periods of 2-6 years is associated with reduced body weight, blood pressure, blood cholesterol, and blood glucose--risk factors for the major killer diseases of cardiovascular disease and diabetes. In addition, recent research has shown that CR for 6 months is able to improve biomarkers for longevity (deep body temperature and plasma insulin) and thus should increase life expectancy. The magnitude of the life-extension effect of CR in humans can only be estimated. The Okinawans, the longest-lived people on earth, consume 40% fewer calories than the Americans and live only 4 years longer. Similarly, women in United States consume 25% fewer calories than men and live 5 years longer. From the survival studies of overweight and obese people, it is estimated that long-term CR to prevent excessive weight gain could add only 3-13 years to life expectancy. Thus the effects of CR on human life extension are probably much smaller than those achieved by medical and public health interventions, which have extended life by about 30 years in developed countries in the 20th century, by greatly reducing deaths from infections, accidents, and cardiovascular disease.

  1. Improved Extension Neural Network and Its Applications

    Directory of Open Access Journals (Sweden)

    Yu Zhou

    2014-01-01

    Full Text Available Extension neural network (ENN is a new neural network that is a combination of extension theory and artificial neural network (ANN. The learning algorithm of ENN is based on supervised learning algorithm. One of important issues in the field of classification and recognition of ENN is how to achieve the best possible classifier with a small number of labeled training data. Training data selection is an effective approach to solve this issue. In this work, in order to improve the supervised learning performance and expand the engineering application range of ENN, we use a novel data selection method based on shadowed sets to refine the training data set of ENN. Firstly, we use clustering algorithm to label the data and induce shadowed sets. Then, in the framework of shadowed sets, the samples located around each cluster centers (core data and the borders between clusters (boundary data are selected as training data. Lastly, we use selected data to train ENN. Compared with traditional ENN, the proposed improved ENN (IENN has a better performance. Moreover, IENN is independent of the supervised learning algorithms and initial labeled data. Experimental results verify the effectiveness and applicability of our proposed work.

  2. Nasal dermoids without intracranial extension in teenagers.

    Science.gov (United States)

    Dolzal, P; Hanzelová, J

    2010-01-01

    Nasal dermoid cysts are benign, cystic midline masses. They contain mature tissues and often pocket hair, fat or sebum. Patients usually present with nasal enlargement or with a wide nasal dorsum with or without a fistula, causing an unacceptable cosmetic appearance. To define a reliable surgical approach and method of removing dermoid with no intracranial extension in adolescent age. We retrospectively present diagnostic and therapeutic procedures in three teenagers ages 15, 17 and 18. All patients underwent prior surgeries at different hospitals. In the first case, the incision and exstirpation of the fistula's opening, followed by the fistula's canal, was performed. In the other two patients, the nasal dermoids were removed via the open approach with the transcollumelar incision. In all patients, we performed rhinoplasty with osteotomies to achieve an improved cosmetic effect. The esthetic results are presented. The diagnosis of nasal swelling requires imaging. Total excision of the cyst is considered the casual treatment. The open rhinoplasty is an adequate method in patients with nasal dermoids without an intracranial extension. Experienced surgeons should manage the functional and esthetical aspects together during the same surgery.

  3. Extension of yeast chronological lifespan by methylamine.

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar

    Full Text Available BACKGROUND: Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast Hansenula polymorpha grown at conditions that require primary peroxisome metabolism for growth. METHODOLOGY/PRINCIPAL FINDINGS: The chronological lifespan of H. polymorpha is strongly enhanced when cells are grown on methanol or ethanol, metabolized by peroxisome enzymes, relative to growth on glucose that does not require peroxisomes. The short lifespan of H. polymorpha on glucose is mainly due to medium acidification, whereas most likely ROS do not play an important role. Growth of cells on methanol/methylamine instead of methanol/ammonium sulphate resulted in further lifespan enhancement. This was unrelated to medium acidification. We show that oxidation of methylamine by peroxisomal amine oxidase at carbon starvation conditions is responsible for lifespan extension. The methylamine oxidation product formaldehyde is further oxidized resulting in NADH generation, which contributes to increased ATP generation and reduction of ROS levels in the stationary phase. CONCLUSION/SIGNIFICANCE: We conclude that primary peroxisome metabolism enhanced chronological lifespan of H. polymorpha. Moreover, the possibility to generate NADH at carbon starvation conditions by an organic nitrogen source supports further extension of the lifespan of the cell. Consequently, the interpretation of CLS analyses in yeast should include possible effects on the energy status of the cell.

  4. On Noisy Extensions of Nonholonomic Constraints

    Science.gov (United States)

    Gay-Balmaz, François; Putkaradze, Vakhtang

    2016-12-01

    We propose several stochastic extensions of nonholonomic constraints for mechanical systems and study the effects on the dynamics and on the conservation laws. Our approach relies on a stochastic extension of the Lagrange-d'Alembert framework. The mechanical system we focus on is the example of a Routh sphere, i.e., a rolling unbalanced ball on the plane. We interpret the noise in the constraint as either a stochastic motion of the plane, random slip or roughness of the surface. Without the noise, this system possesses three integrals of motion: energy, Jellet and Routh. Depending on the nature of noise in the constraint, we show that either energy, or Jellet, or both integrals can be conserved, with probability 1. We also present some exact solutions for particular types of motion in terms of stochastic integrals. Next, for an arbitrary nonholonomic system, we consider two different ways of including stochasticity in the constraints. We show that when the noise preserves the linearity of the constraints, then energy is preserved. For other types of noise in the constraint, e.g., in the case of an affine noise, the energy is not conserved. We study in detail a class of Lagrangian mechanical systems on semidirect products of Lie groups, with "rolling ball type" constraints. We conclude with numerical simulations illustrating our theories, and some pedagogical examples of noise in constraints for other nonholonomic systems popular in the literature, such as the nonholonomic particle, the rolling disk and the Chaplygin sleigh.

  5. Competitive differentiation through brand extensions in the era of hyper competition

    Directory of Open Access Journals (Sweden)

    Claudiu-Catalin Munteanu

    2015-03-01

    Full Text Available In the era of hyper competition, competitive differentiation has become increasingly important. Brand extensions are used by companies across various industries for competitive differentiation. But in the era of hyper competition, a successful differentiation strategy requires that a brand emphasizes on uniqueness rather than commoditization. In this article, we make a case for creating a meaningful differentiation strategy. We emphasize the role of brand extensions for competitive differentiation and highlight the main perils of using brand extensions as a primary differentiation strategy. By using qualitative research, we identify primary objectives for brand extensions in practice. This investigation uses in-depth interviews with 14 senior brand managers across various industries to highlight brand portfolio strategies in relation to the brand differentiation strategy. Findings reveal that for business at the base of the pyramid, in markets such as Romania, brand managers are using brand extensions to increase sales or to boost short-term revenue rather than to implement a coherent differentiation strategy. We conclude with multiple recommendations for improving brand extension usage as a strategic instrument for creating meaningful differentiation in the era of hyper competition.

  6. Image Segmentation and Analysis of Flexion-Extension Radiographs of Cervical Spines

    Directory of Open Access Journals (Sweden)

    Eniko T. Enikov

    2014-01-01

    Full Text Available We present a new analysis tool for cervical flexion-extension radiographs based on machine vision and computerized image processing. The method is based on semiautomatic image segmentation leading to detection of common landmarks such as the spinolaminar (SL line or contour lines of the implanted anterior cervical plates. The technique allows for visualization of the local curvature of these landmarks during flexion-extension experiments. In addition to changes in the curvature of the SL line, it has been found that the cervical plates also deform during flexion-extension examination. While extension radiographs reveal larger curvature changes in the SL line, flexion radiographs on the other hand tend to generate larger curvature changes in the implanted cervical plates. Furthermore, while some lordosis is always present in the cervical plates by design, it actually decreases during extension and increases during flexion. Possible causes of this unexpected finding are also discussed. The described analysis may lead to a more precise interpretation of flexion-extension radiographs, allowing diagnosis of spinal instability and/or pseudoarthrosis in already seemingly fused spines.

  7. Utilization of Educational Innovations and Technology in Research and Extension Functions of State Universities

    Directory of Open Access Journals (Sweden)

    Rosalinda M. Comia

    2017-11-01

    Full Text Available The study focused on the extent of utilization of the educational innovations and technology in research and extension functions of SUs. The descriptive design, triangulation method, and purposive sampling were applied in this study. The findings revealed that majority of the respondents are married adults and master’s degree graduates with education as their area of specialization. They are permanent in status and have considerable years in the University serving as research or extension officer. Research of SUs have common research thrusts in terms of environment and natural resources management but differ in their own respective agenda; similarly the SUs share common extension thrusts and concerns but differ in their programs, activities and projects related to community services. Commonly encountered problems concern inadequate funds and inability to access the available technology. Officers utilized educational innovations on research and extension to a moderate extent but software and hardware were utilized to a great extent; likewise internet-based communication was utilized to a great extent for research but used moderately for extension. This implies that compared to research, most of the extension functions do not require the use of internet-based communication. From the results of the study, it was recommended that review of the existing allocation of funds for technology development may be done to improve the existing hardware, software and communication facilities.

  8. Extensive hypertrophic lupus erythematosus: Atypical presentation

    Directory of Open Access Journals (Sweden)

    Tarun Narang

    2012-01-01

    Full Text Available Lupus erythematosus (LE is a disease with a wide spectrum of cutaneous and systemic manifestations. Clinical features of patients with LE show a great variation, and for this reason it is difficult to develop a unifying concept of this disease. Our objective is to present a case of hypertrophic LE with atypical morphology and extensive involvement, who responded favorably to isotretinoin. Diagnosis of hypertrophic lupus erythematosus (HLE was confirmed by characteristic histopathological findings. Combination therapy with isotretinoin and hydroxychloroquine resulted in flattening and repression of previously refractory skin lesions. Sometimes, HLE lesions may present a diagnostic and therapeutic dilemma. In long standing lesions, squamous cell carcinoma may arise. Therefore, HLE requires adequate therapy with clinical and histopathological follow up.

  9. BB-CLIPS: Blackboard extensions to CLIPS

    Science.gov (United States)

    Orchard, Robert A.; Diaz, Aurora C.

    1990-01-01

    This paper describes a set of extensions made to CLIPS version 4.3 that provide capabilities similar to the blackboard control architecture described by Hayes-Roth. There are three types of additions made to the CLIPS shell. The first extends the syntax to allow the specification of blackboard locations for CLIPS facts. The second implements changes in CLIPS rules and the agenda manager that provide some of the powerful features of the blackboard control architecture. These additions provide dynamic prioritization of rules on the agenda allowing control strategies to be implemented that respond to the changing goals of the system. The final category of changes support the needs of continuous systems, including the ability for CLIPS to continue execution with an empty agenda.

  10. An Extension of Gregus Fixed Point Theorem

    Directory of Open Access Journals (Sweden)

    J. O. Olaleru

    2007-03-01

    Full Text Available Let C be a closed convex subset of a complete metrizable topological vector space (X,d and T:C→C a mapping that satisfies d(Tx,Ty≤ad(x,y+bd(x,Tx+cd(y,Ty+ed(y,Tx+fd(x,Ty for all x,y∈C, where 0extension of the results of several authors, is proved in this paper. In addition, we use the Mann iteration to approximate the fixed point of T.

  11. Learning investment indicators through data extension

    Science.gov (United States)

    Dvořák, Marek

    2017-07-01

    Stock prices in the form of time series were analysed using single and multivariate statistical methods. After simple data preprocessing in the form of logarithmic differences, we augmented this single variate time series to a multivariate representation. This method makes use of sliding windows to calculate several dozen of new variables using simple statistic tools like first and second moments as well as more complicated statistic, like auto-regression coefficients and residual analysis, followed by an optional quadratic transformation that was further used for data extension. These were used as a explanatory variables in a regularized logistic LASSO regression which tried to estimate Buy-Sell Index (BSI) from real stock market data.

  12. Post-traumatic extensive knee ganglion cyst

    Directory of Open Access Journals (Sweden)

    Mehran Mahvash

    2011-08-01

    Full Text Available A rare case of a posttraumatic extensive ganglion cyst of the anterolateral thigh with connection to the knee joint is presented. A 54- year-old man presented a palpable mass in the anterolateral region of his right thigh with a 15 months existing sense of fullness and tightness. He had an accident with his bicycle 21 months ago. Magnetic resonance imaging (MRI was performed showing a cyst inside the quadriceps femoris muscle between vastus lateralis and intermedius with connection to recessus suprapatellaris and knee joint. In addition MRI detected a traumatic lesion in the quadriceps femoris tendon in the near of the knee joint. The ganglion cyst was 18 cm long and was excised completely. Intraope - ratively, the knee joint connection was confirmed and excised as well. The ganglion cyst was filled with a gelatinous and viscous fluid.

  13. Extensive IT outsourcing: advice from providers.

    Science.gov (United States)

    Smith, Mike; Whiting, Stacilee

    2007-01-01

    In summary, providers are reporting some benefits related to resources and knowledge, improved service levels/performance and stronger IT staff/leadership. Also, on average, providers are reporting satisfactory experiences with application support and CIO outsourcing. However, not all of their expectations are being met, and some providers have discontinued outsourcing due to unmet expectations. Clearly, outsourcing is an option one must research in depth--it is not for everyone. When one evaluates the results of extensive IT outsourcing, it becomes easier to see what outsourcing mix and firm may be a good match for your organization's needs and expected outcomes. As you decide upon the outsourcing mix and firm that is right for you, providers advise you to pay special attention to contractual arrangements. With adequate research and contractual provisions, organizations can find the outsourcing mix that is right for them.

  14. Supersymmetric Extension of Technicolor & Fermion Mass Generation

    DEFF Research Database (Denmark)

    Antola, Matti; Di Chiara, Stefano; Sannino, Francesco

    2012-01-01

    We provide a complete extension of Minimal Walking Technicolor able to account for the standard model fermion masses. The model is supersymmetric at energies greater or equal to the technicolor compositeness scale. We integrate out, at the supersymmetry breaking scale, the elementary Higgses. We...... use the resulting four-fermion operators to derive the low energy effective theory. We then determine the associated tree-level vacuum and low energy spectrum properties. Furthermore we investigate the phenomenological viability of the model by comparing its predictions with electroweak precision...... tests and experimental bounds on the mass spectrum. We then turn to the composite Higgs phenomenology at the LHC and show that current data are already constraining the parameter space of the model....

  15. Gemcitabine-Induced Extensive Skin Necrosis

    Directory of Open Access Journals (Sweden)

    Sara D'epiro

    2012-01-01

    Full Text Available An 82-year-old woman presented with oedema and extensive necrotic ulcerative lesions on the back side of her lower limbs, emerging after the second cycle of chemotherapy consisting of Gemcitabine for metastatic pancreatic cancer. The absence of any convincing argument in favor of cardiovascular or autoimmune disease led us to attribute the onset of skin necrosis to chemotherapy administration. Although skin ischemia has also been described as a paraneoplastic syndrome, in this case we could observe a temporal and causal relationship to Gemcitabine infusion. Recently, this drug has been associated with important vascular side effects; its vascular toxicity is in fact higher than previously estimated. To our knowledge, careful attention should be reserved to neoplastic patients candidated to Gemcitabine administration, especially if previously affected by arterial vascular disease, venous thromboembolism, or collagenoses.

  16. Extensive enactivism: why keep it all in?

    Science.gov (United States)

    Hutto, Daniel D; Kirchhoff, Michael D; Myin, Erik

    2014-01-01

    Radical enactive and embodied approaches to cognitive science oppose the received view in the sciences of the mind in denying that cognition fundamentally involves contentful mental representation. This paper argues that the fate of representationalism in cognitive science matters significantly to how best to understand the extent of cognition. It seeks to establish that any move away from representationalism toward pure, empirical functionalism fails to provide a substantive "mark of the cognitive" and is bereft of other adequate means for individuating cognitive activity. It also argues that giving proper attention to the way the folk use their psychological concepts requires questioning the legitimacy of commonsense functionalism. In place of extended functionalism-empirical or commonsensical-we promote the fortunes of extensive enactivism, clarifying in which ways it is distinct from notions of extended mind and distributed cognition.

  17. Extensive Enactivism: Why Keep it All in?

    Directory of Open Access Journals (Sweden)

    Daniel Douglas Hutto

    2014-09-01

    Full Text Available Radical enactive and embodied approaches to cognitive science oppose the received view in the sciences of the mind in denying that cognition fundamentally involves contentful mental representation. This paper argues that the fate of representationalism in cognitive science matters significantly to how best to understand the extent of cognition. It seeks to establish that any move away from representationalism towards pure, empirical functionalism fails to provide a substantive ‘mark of the cognitive’ and is bereft of other adequate means for individuating cognitive activity. It also argues that giving proper attention to the way the folk use their psychological concepts requires questioning the legitimacy of commonsense functionalism. In place of extended functionalism – empirical or commonsensical – we promote the fortunes of extensive enactivism, clarifying in which ways it is distinct from notions of extended mind and distributed cognition.

  18. Adaptive distributional extensions to DFR ranking

    DEFF Research Database (Denmark)

    Petersen, Casper; Simonsen, Jakob Grue; Järvelin, Kalervo

    2016-01-01

    Divergence From Randomness (DFR) ranking models assume that informative terms are distributed in a corpus differently than non-informative terms. Different statistical models (e.g. Poisson, geometric) are used to model the distribution of non-informative terms, producing different DFR models....... An informative term is then detected by measuring the divergence of its distribution from the distribution of non-informative terms. However, there is little empirical evidence that the distributions of non-informative terms used in DFR actually fit current datasets. Practically this risks providing a poor...... separation between informative and non-informative terms, thus compromising the discriminative power of the ranking model. We present a novel extension to DFR, which first detects the best-fitting distribution of non-informative terms in a collection, and then adapts the ranking computation to this best...

  19. A Moodle extension to book online labs

    Directory of Open Access Journals (Sweden)

    Antonio C. Cardoso

    2005-11-01

    Full Text Available The social constructivist philosophy of Moodle makes it an excellent choice to deliver e-learning contents that require collaborative activities, such as those that are associated with online labs. In the case of online labs that enable web access to real devices (remote workbenches, access time should be reserved beforehand. A booking tool will avoid access conflicts and at the same time will help the students to organise their time and activities. This paper presents a Moodle extension that was developed within the Leonardo da Vinci MARVEL project, with the objective of meeting this requirement. The booking tool presented enables resource sharing in general and may be used to organise access to any type of scarce resources, such as to online labs and to the videoconferencing rooms that are needed to support collaborative activities.

  20. Extension of association models to complex chemicals

    DEFF Research Database (Denmark)

    Avlund, Ane Søgaard

    Summary of “Extension of association models to complex chemicals”. Ph.D. thesis by Ane Søgaard Avlund The subject of this thesis is application of SAFT type equations of state (EoS). Accurate and predictive thermodynamic models are important in many industries including the petroleum industry....... The SAFT EoS was developed 20 years ago, and a large number of papers on the subject has been published since, but many issues still remain unsolved. These issues are both theoretical and practical. The SAFT theory does not account for intramolecular association, it can only treat flexible chains, and does...... functional groups. It is also tested whether increasing the number of sites for DEA (diethanolamine) improves the results. It can be shown from experimental data that intramolecular association is dominating compared to intermolecular association in certain systems, and that the intramolecular association...

  1. Estimating Extensive Form Games in R

    Directory of Open Access Journals (Sweden)

    Brenton Kenkel

    2014-01-01

    Full Text Available This article introduces new software, the games package, for estimating strategic statistical models in R. In these models, the probability distribution over outcomes corresponds to the equilibrium of an underlying game form. We review such models and provide derivations for one example, including discussion of alternative motivations for the stochastic component of the models. We introduce the basic functionality of the games package, such as how to estimate players utilities for outcomes as a function of covariates. The package implements maximum likelihood estimation for the most commonly used models of strategic choice, including three extensive form games and an ultimatum bargaining model. The software also includes functions for bootstrapping, plotting fitted values with their confidence intervals, performing non-nested model comparisons, and checking global convergence failures. We use the new software to replicate Leblangs (2003 analysis of speculative currency attacks.

  2. Energy Extension Service Program planning manual

    Energy Technology Data Exchange (ETDEWEB)

    Liersch, Judith M.

    1979-06-01

    The manual is the first revision of the EES Program Planning Manual. At the states' request, there have been a number of changes to the state EES contacts list, and an updated list is included in this package as the revised Appendix D. Part I, Introduction, presents: How to Use the State Program Planning Manual and The Energy Extension Service Program. Part II, Applying for an EES Grant, presents: The Annual State Application for Financial Assistance; State Financial Assistance and Associated Requirements; Preparing the State Plan. Part III, Operating a State EES, presents: Start-Up Considerations; State Program Reporting; Recordkeeping and Financial Management. Part IV, DOE's Role, presents DOE Functions and Responsibilities and Special Cases: Development and Implementation of a State Plan by the EES Director and Administrative Review.

  3. Production Flexibility in Extensive Beef Farming Systems

    Directory of Open Access Journals (Sweden)

    Laura Astigarraga

    2011-03-01

    Full Text Available The aim of this work is to assess the flexibility of production allowed by extensive production conditions faced with variations in the environment, i.e., market variations and climatic fluctuations, of Limousin beef systems. The study used a case-based methodology in which seven beef farms with less than 1 LU/ha were chosen. Data collection was based on three interviews using a semistructured questionnaire and on the analysis of productive and economic results over a 15-year period (1991-2005. The main evolution of these farms is related to a rise in work productivity associated with an increase in herd size. Herd increase was made possible by enlarging the area, the margin of intensification being limited in these regions. To take advantage of the enlarged land area, females were reared for fattening or for reproduction instead of selling them at weaning. The Limousin female provides a wide product mix because of its plasticity, as has been studied by several researchers. This mix flexibility is achieved by delaying product differentiation, a form of production flexibility that can reduce the risk of under-producing or over-producing varied product configurations. On the other hand, calves sold to the Italian market after weaning are generic products, associated with a flexible production process to overcome fluctuations in forage availability due to climatic variations. The introduction of maize silage for feeding acts as an alternative route, actual and potential, through the system to overcome unexpected forage shortage from natural grasslands as a result of droughts. The study shows that extensive farming systems have developed types of flexibility to match different factors of uncertainty from the environment. Finally, the issue of farm system performance is thus not so much a question of whether a farm is fit at a specific moment in time, but whether it transforms into a less or more sustainable orientation.

  4. Extensive Cryopegs on Barter Island, North Slope, Alaska

    Science.gov (United States)

    Lorenson, T. D.; Swarzenski, P. W.; Conaway, C. H.; Oberle, F. J.; Johnson, C. D.; Richmond, B. M.; Gibbs, A.

    2016-12-01

    Erosion rates are accelerating along portions of Northern Alaska due to recent warming trends and associated ice-free days along the coastline. We are assessing the composition and dynamics of permafrost on Barter Island to constrain how permafrost thawing and erosion contribute to release of permafrost constituents into the atmosphere and the ocean. We discovered a large basal cryopeg (high-salinity talik) at least 2 km long along the coast extending at least 300 m inland while conducting surface multichannel electrical resistivity tomography (ERT) to image and characterize shallow subsurface permafrost. The ERT surveys showed the extensive subsurface occurrence of low resistivity sediment suggesting the presence of freshwater overlying a less resistive layer about 5 m below. Borehole temperature data from a nearby inland location showed that at 10 m, the temperature -8° C, too cold to for liquid fresh water needed to explain a less resistive layer below the frozen active layer. We confirmed the presence of the cryopegs by coring up to 8 m deep in four locations. Extracted pore water from the cores is fresh in the upper 2 m within the active layer, and increasing salinity with depth. Enhanced salinity was found below 2.5 m. Salinity of up to 58 was extracted from stiff marine microfossil-bearing clay from 5 to 8 m deep. Pore water sulfate concentrations are depleted relative to seawater. XRD analyses material reveal the presence of the CaSO4 containing minerals of gypsum and anhydrite, the likely sink of sulfate. The source of saline water is actively being investigated. A 87/86Sr isotopic measurement of .0711, a value greater than observed in modern seawater, suggests that weathering processes or water-rock interaction affect the chemical composition of the brine. Regardless, the presence of extensive taliks beneath permafrost at elevations very near present-day sea level will be an unexpected factor in the assessment of future shoreline erosion rates.

  5. A Needs Assessment of Aquaculture Extension Agents, Specialists, and Program Administrators in Extension Programming

    Science.gov (United States)

    Schwarz, Michael H.; Gibson, Jerry

    2010-01-01

    The study reported here identified continuing education and training needs of aquaculture Extension agents, specialists, and program administrators in 10 competency areas relating to the need for continuing education or training. Fourteen resources on the AquaNIC Web site were also evaluated, as was the efficacy of the AQUA-EXT listserv. Data were…

  6. Bibliography of U.S. Extension and Extension-related Publications on Nematodes.

    Science.gov (United States)

    1988-10-01

    A listing was compiled of hematology publications available through the Cooperative Extension Service and similar organizations in the United States. It provides a convenient reference to current articles addressing many of the more applied aspects of plant nematology and nematode management.

  7. Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma

    DEFF Research Database (Denmark)

    Nepal, Chirag; O'Rourke, Colm J; Oliveira, Douglas Vnp

    2018-01-01

    -exome sequencing, targeted exome sequencing) and epigenomic data from 496 patients, and used the three most recurrently mutated genes to stratify patients (IDH, KRAS, TP53, 'undetermined'). Using this molecular dissection approach, each subgroup was determined to possess unique mutational signature preferences, co...... all 3 mutations ('undetermined') harbored the most extensive structural alterations while IDH mutant tumors displayed the most extensive DNA methylome dysregulation, consistent with previous findings. CONCLUSION: Stratification of iCCA patients based on occurrence of mutations in three classifier...... genes (IDH, KRAS, TP53) revealed unique oncogenic programs (mutational, structural, epi-mutational) that influence pharmacologic response in drug repositioning protocols. This genome dissection approach highlights the potential of individual mutations to induce extensive molecular heterogeneity...

  8. sources and use of extension information among maize farmers

    African Journals Online (AJOL)

    DR ADESOPE

    JOURNAL OF AGRICULTURE AND SOCIAL RESEARCH (JASR) Vol. ... extension information is sourced through extension worker, the mass media ..... Finally, farmers in general, and rural farmers in particular, should be encouraged to seek.

  9. Achieving Impact at Scale through ICT-Enabled Extension Services ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    CIFSRF Phase 2). In Africa, agricultural extension services have the potential to grow markets and enhance food security for smallholder farmers. Agricultural extension uses scientific research to educate farmers and improve agricultural ...

  10. Lightweight Nozzle Extension for Liquid Rocket Engines Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The ARES J-2X requires a large nozzle extension. Currently, a metallic nozzle extension is being considered with carbon-carbon composite as a backup. In Phase 1,...

  11. Journal of Agricultural Extension Vol.17 (2) December, 2013 ISSN ...

    African Journals Online (AJOL)

    ONIKOYI

    ). However, the experiences of farmers are fast changing. Traditional extension services linked with production objectives and blanket recommendations can no longer meet farmers' expectations. Therefore, extension practitioners need to ...

  12. The XML approach to implementing space link extension service management

    Science.gov (United States)

    Tai, W.; Welz, G. A.; Theis, G.; Yamada, T.

    2001-01-01

    A feasibility study has been conducted at JPL, ESOC, and ISAS to assess the possible applications of the eXtensible Mark-up Language (XML) capabilities to the implementation of the CCSDS Space Link Extension (SLE) Service Management function.

  13. Extensible automated dispersive liquid–liquid microextraction

    Energy Technology Data Exchange (ETDEWEB)

    Li, Songqing; Hu, Lu; Chen, Ketao; Gao, Haixiang, E-mail: hxgao@cau.edu.cn

    2015-05-04

    Highlights: • An extensible automated dispersive liquid–liquid microextraction was developed. • A fully automatic SPE workstation with a modified operation program was used. • Ionic liquid-based in situ DLLME was used as model method. • SPE columns packed with nonwoven polypropylene fiber was used for phase separation. • The approach was applied to the determination of benzoylurea insecticides in water. - Abstract: In this study, a convenient and extensible automated ionic liquid-based in situ dispersive liquid–liquid microextraction (automated IL-based in situ DLLME) was developed. 1-Octyl-3-methylimidazolium bis[(trifluoromethane)sulfonyl]imide ([C{sub 8}MIM]NTf{sub 2}) is formed through the reaction between [C{sub 8}MIM]Cl and lithium bis[(trifluoromethane)sulfonyl]imide (LiNTf{sub 2}) to extract the analytes. Using a fully automatic SPE workstation, special SPE columns packed with nonwoven polypropylene (NWPP) fiber, and a modified operation program, the procedures of the IL-based in situ DLLME, including the collection of a water sample, injection of an ion exchange solvent, phase separation of the emulsified solution, elution of the retained extraction phase, and collection of the eluent into vials, can be performed automatically. The developed approach, coupled with high-performance liquid chromatography–diode array detection (HPLC–DAD), was successfully applied to the detection and concentration determination of benzoylurea (BU) insecticides in water samples. Parameters affecting the extraction performance were investigated and optimized. Under the optimized conditions, the proposed method achieved extraction recoveries of 80% to 89% for water samples. The limits of detection (LODs) of the method were in the range of 0.16–0.45 ng mL{sup −1}. The intra-column and inter-column relative standard deviations (RSDs) were <8.6%. Good linearity (r > 0.9986) was obtained over the calibration range from 2 to 500 ng mL{sup −1}. The proposed

  14. The Methanosarcina barkeri genome: comparative analysis withMethanosarcina acetivorans and Methanosarcina mazei reveals extensiverearrangement within methanosarcinal genomes

    Energy Technology Data Exchange (ETDEWEB)

    Maeder, Dennis L.; Anderson, Iain; Brettin, Thomas S.; Bruce,David C.; Gilna, Paul; Han, Cliff S.; Lapidus, Alla; Metcalf, William W.; Saunders, Elizabeth; Tapia, Roxanne; Sowers, Kevin R.

    2006-05-19

    We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the large M. acetivorans is the result of multiple gene-scale insertions and duplications uniformly distributed in that genome, while M. barkeri is characterized by localized inversions associated with the loss of gene content. In contrast, the relatively short M. mazei most closely approximates the ancestral organizational state.

  15. Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments.

    Science.gov (United States)

    Cenci, Alberto; Combes, Marie-Christine; Lashermes, Philippe

    2012-01-01

    Sequence comparison of orthologous regions enables estimation of the divergence between genomes, analysis of their evolution and detection of particular features of the genomes, such as sequence rearrangements and transposable elements. Despite the economic importance of Coffea species, little genomic information is currently available. Coffea is a relatively young genus that includes more than one hundred diploid species and a single tetraploid species. Three Coffea orthologous regions of 470-900 kb were analyzed and compared: both subgenomes of allotetraploid Coffea arabica (contributed by the diploid species Coffea eugenioides and Coffea canephora) and the genome of diploid C. canephora. Sequence divergence was calculated on global alignments or on coding and non-coding sequences separately. A search for transposable elements detected 43 retrotransposons and 198 transposons in the sequences analyzed. Comparative insertion analysis made it possible to locate 165 TE insertions in the phylogenetic tree of the three genomes/subgenomes. In the tetraploid C. arabica, a homoeologous non-reciprocal transposition (HNRT) was detected and characterized: a 50 kb region of the C. eugenioides derived subgenome replaced the C. canephora derived counterpart. Comparative sequence analysis on three Coffea genomes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of shared transposable elements. Compared to the results of similar analysis in other genera (Aegilops/Triticum and Oryza), Coffea genomes/subgenomes appeared to be dramatically less diverged, which is consistent with the relatively recent radiation of the Coffea genus. Based on nucleotide substitution frequency, the HNRT was dated at 10,000-50,000 years BP, which is also the most recent estimation of the origin of C. arabica.

  16. Expanding the Reach of Extension through Social Media

    Science.gov (United States)

    Gharis, Lauri W.; Bardon, Robert E.; Evans, Jennifer L.; Hubbard, William G.; Taylor, Eric

    2014-01-01

    With increasing numbers of the public using social media applications, Extension professionals have the ability to apply these same tools to connect with their clients. This article demonstrates how a social media toolset can be employed by Extension professionals by identifying how Extension professionals are currently using social media,…

  17. Use of Internet for Innovation Management by Extension Agents in ...

    African Journals Online (AJOL)

    User

    agents' increases, the perception of the Internet uses for innovation management also increases in the same direction. The extension agent that uses Internet extensively is likely to have a favourable perception of its use in innovation management. Therefore, it is important to encourage extension agents in the use of.

  18. Evaluation of the agricultural extension programmes of Shell ...

    African Journals Online (AJOL)

    Evaluation of the agricultural extension programmes of Shell Petroleum Development Company in Rivers State, Nigeria. ... The effectiveness of field extension agents was limited by inadequate communication and transport facilities, non-repayment of soft loans and irregular attendance to scheduled extension meetings by ...

  19. Documentation of Extension Specialists' Involvement in Graduate Education.

    Science.gov (United States)

    Murdock, Edward C.; York, Alan C.

    1996-01-01

    Describes the changes in the roles of the Cooperative Extension Service and extension specialists affiliated with universities. Reports the results of survey research and concludes that extension specialists should actively pursue the opportunity to direct graduate students. Contains 16 references. (DDR)

  20. Stress coping strategies among agricultural extension agents in Oyo ...

    African Journals Online (AJOL)

    The study examined the coping strategies used by extension agents A total of seventy 72agricultural extension agents were randomly sampled out of 288 agricultural extension agents from the four zones (Saki, Oyo, Ogbomosho, and Ibadan) in the Oyo State Agricultural Development Programme (OYSADEP).

  1. The role of a pluralistic extension system in enhancing agriculture ...

    African Journals Online (AJOL)

    The role of a pluralistic extension system in enhancing agriculture productivity in Mozambique. ... This is unlike in the recent past when agricultural services were mainly delivered by the public sector. The 25 years ... The expansion of public extension services created new challenges for the delivering of extension services.

  2. Journal of Agricultural Extension Vol.17 (2) December, 2013 ISSN ...

    African Journals Online (AJOL)

    ONIKOYI

    Abstract. The study assessed the availability and dissemination of information to farmers using mobile phones by public extension agents in Delta state, Nigeria. Data were collected from 64 randomly selected public extension agents from the three agricultural zones in the state. Majority (98.4%) of the extension agents were ...

  3. Using Authentic Materials for Extensive Reading to Promote English Proficiency

    Science.gov (United States)

    Guo, Siao-cing

    2012-01-01

    Current literature points to the importance and benefits of extensive reading. Extensive reading provides contextualized clues for better reading comprehension (Krashen, 1982), and substantial linguistic input (Bell, 1998) needed for language development. Several studies have found a correlation between extensive reading and specific linguistic…

  4. Job burnout and coping strategies among extension agents in south ...

    African Journals Online (AJOL)

    The need to maintain a non-mineral dependent economy and daunting food import bills have been the drive for the provision of extension services, which is dependent on motivated extension work force.. Extension personnel will not stay motivated under circumstances where the risk of job burnout is high. A simple random ...

  5. Legislated Policy as the Basis for Effective Extension Delivery ...

    African Journals Online (AJOL)

    The paper compares the extension policies and programmes of Britain and Nigeria. Extension policy in Nigeria is characterized as stemming from ad hoc arrangements which are compounded by political instability and external locus of control. The United Kingdom in contrast has had focused extension policies supported ...

  6. Determinants of training needs of extension personnel of agricultural ...

    African Journals Online (AJOL)

    The dynamics experienced in agricultural practice has put extension service delivery on a new platform that requires regular updating of the extension staff knowledge for new competences, to meet the changing needs of the clientele they serve. This study therefore sought to determine the training needs of extension ...

  7. America’s Changing Urban Landscape: Positioning Extension for Success

    Directory of Open Access Journals (Sweden)

    Marie A. Ruemenapp

    2017-06-01

    Full Text Available For the Cooperative Extension Service (Extension to have a substantive urban presence and impact, it will be vital for local Extension staff, state Extension systems, and the national Extension system to understand how to position Extension for success in large metropolitan regions. To do this, Extension should examine its history of working in cities, work to overcome a number of internal barriers or challenges that are defined in Extension literature, and develop a deeper understanding of the unique and complex set of characteristics and features of urban environments. As Extension does this, it will be important for it to move forward in a manner that ensures it is relevant to local metropolitan residents while being responsive to the needs of communities statewide. It will also be imperative that Extension be recognized locally, statewide, and nationally for its work; however, Extension is not starting from scratch as it has more than a 60-year history of working in cities. Extension should learn from best practices within the numerous strong urban and suburban operational and educational models present in a number of states.

  8. Why and How Textbooks Should Encourage Extensive Reading

    Science.gov (United States)

    Brown, Dale

    2009-01-01

    Extensive reading is believed to have considerable benefits for learners both in terms of learning gains and motivation and seems to be becoming ever more popular in the ELT world. So far, however, there seems to be almost no integration of extensive reading and textbooks. This article argues that textbooks should be encouraging extensive reading,…

  9. Integrating Extensive Reading into an English for Academic Purposes Program

    Science.gov (United States)

    Macalister, John

    2008-01-01

    This paper reports on the inclusion of extensive reading in three separate 12-week courses taught by different teachers on an EAP programme at a New Zealand university. The inclusion of extensive reading was experimental and sought answers to two questions: would students respond positively to the extensive reading component, and how could…

  10. Evaluation of performance of extension workers in Lesotho | Mokone ...

    African Journals Online (AJOL)

    The extension service in Lesotho and other developing countries have been criticized for not being able to bring the necessary change in the farming populace, especially the rural and resource poor. Extension workers are faced with problems that need to be dealt with in order for them and extension as a whole to be ...

  11. Farmers and Extension Personnel View of Constraints to Effective ...

    African Journals Online (AJOL)

    This study examined farmers' and extension personnel's View of constraints to effectiveness of agricultural extension services in Oyo State, Nigeria. Simple random sampling technique was used to select 100 farmers and 20 extension personnel. Data subjected to descriptive and correlation analyses were collected using ...

  12. Public Sector Agricultural Extension System Reform and the Challenges Ahead

    Science.gov (United States)

    Rivera, William M.

    2011-01-01

    This paper is organized into two main sections. The first section examines extension as an engine for innovation and reviews the numerous priorities confronting extension systems. Section two highlights the current knowledge imperative and the critical connection of extension to post-secondary higher education and training, organizational…

  13. 34 CFR 101.42 - Extension of time or postponement.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Extension of time or postponement. 101.42 Section 101.42 Education Regulations of the Offices of the Department of Education OFFICE FOR CIVIL RIGHTS... Extension of time or postponement. Requests for extension of time should be served on all parties and should...

  14. 38 CFR 18b.27 - Extension of time or postponement.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Extension of time or postponement. 18b.27 Section 18b.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Time § 18b.27 Extension of time or postponement. Requests for extension of time should be served on all...

  15. evaluation of job performance of village extension agents in lagos ...

    African Journals Online (AJOL)

    AFINNI IMAM

    factors influencing dissemination of improved technology, age, education and gender were significant at 5% level of ... agricultural production and in marketing of their produce (Williams, 1989). On the other hand, ... extension agents often determines the success or failure of an extension programme. An extension agent ...

  16. Evaluating retail format extensions : The role of shopping goals

    NARCIS (Netherlands)

    Haans, A.J.

    2011-01-01

    Although retail extensions have become a common growth strategy, more than 50% fail to survive. The question what drives extension success, therefore remains a key issue. This research tests the hypothesis that expectations about the attributes of extensions, and as a result of their evaluations,

  17. Evaluation of extension agents effectiveness in transferring agro ...

    African Journals Online (AJOL)

    Evaluation of extension agents effectiveness in transferring agro-forestry technologies to farmers in Imo state, Nigeria. ... The paper recommended adequate motivation and training of the change agents to equip them more in their extension delivery. Keyword: Agroforestry technologies, conservation, extension agents, ...

  18. Facilitating protein solubility by use of peptide extensions

    Science.gov (United States)

    Freimuth, Paul I; Zhang, Yian-Biao; Howitt, Jason

    2013-09-17

    Expression vectors for expression of a protein or polypeptide of interest as a fusion product composed of the protein or polypeptide of interest fused at one terminus to a solubility enhancing peptide extension are provided. Sequences encoding the peptide extensions are provided. The invention further comprises antibodies which bind specifically to one or more of the solubility enhancing peptide extensions.

  19. Evaluation of the effectiveness of the Imo State fisheriers extension ...

    African Journals Online (AJOL)

    Evaluation of the effectiveness of the Imo State fisheriers extension programme. DO Ohajianya, DO Onu, JA Echetama. Abstract. This study evaluated the Imo State Ministry of Agriculture Fisheries Extension Programmes. Questionnaires were used to collect data from 15 randomly selected extension staff and 200 ...

  20. Perspective of agricultural extension in livestock production in ...

    African Journals Online (AJOL)

    The main source of extension services was the private sector and the services rendered were educational, health, technical, management and marketing. The extension communication methods used were visits, demonstration, workshop, training and excursion. The benefits of extension services were introduction of ...