WorldWideScience

Sample records for high genome plasticity

  1. Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium

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    Latifi Amel

    2008-06-01

    Full Text Available Abstract Background The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There has been little investigation of the genomics of these cyanobacteria. Results Deciphering the 5,172,804 bp sequence of Microcystis aeruginosa PCC 7806 has revealed the high plasticity of its genome: 11.7% DNA repeats containing more than 1,000 bases, 6.8% putative transposases and 21 putative restriction enzymes. Compared to the genomes of other cyanobacterial lineages, strain PCC 7806 contains a large number of atypical genes that may have been acquired by lateral transfers. Metabolic pathways, such as fermentation and a methionine salvage pathway, have been identified, as have genes for programmed cell death that may be related to the rapid disappearance of Microcystis blooms in nature. Analysis of the PCC 7806 genome also reveals striking novel biosynthetic features that might help to elucidate the ecological impact of secondary metabolites and lead to the discovery of novel metabolites for new biotechnological applications. M. aeruginosa and other large cyanobacterial genomes exhibit a rapid loss of synteny in contrast to other microbial genomes. Conclusion Microcystis aeruginosa PCC 7806 appears to have adopted an evolutionary strategy relying on unusual genome plasticity to adapt to eutrophic freshwater ecosystems, a property shared by another strain of M. aeruginosa (NIES-843. Comparisons of the genomes of PCC 7806 and other cyanobacterial strains indicate that a similar strategy may have also been used by the marine strain Crocosphaera watsonii WH8501 to adapt to other ecological niches, such as oligotrophic open oceans.

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

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    Pesole Graziano

    2007-08-01

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

  3. Genome plasticity and systems evolution in Streptomyces

    Science.gov (United States)

    2012-01-01

    Background Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation. Results We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication. Conclusions Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A

  4. Functional genomics of physiological plasticity and local adaptation in killifish.

    Science.gov (United States)

    Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F

    2011-01-01

    Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.

  5. Young men with low birthweight exhibit decreased plasticity of genome-wide muscle DNA methylation by high-fat overfeeding

    DEFF Research Database (Denmark)

    Jacobsen, Stine C; Gillberg, Linn; Bork-Jensen, Jette

    2014-01-01

    The association between low birthweight (LBW) and risk of developing type 2 diabetes may involve epigenetic mechanisms, with skeletal muscle being a prime target tissue. Differential DNA methylation patterns have been observed in single genes in muscle tissue from type 2 diabetic and LBW...... individuals, and we recently showed multiple DNA methylation changes during short-term high-fat overfeeding in muscle of healthy people. In a randomised crossover study, we analysed genome-wide DNA promoter methylation in skeletal muscle of 17 young LBW men and 23 matched normal birthweight (NBW) men after...... a control and a 5 day high-fat overfeeding diet....

  6. Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

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    Liu Xiumei

    2008-11-01

    Full Text Available Abstract Background Outbreak of V. parahaemolyticus infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of V. parahaemolyticus. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of V. parahaemolyticus. Results Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5, and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (trh-, tdh+ and GS-PCR+, while C2 contained 12 pre-1996 'old' O3:K6 strains (trh+, tdh- and GS-PCR- tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18 might be emerged from the old-O3:K6 clone, which was promoted by acquisition of toxRS/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (trh-, tdh- and GS-PCR+ was identified between the pandemic and old-O3:K6 clones. Conclusion A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of V. parahaemolyticus and an evolutionary history of the pandemic group (clone of this pathogen.

  7. Plastic

    International Nuclear Information System (INIS)

    Jeong Gi Hyeon

    1987-04-01

    This book deals with plastic, which includes introduction for plastic, chemistry of high polymers, polymerization, speciality and structure of a high molecule property of plastic, molding, thermosetting plastic, such as polyethylene, polyether, polyamide and polyvinyl acetyl, thermal plastic like phenolic resins, xylene resins, melamine resin, epoxy resin, alkyd resin and poly urethan resin, new plastic like ionomer and PPS resin, synthetic laminated tape and synthetic wood, mixed materials in plastic, reprocessing of waste plastic, polymer blend, test method for plastic materials and auxiliary materials of plastic.

  8. Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

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    Zhiliang Yu

    2017-07-01

    Full Text Available Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.

  9. Keeping it complicated: Mitochondrial genome plasticity across diplonemids.

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    Valach, Matus; Moreira, Sandrine; Hoffmann, Steve; Stadler, Peter F; Burger, Gertraud

    2017-10-26

    Chromosome rearrangements are important drivers in genome and gene evolution, with implications ranging from speciation to development to disease. In the flagellate Diplonema papillatum (Euglenozoa), mitochondrial genome rearrangements have resulted in nearly hundred chromosomes and a systematic dispersal of gene fragments across the multipartite genome. Maturation into functional RNAs involves separate transcription of gene pieces, joining of precursor RNAs via trans-splicing, and RNA editing by substitution and uridine additions both reconstituting crucial coding sequence. How widespread these unusual features are across diplonemids is unclear. We have analyzed the mitochondrial genomes and transcriptomes of four species from the Diplonema/Rhynchopus clade, revealing a considerable genomic plasticity. Although gene breakpoints, and thus the total number of gene pieces (~80), are essentially conserved across this group, the number of distinct chromosomes varies by a factor of two, with certain chromosomes combining up to eight unrelated gene fragments. Several internal protein-coding gene pieces overlap substantially, resulting, for example, in a stretch of 22 identical amino acids in cytochrome c oxidase subunit 1 and NADH dehydrogenase subunit 5. Finally, the variation of post-transcriptional editing patterns across diplonemids indicates compensation of two adverse trends: rapid sequence evolution and loss of genetic information through unequal chromosome segregation.

  10. Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

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    I-Hsuan Lin

    Full Text Available Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I and S. pasteurianus ATCC 43144 (biotype II.2. The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92% and 1607 (86% of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

  11. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location.

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    Zmienko, Agnieszka; Samelak-Czajka, Anna; Kozlowski, Piotr; Szymanska, Maja; Figlerowicz, Marek

    2016-11-08

    Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted. We analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2-14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV. We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular

  12. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

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    Romain Blanc-Mathieu

    2017-06-01

    Full Text Available Root-knot nematodes (genus Meloidogyne exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by

  13. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

    DEFF Research Database (Denmark)

    Pearce, S L; Clarke, D F; East, P D

    2017-01-01

    BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptom......BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics......, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100...... lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show...

  14. Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

    Energy Technology Data Exchange (ETDEWEB)

    McMurdie, Paul J.; Behrens, Sebastien F.; Muller, Jochen A.; Goke, Jonathan; Ritalahti, Kirsti M.; Wagner, Ryan; Goltsman, Eugene; Lapidus, Alla; Holmes, Susan; Loffler, Frank E.; Spormann, Alfred M.

    2009-06-30

    Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.

  15. Genome landscape and evolutionary plasticity of chromosomes in malaria mosquitoes.

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    Ai Xia

    2010-05-01

    Full Text Available Nonrandom distribution of rearrangements is a common feature of eukaryotic chromosomes that is not well understood in terms of genome organization and evolution. In the major African malaria vector Anopheles gambiae, polymorphic inversions are highly nonuniformly distributed among five chromosomal arms and are associated with epidemiologically important adaptations. However, it is not clear whether the genomic content of the chromosomal arms is associated with inversion polymorphism and fixation rates.To better understand the evolutionary dynamics of chromosomal inversions, we created a physical map for an Asian malaria mosquito, Anopheles stephensi, and compared it with the genome of An. gambiae. We also developed and deployed novel Bayesian statistical models to analyze genome landscapes in individual chromosomal arms An. gambiae. Here, we demonstrate that, despite the paucity of inversion polymorphisms on the X chromosome, this chromosome has the fastest rate of inversion fixation and the highest density of transposable elements, simple DNA repeats, and GC content. The highly polymorphic and rapidly evolving autosomal 2R arm had overrepresentation of genes involved in cellular response to stress supporting the role of natural selection in maintaining adaptive polymorphic inversions. In addition, the 2R arm had the highest density of regions involved in segmental duplications that clustered in the breakpoint-rich zone of the arm. In contrast, the slower evolving 2L, 3R, and 3L, arms were enriched with matrix-attachment regions that potentially contribute to chromosome stability in the cell nucleus.These results highlight fundamental differences in evolutionary dynamics of the sex chromosome and autosomes and revealed the strong association between characteristics of the genome landscape and rates of chromosomal evolution. We conclude that a unique combination of various classes of genes and repetitive DNA in each arm, rather than a single type

  16. Radiation crosslinking of highly plasticized PVC

    Science.gov (United States)

    Mendizabal, E.; Cruz, L.; Jasso, C. F.; Burillo, G.; Dakin, V. I.

    1996-02-01

    To improve the physical properties of highly plasticized PVC, the polymer was crosslinked by gamma irradiation using a dose rate of 91 kGy/h. The effect of plasticizer type was studied by using three different plasticizers, 2,2,4-trimethyl-1,3-pentanediol diisobutyrate (TXIB), di(2-ethyl hexyl) phthalate (DOP), and di(2-ethylhexyl terephthalate) (DOTP), and varying irradiation doses. Gel content was determined by soxhlet extraction, tensile measurements were made on a universal testing machine and the mechano-dynamic measurements were made in a dynamic rheometer. It was found that a considerable bonding of plasticizer molecules to macromolelcules takes place along with crosslinking, so that the use of the solvent extraction method for measuring the degree of crosslinking can give erroneous information. Radiation-chemical crosslinking yield ( Gc) and molecular weight of interjunctions chains ( Mc), were calculated for different systems studied. Addition of ethylene glycol dimethacrylate (EGDM) as a crosslinking coagent and dioctyl tin oxide (DOTO) as a stabilizer was also studied. Plasticizers extraction resistance was increased by irradiation treatment.

  17. Radiation crosslinking of highly plasticized PVC

    International Nuclear Information System (INIS)

    Mendizabal, E.; Cruz, L.; Jasso, C.F.; Burillo, G.; Dakin, V.I.

    1996-01-01

    To improve the physical properties of highly plasticized PVC, the polymer was crosslinked by gamma irradiation using a dose rate of 91 kGy/h. The effect of plasticizer type was studied by using three different plasticizers, 2,2,4-trimethyl-1,3-pentanediol diisobutyrate (TXIB), di(2-ethyl hexyl) phthalate (DOP), and di(2-ethylhexyl terephthalate) (DOTP), and varying irradiation doses. Gel content was determined by soxhlet extraction, tensile measurements were made on a universal testing machine and the mechano-dynamic measurements were made in a dynamic rheometer. It was found that a considerable bonding of plasticizer molecules to macromolecules takes place along with crosslinking, so that the use of the solvent extraction method for measuring the degree of crosslinking can give erroneous information. Radiation-chemical crosslinking yield (G c ) and molecular weight of interjunctions chains (M c ), were calculated for different systems studied. Addition of ethylene glycol dimethyacrylate (EGDM) as a crosslinking coagent and dioctyl tin oxide (DOTO) as a stabilizer was also studied. Plasticizers extraction resistance was increased by irradiation treatment. (author)

  18. Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans

    NARCIS (Netherlands)

    Li, Y.; Alda Alvarez, O.; Gutteling, E.W.; Tijsterman, M.; Fu, J.; Riksen, J.A.G.; Hazendonk, E.; Prins, J.C.P.; Plasterk, R.H.A.; Jansen, R.C.; Breitling, R.; Kammenga, J.E.

    2006-01-01

    Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals have been mapped to the causal regulatory regions, termed expression quantitative trait loci. Whether the environment-induced plastic

  19. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.

    NARCIS (Netherlands)

    Li, Y.; Alvarez, O.A.; Gutteling, E.W.; Tijsterman, M.; Fu, J.; Riksen, J.A.; Hazendonk, M.G.A.; Prins, P.; Plasterk, R.H.A.; Jansen, R.C.; Breitling, R.; Kammenga, J.E.

    2006-01-01

    Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals have been mapped to the causal regulatory regions, termed expression quantitative trait loci. Whether the environment-induced plastic

  20. Genome 3D-architecture: Its plasticity in relation to function

    Indian Academy of Sciences (India)

    Kundan Sengupta

    Mini-Review. Genome 3D-architecture: Its plasticity in relation to function. KUNDAN ... MS received 23 October 2017; accepted 14 February 2018; published online 7 April 2018 .... moter Communication and T Cell Fate. Cell 171 103–119.

  1. Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

    Science.gov (United States)

    Liscovitch-Brauer, Noa; Alon, Shahar; Porath, Hagit T; Elstein, Boaz; Unger, Ron; Ziv, Tamar; Admon, Arie; Levanon, Erez Y; Rosenthal, Joshua J C; Eisenberg, Eli

    2017-04-06

    RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

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    Beverly E. Flood

    2016-05-01

    Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

  3. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity.

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    Lisa L Ellis

    2014-07-01

    Full Text Available We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

  4. Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity

    Science.gov (United States)

    Ellis, Lisa L.; Huang, Wen; Quinn, Andrew M.; Ahuja, Astha; Alfrejd, Ben; Gomez, Francisco E.; Hjelmen, Carl E.; Moore, Kristi L.; Mackay, Trudy F. C.; Johnston, J. Spencer; Tarone, Aaron M.

    2014-01-01

    We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions. PMID:25057905

  5. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  6. Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.

  7. High-temperature discrete dislocation plasticity

    Science.gov (United States)

    Keralavarma, S. M.; Benzerga, A. A.

    2015-09-01

    A framework for solving problems of dislocation-mediated plasticity coupled with point-defect diffusion is presented. The dislocations are modeled as line singularities embedded in a linear elastic medium while the point defects are represented by a concentration field as in continuum diffusion theory. Plastic flow arises due to the collective motion of a large number of dislocations. Both conservative (glide) and nonconservative (diffusion-mediated climb) motions are accounted for. Time scale separation is contingent upon the existence of quasi-equilibrium dislocation configurations. A variational principle is used to derive the coupled governing equations for point-defect diffusion and dislocation climb. Superposition is used to obtain the mechanical fields in terms of the infinite-medium discrete dislocation fields and an image field that enforces the boundary conditions while the point-defect concentration is obtained by solving the stress-dependent diffusion equations on the same finite-element grid. Core-level boundary conditions for the concentration field are avoided by invoking an approximate, yet robust kinetic law. Aspects of the formulation are general but its implementation in a simple plane strain model enables the modeling of high-temperature phenomena such as creep, recovery and relaxation in crystalline materials. With emphasis laid on lattice vacancies, the creep response of planar single crystals in simple tension emerges as a natural outcome in the simulations. A large number of boundary-value problem solutions are obtained which depict transitions from diffusional to power-law creep, in keeping with long-standing phenomenological theories of creep. In addition, some unique experimental aspects of creep in small scale specimens are also reproduced in the simulations.

  8. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  9. Hapsembler: An Assembler for Highly Polymorphic Genomes

    Science.gov (United States)

    Donmez, Nilgun; Brudno, Michael

    As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.

  10. Diffusion and plasticity at high temperature

    Science.gov (United States)

    Philibert, J.

    1991-06-01

    High temperature plastic deformation requires atomic migration whatever the mechanism of deformation. The constitutive equations contain a diffusion coefficient and the deformation rate follows an Arrhenius law. This paper will only discuss the case of viscous creep in order to elucidate the nature of the diffusion processes and the expression of the diffusion coefficient involved in alloys or compounds. La déformation plastique à haute température met en jeu des migrations atomiques, quel que soit le mécanisme de déformation. Les lois de comportement contiennent donc un coefficient de diffusion et la vitesse de déformation obéit à une loi d'Arrhenius. Dans cet article, qui ne conceme qu'un seul type de déformation, lefluage visqueux, on s'efforce de préciser la nature des processus de diffusion et du coefficient de diffusion mis en jeu dans le cas des alliages et des composés.

  11. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.

    Directory of Open Access Journals (Sweden)

    Yang Li

    2006-12-01

    Full Text Available Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals have been mapped to the causal regulatory regions, termed expression quantitative trait loci. Whether the environment-induced plastic response of gene expression also shows heritable difference has not yet been studied. Here we show that differential expression induced by temperatures of 16 degrees C and 24 degrees C has a strong genetic component in Caenorhabditis elegans recombinant inbred strains derived from a cross between strains CB4856 (Hawaii and N2 (Bristol. No less than 59% of 308 trans-acting genes showed a significant eQTL-by-environment interaction, here termed plasticity quantitative trait loci. In contrast, only 8% of an estimated 188 cis-acting genes showed such interaction. This indicates that heritable differences in plastic responses of gene expression are largely regulated in trans. This regulation is spread over many different regulators. However, for one group of trans-genes we found prominent evidence for a common master regulator: a transband of 66 coregulated genes appeared at 24 degrees C. Our results suggest widespread genetic variation of differential expression responses to environmental impacts and demonstrate the potential of genetical genomics for mapping the molecular determinants of phenotypic plasticity.

  12. Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira

    Science.gov (United States)

    Xu, Yinghua; Zhu, Yongzhang; Wang, Yuezhu; Chang, Yung-Fu; Zhang, Ying; Jiang, Xiugao; Zhuang, Xuran; Zhu, Yongqiang; Zhang, Jinlong; Zeng, Lingbing; Yang, Minjun; Li, Shijun; Wang, Shengyue; Ye, Qiang; Xin, Xiaofang; Zhao, Guoping; Zheng, Huajun; Guo, Xiaokui; Wang, Junzhi

    2016-01-01

    Leptospirosis, caused by pathogenic Leptospira spp., has recently been recognized as an emerging infectious disease worldwide. Despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of Leptospira spp. remains limited. Here we sequenced and analyzed 102 isolates representing global sources. A high genomic variability were observed among different Leptospira species, which was attributed to massive gene gain and loss events allowing for adaptation to specific niche conditions and changing host environments. Horizontal gene transfer and gene duplication allowed the stepwise acquisition of virulence factors in pathogenic Leptospira evolved from a recent common ancestor. More importantly, the abundant expansion of specific virulence-related protein families, such as metalloproteases-associated paralogs, were exclusively identified in pathogenic species, reflecting the importance of these protein families in the pathogenesis of leptospirosis. Our observations also indicated that positive selection played a crucial role on this bacteria adaptation to hosts. These novel findings may lead to greater understanding of the global diversity and virulence evolution of Leptospira spp. PMID:26833181

  13. Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains

    Directory of Open Access Journals (Sweden)

    Runa Kuley

    2017-08-01

    in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.

  14. The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

    Directory of Open Access Journals (Sweden)

    Nicholas R Thomson

    2006-12-01

    Full Text Available The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common

  15. Recovery of Porosity and Permeability for High Plasticity Clays

    DEFF Research Database (Denmark)

    Krogsbøll, Anette; Foged, Niels Nielsen

    to be the case for high plasticity clays that are uncemented, and with a high content of clay minerals, especially smectite. Oedometer tests on samples from the Paleogene period show that 80% or more of the compaction will recover when unloaded, and if unloaded to a stress lower than in situ stress level...

  16. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  17. Plasticity of the Leishmania genome leading to gene copy number variations and drug resistance [version 1; referees: 5 approved

    Directory of Open Access Journals (Sweden)

    Marie-Claude N. Laffitte

    2016-09-01

    Full Text Available Leishmania has a plastic genome, and drug pressure can select for gene copy number variation (CNV. CNVs can apply either to whole chromosomes, leading to aneuploidy, or to specific genomic regions. For the latter, the amplification of chromosomal regions occurs at the level of homologous direct or inverted repeated sequences leading to extrachromosomal circular or linear amplified DNAs. This ability of Leishmania to respond to drug pressure by CNVs has led to the development of genomic screens such as Cos-Seq, which has the potential of expediting the discovery of drug targets for novel promising drug candidates.

  18. High-speed and high-ratio referential genome compression.

    Science.gov (United States)

    Liu, Yuansheng; Peng, Hui; Wong, Limsoon; Li, Jinyan

    2017-11-01

    The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio. We present a high-performance referential genome compression algorithm named HiRGC. It is based on a 2-bit encoding scheme and an advanced greedy-matching search on a hash table. We compare the performance of HiRGC with four state-of-the-art compression methods on a benchmark dataset of eight human genomes. HiRGC takes compress about 21 gigabytes of each set of the seven target genomes into 96-260 megabytes, achieving compression ratios of 217 to 82 times. This performance is at least 1.9 times better than the best competing algorithm on its best case. Our compression speed is also at least 2.9 times faster. HiRGC is stable and robust to deal with different reference genomes. In contrast, the competing methods' performance varies widely on different reference genomes. More experiments on 100 human genomes from the 1000 Genome Project and on genomes of several other species again demonstrate that HiRGC's performance is consistently excellent. The C ++ and Java source codes of our algorithm are freely available for academic and non-commercial use. They can be downloaded from https://github.com/yuansliu/HiRGC. jinyan.li@uts.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    OpenAIRE

    Henrique Machado; Henrique Machado; Lone Gram

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

  20. High pressure studies of fluorenone emission in plastic media

    International Nuclear Information System (INIS)

    Mitchell, D.J.; Schuster, G.B.; Drickamer, H.G.

    1977-01-01

    The energy and the quantum efficiency for fluorenone fluorescence in the crystalline state and in polymeric matrices was measured as a function of external pressure over the range 0--140 kbar. The application of high pressure induces changes in the quantum yield, which ranges from 0.001 at low pressure to a maximum of approx.0.1 at high pressure in hydrocarbon plastics. These results are interpreted as arising from the decrease in the energy of the lowest ππ excited singlet state relative to other relevant states as the external pressure is increased

  1. Analysis of high-identity segmental duplications in the grapevine genome

    Directory of Open Access Journals (Sweden)

    Carelli Francesco N

    2011-08-01

    Full Text Available Abstract Background Segmental duplications (SDs are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera genome (PN40024. Results We demonstrate that recent SDs (> 94% identity and >= 10 kb in size are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence. We detected mitochondrial and plastid DNA and genes (10% of gene annotation in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress. Conclusions These data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.

  2. A Legionella pneumophila effector protein encoded in a region of genomic plasticity binds to Dot/Icm-modified vacuoles.

    Directory of Open Access Journals (Sweden)

    Shira Ninio

    2009-01-01

    Full Text Available Legionella pneumophila is an opportunistic pathogen that can cause a severe pneumonia called Legionnaires' disease. In the environment, L. pneumophila is found in fresh water reservoirs in a large spectrum of environmental conditions, where the bacteria are able to replicate within a variety of protozoan hosts. To survive within eukaryotic cells, L. pneumophila require a type IV secretion system, designated Dot/Icm, that delivers bacterial effector proteins into the host cell cytoplasm. In recent years, a number of Dot/Icm substrate proteins have been identified; however, the function of most of these proteins remains unknown, and it is unclear why the bacterium maintains such a large repertoire of effectors to promote its survival. Here we investigate a region of the L. pneumophila chromosome that displays a high degree of plasticity among four sequenced L. pneumophila strains. Analysis of GC content suggests that several genes encoded in this region were acquired through horizontal gene transfer. Protein translocation studies establish that this region of genomic plasticity encodes for multiple Dot/Icm effectors. Ectopic expression studies in mammalian cells indicate that one of these substrates, a protein called PieA, has unique effector activities. PieA is an effector that can alter lysosome morphology and associates specifically with vacuoles that support L. pneumophila replication. It was determined that the association of PieA with vacuoles containing L. pneumophila requires modifications to the vacuole mediated by other Dot/Icm effectors. Thus, the localization properties of PieA reveal that the Dot/Icm system has the ability to spatially and temporally control the association of an effector with vacuoles containing L. pneumophila through activities mediated by other effector proteins.

  3. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar

    Directory of Open Access Journals (Sweden)

    Fabbrini Francesco

    2012-04-01

    Full Text Available Abstract Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5, the transition from shoot to bud (date1.5, the duration of bud formation (subproc1 and bud maturation (subproc2 eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs. These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set

  4. Modular architecture of the T4 phage superfamily: A conserved core genome and a plastic periphery

    International Nuclear Information System (INIS)

    Comeau, Andre M.; Bertrand, Claire; Letarov, Andrei; Tetart, Francoise; Krisch, H.M.

    2007-01-01

    Among the most numerous objects in the biosphere, phages show enormous diversity in morphology and genetic content. We have sequenced 7 T4-like phages and compared their genome architecture. All seven phages share a core genome with T4 that is interrupted by several hyperplastic regions (HPRs) where most of their divergence occurs. The core primarily includes homologues of essential T4 genes, such as the virion structure and DNA replication genes. In contrast, the HPRs contain mostly novel genes of unknown function and origin. A few of the HPR genes that can be assigned putative functions, such as a series of novel Internal Proteins, are implicated in phage adaptation to the host. Thus, the T4-like genome appears to be partitioned into discrete segments that fulfil different functions and behave differently in evolution. Such partitioning may be critical for these large and complex phages to maintain their flexibility, while simultaneously allowing them to conserve their highly successful virion design and mode of replication

  5. Comparison of Liquid Limit of Highly Plastic Clay by Means of Casagrande and Fall Cone Apparatus

    DEFF Research Database (Denmark)

    Grønbech, Gitte Lyng; Nielsen, Benjaminn Nordahl; Ibsen, Lars Bo

    2011-01-01

    The connection between the Liquid Limit found using the Casagrande and the Fall Cone Apparatus is tested for the Danish Eocene Clay that has Liquid Limits up to 350% and Plasticity Index up to 300%, which is well outside the normal range of Casagrande’s Plasticity Chart. Based on the high plastic...

  6. High-carbon chromium steel resistance to small plastic deformation

    International Nuclear Information System (INIS)

    Gajduchenya, V.F.; Madyanov, S.A.; Apaev, B.A.; Kirillov, Yu.V.; Sokolov, L.D.

    1978-01-01

    The phase composition of a steel with 1.08% C and 2.1% Cr, and the variation in the level of microstresses in the matrix as related to the annealing temperature in the range of 400-600 deg C and in the applied compression stress were investigated. To study the phase composition, and chromium content in the α-solution and the carbide phases, magnetic, chemical, and X-ray spectrum analyses were carried out. The change in the level of microstresses was determined roentgenographically. During the stress relaxation test at temperatures of 20-180 deg C, the mechanism of plastic deformation near the yield point was investigated. It is shown that three dislocation mechanisms operate in high-carbon chromium steel under the conditions at hand: overcoming the Pierls-Nabarro barriers by the dislocations, overcoming the stress fields of coherent carbide particles by dislocations, and circumvention of second-phase particles by dislocations. The dependence of the realization of the different plastic deformation mechanisms on the number of carbide particles and the chromium concentration in the matrix was established. The thermally activated nature of the motion of the dislocations under conditions of stress relaxation at an elevated temperature is noted

  7. Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

    Science.gov (United States)

    Iguchi, Atsushi; Nagaya, Yutaka; Pradel, Elizabeth; Ooka, Tadasuke; Ogura, Yoshitoshi; Katsura, Keisuke; Kurokawa, Ken; Oshima, Kenshiro; Hattori, Masahira; Parkhill, Julian; Sebaihia, Mohamed; Coulthurst, Sarah J; Gotoh, Naomasa; Thomson, Nicholas R; Ewbank, Jonathan J; Hayashi, Tetsuya

    2014-08-01

    Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Plastic reactor suitable for high pressure and supercritical fluid electrochemistry

    DEFF Research Database (Denmark)

    Branch, Jack; Alibouri, Mehrdad; Cook, David A.

    2017-01-01

    The paper describes a reactor suitable for high pressure, particularly supercritical fluid, electrochemistry and electrodeposition at pressures up to 30 MPa at 115◦C. The reactor incorporates two key, new design concepts; a plastic reactor vessel and the use of o-ring sealed brittle electrodes...... by the deposition of Bi. The application of the reactor to the production of nanostructures is demonstrated by the electrodeposition of ∼80 nm diameter Te nanowires into an anodic alumina on silicon template. Key advantages of the new reactor design include reduction of the number of wetted materials, particularly...... glues used for insulating electrodes, compatability with reagents incompatible with steel, compatability with microfabricated planar multiple electrodes, small volume which brings safety advantages and reduced reagent useage, and a significant reduction in experimental time....

  9. Clay membrane made of natural high plasticity clay

    DEFF Research Database (Denmark)

    Foged, Niels; Baumann, Jens

    1998-01-01

    Leachate containment in Denmark has through years been regulated by the DIF Recommendation for Sanitary Landfill Liners (DS/R 466). It states natural clay deposits may be used for membrane material provided the membrane and drainage system may contain at least 95% of all leachate created throughout...... ion transport as well as diffusion.Clay prospection for clays rich in smectite has revealed large deposits of Tertiary clay of very high plasticity in the area around Rødbyhavn on the Danish island Lolland. The natural clay contains 60 to 75% smectite, dominantly as a sodium-type. The clay material...... has been evaluated using standardised methods related to mineralogy, classification, compaction and permeability, and initial studies of diffusion properties have been carried out. Furthermore, at a test site the construction methods for establishing a 0.15 to 0.3m thick clay membrane have been tested...

  10. Clay membrane made of natural high plasticity clay:

    DEFF Research Database (Denmark)

    Foged, Niels; Baumann, Jens

    1999-01-01

    Leachate containment in Denmark has throughout the years been regulated by the DIF Recommendation for Sanitary Landfill Liners (DS/R4669. It states that natural clay deposits may be used as membrane material provided the membrane and drainage system contains at least 95% of all leachate created...... into account advective ion transport as well as diffusion. Clay prospecting for clays rich in smectite has revealed large deposits of Tertiary clay of very high plasticity in the area around Rødbyhavn on the Danish island of Lolland. The natural clay contains 60-75% smectite, dominantly as a sodium......-type. The clay material has been evaluated using the standardized methods related to mineralogy, classification, compaction and permeability, and initial studies of diffusion properties have been carried out. Furthermore, at a test site the construction methods for establishing a 0.15-0.3 m thick clay membrane...

  11. Compression cracking of plastic spheres: a high speed photography study

    International Nuclear Information System (INIS)

    Majzoub, R.; Chaudhri, M.M.

    1999-01-01

    Failure of brittle spheres under compressive loading, both quasi static and dynamic, is a technologically important problem. However, so far, neither the stress state in a loaded nor the failure process in understood clearly. In fact, because the process of the failure of a loaded sphere is very rapid, it has not been possible to follow it when making static observations. We have, therefore, carried out a high-speed photographic study using framing rates of up to 200,000 frames per second to follow the sequence of events when polished 12.7 mm diameter spheres of acrylic resin are fragmented using a low-velocity impact apparatus. The latter consist of a 5.7 kg hammer, which is allowed to drop on to the test sphere from a height of 1.3 m and the entire event of impact and ensuing fracture is photographed with a rotating mirror camera (C-4). Form numerous impact experiments it has been found that as the impact load increases gradually, plastic flow and flattering of the sphere occurs at the contact region. The size of the flattened region continuous to grow with increasing impact load and when this region becomes sufficiently large, usually one or two cracks initiate at the periphery of the contact rather than in the bulk of the sphere. The surface cracks then grow into the bulk of the sphere at velocities in the range of 600-800 m s/sup -1/. It is interesting to note these crack velocities are the maximum observed velocities in this material, but these are only approx. 0.8 of the Rayleigh wave velocity, which is the theoretically predicted maximum crack velocity in brittle materials. It is argued that in order to cause the catastrophic failure of a solid sphere, it is necessary to cause plasticity in it which then leads to the generation of tensile hoop stresses at the circle of contact between the sphere and platen. (author)

  12. Response function measurement of plastic scintillator for high energy neutrons

    International Nuclear Information System (INIS)

    Sanami, Toshiya; Ban, Syuichi; Takahashi, Kazutoshi; Takada, Masashi

    2003-01-01

    The response function and detection efficiency of 2''φ x 2''L plastic (PilotU) and NE213 liquid (2''NE213) scintillators, which were used for the measurement of secondary neutrons from high energy electron induced reactions, were measured at Heavy Ion Medical Accelerator in Chiba (HIMAC). High energy neutrons were produced via 400 MeV/n C beam bombardment on a thick graphite target. The detectors were placed at 15 deg with respect to C beam axis, 5 m away from the target. As standard, a 5''φ x 5''L NE213 liquid scintillator (5''NE213) was also placed at same position. Neutron energy was determined by the time-of-flight method with the beam pickup scintillator in front of the target. In front of the detectors, veto scintillators were placed to remove charged particle events. All detector signals were corrected with list mode event by event. We deduce neutron spectrum for each detectors. The efficiency curves for pilotU and 2''NE213 were determined on the bases of 5 N E213 neutron spectrum and its efficiency calculated by CECIL code. (author)

  13. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  14. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.; Michell, Craig; Apprill, Amy; Voolstra, Christian R.

    2017-01-01

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  15. Magical Engineering Plastic

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Gwang Ung

    1988-01-15

    This book introduces engineering plastic about advantage of engineering plastic, plastic material from processing method, plastic shock, plastic until now, background of making of engineering plastic, wonderful engineering plastic science such as a high molecule and molecule, classification of high molecule, difference between metal and high molecule, heat and high molecule materials, and property of surface, engineering plastic of dream like from linseed oil to aramid, small dictionary of engineering plastic.

  16. Magical Engineering Plastic

    International Nuclear Information System (INIS)

    Kim, Gwang Ung

    1988-01-01

    This book introduces engineering plastic about advantage of engineering plastic, plastic material from processing method, plastic shock, plastic until now, background of making of engineering plastic, wonderful engineering plastic science such as a high molecule and molecule, classification of high molecule, difference between metal and high molecule, heat and high molecule materials, and property of surface, engineering plastic of dream like from linseed oil to aramid, small dictionary of engineering plastic.

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

    DEFF Research Database (Denmark)

    Zhan, Bujie; Fadista, João; Thomsen, Bo

    2011-01-01

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

  18. Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance.

    Science.gov (United States)

    Patel, Seema

    2016-11-01

    Despite the advent of next-generation sequencing (NGS) technologies, sophisticated data analysis and drug development efforts, bacterial drug resistance persists and is escalating in magnitude. To better control the pathogens, a thorough understanding of their genomic architecture and dynamics is vital. Bacterial genome is extremely complex, a mosaic of numerous co-operating and antagonizing components, altruistic and self-interested entities, behavior of which are predictable and conserved to some extent, yet largely dictated by an array of variables. In this regard, mobile genetic elements (MGE), DNA repair systems, post-segregation killing systems, toxin-antitoxin (TA) systems, restriction-modification (RM) systems etc. are dominant agents and horizontal gene transfer (HGT), gene redundancy, epigenetics, phase and antigenic variation etc. processes shape the genome. By illegitimate recombinations, deletions, insertions, duplications, amplifications, inversions, conversions, translocations, modification of intergenic regions and other alterations, bacterial genome is modified to tackle stressors like drugs, and host immune effectors. Over the years, thousands of studies have investigated this aspect and mammoth amount of insights have been accumulated. This review strives to distillate the existing information, formulate hypotheses and to suggest directions, that might contribute towards improved mitigation of the vicious pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. High Plasticity of New Granule Cells in the Aging Hippocampus

    Directory of Open Access Journals (Sweden)

    Mariela F. Trinchero

    2017-10-01

    Full Text Available Summary: During aging, the brain undergoes changes that impair cognitive capacity and circuit plasticity, including a marked decrease in production of adult-born hippocampal neurons. It is unclear whether development and integration of those new neurons are also affected by age. Here, we show that adult-born granule cells (GCs in aging mice are scarce and exhibit slow development, but they display a remarkable potential for structural plasticity. Retrovirally labeled 3-week-old GCs in middle-aged mice were small, underdeveloped, and disconnected. Neuronal development and integration were accelerated by voluntary exercise or environmental enrichment. Similar effects were observed via knockdown of Lrig1, an endogenous negative modulator of neurotrophin receptors. Consistently, blocking neurotrophin signaling by Lrig1 overexpression abolished the positive effects of exercise. These results demonstrate an unparalleled degree of plasticity in the aging brain mediated by neurotrophins, whereby new GCs remain immature until becoming rapidly recruited to the network by activity. : Trinchero et al. show that development of new granule cells born in the adult hippocampus is strongly influenced by age. In the aging hippocampus, new neurons remain immature for prolonged intervals, yet voluntary exercise triggers their rapid growth and functional synaptogenesis. This extensive structural remodeling is mediated by neurotrophins. Keywords: adult neurogenesis, dentate gyrus, functional integration, neurotrophins, synaptogenesis, exercise

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

    Science.gov (United States)

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

    2006-11-01

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

  1. Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2007-09-01

    Full Text Available Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes. Results From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression. Conclusion The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements

  2. Scrutinizing virus genome termini by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Shasha Li

    Full Text Available Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.

  3. Improving the circular economy via hydrothermal processing of high-density waste plastics.

    Science.gov (United States)

    Helmer Pedersen, Thomas; Conti, Federica

    2017-10-01

    Rising environmental concerns on climate changes are causing an increasing attention on circular economies. The plastic economy, in particular, is in focus due to the accelerating consumption of plastics, mainly derived from virgin feedstock, combined with the lack of plastic recycling strategies. This work presents a novel outlook on the potential of using supercritical hydrothermal processing of waste plastic fractions for tertiary recycling. The study investigates hydrothermal processing of nine different, high-density types of plastics into original resin monomers and other value-added chemical compounds. The outlook presents conversion yields, carbon balances, and chemical details on the products obtained. It is found that all the investigated resins are prone to hydrothermal treatment, and that high yields of monomers and high value compounds (up to nearly 100%), suitable for chemicals and fuels applications, can be obtained. For instance, for polycarbonate, styrene-butadiene, poly(lactic acid), poly(ethylene terephthalate), and poly(butylene terephthalate), original monomeric compounds can be reclaimed for manufacturing new resins. The promising results presented demonstrate that hydrothermal processing of high-density plastics is a prospective technology for increasing the circularity of the plastic economy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. The plasticizer butyl benzyl phthalate induces genomic changes in rat mammary gland after neonatal/prepubertal exposure

    Directory of Open Access Journals (Sweden)

    Lamartiniere Coral A

    2007-12-01

    Full Text Available Abstract Background Phthalate esters like n-butyl benzyl phthalate (BBP are widely used plasticizers. BBP has shown endocrine-disrupting properties, thus having a potential effect on hormone-sensitive tissues. The aim of this study is to determine the effect of neonatal/prepubertal exposure (post-natal days 2–20 to BBP on maturation parameters and on the morphology, proliferative index and genomic signature of the rat mammary gland at different ages of development (21, 35, 50 and 100 days. Results Here we show that exposure to BBP increased the uterine weight/body weight ratio at 21 days and decreased the body weight at time of vaginal opening. BBP did not induce significant changes on the morphology of the mammary gland, but increased proliferative index in terminal end buds at 35 days and in lobules 1 at several ages. Moreover, BBP had an effect on the genomic profile of the mammary gland mainly at the end of the exposure (21 days, becoming less prominent thereafter. By this age a significant number of genes related to proliferation and differentiation, communication and signal transduction were up-regulated in the glands of the exposed animals. Conclusion These results suggest that BBP has an effect in the gene expression profile of the mammary gland.

  5. Plastic responses to elevated temperature in low and high elevation populations of three grassland species.

    Science.gov (United States)

    Frei, Esther R; Ghazoul, Jaboury; Pluess, Andrea R

    2014-01-01

    Local persistence of plant species in the face of climate change is largely mediated by genetic adaptation and phenotypic plasticity. In species with a wide altitudinal range, population responses to global warming are likely to differ at contrasting elevations. In controlled climate chambers, we investigated the responses of low and high elevation populations (1200 and 1800 m a.s.l.) of three nutrient-poor grassland species, Trifolium montanum, Ranunculus bulbosus, and Briza media, to ambient and elevated temperature. We measured growth-related, reproductive and phenological traits, evaluated differences in trait plasticity and examined whether trait values or plasticities were positively related to approximate fitness and thus under selection. Elevated temperature induced plastic responses in several growth-related traits of all three species. Although flowering phenology was advanced in T. montanum and R. bulbosus, number of flowers and reproductive allocation were not increased under elevated temperature. Plasticity differed between low and high elevation populations only in leaf traits of T. montanum and B. media. Some growth-related and phenological traits were under selection. Moreover, plasticities were not correlated with approximate fitness indicating selectively neutral plastic responses to elevated temperature. The observed plasticity in growth-related and phenological traits, albeit variable among species, suggests that plasticity is an important mechanism in mediating plant responses to elevated temperature. However, the capacity of species to respond to climate change through phenotypic plasticity is limited suggesting that the species additionally need evolutionary adaptation to adjust to climate change. The observed selection on several growth-related and phenological traits indicates that the study species have the potential for future evolution in the context of a warming climate.

  6. Drying shrinkage problems in high-plastic clay soils in Oklahoma.

    Science.gov (United States)

    2013-08-01

    Longitudinal cracking in pavements due to drying shrinkage of high-plastic subgrade soils has been a major : problem in Oklahoma. Annual maintenance to seal and repair these distress problems costs significant amount of : money to the state. The long...

  7. High Rate Plastic Deformation and Failure of Tungsten-Sintered Metals

    National Research Council Canada - National Science Library

    Bjerke, Todd

    2004-01-01

    The competition between plastic deformation and brittle fracture during high rate loading of a tungsten-sintered metal is examined through impact experiments, post-experiment microscopy, and numerical simulation...

  8. Comparison of elastic-viscous-plastic and viscous-plastic dynamics models using a high resolution Arctic sea ice model

    Energy Technology Data Exchange (ETDEWEB)

    Hunke, E.C. [Los Alamos National Lab., NM (United States); Zhang, Y. [Naval Postgraduate School, Monterey, CA (United States)

    1997-12-31

    A nonlinear viscous-plastic (VP) rheology proposed by Hibler (1979) has been demonstrated to be the most suitable of the rheologies commonly used for modeling sea ice dynamics. However, the presence of a huge range of effective viscosities hinders numerical implementations of this model, particularly on high resolution grids or when the ice model is coupled to an ocean or atmosphere model. Hunke and Dukowicz (1997) have modified the VP model by including elastic waves as a numerical regularization in the case of zero strain rate. This modification (EVP) allows an efficient, fully explicit discretization that adapts well to parallel architectures. The authors present a comparison of EVP and VP dynamics model results from two 5-year simulations of Arctic sea ice, obtained with a high resolution sea ice model. The purpose of the comparison is to determine how differently the two dynamics models behave, and to decide whether the elastic-viscous-plastic model is preferable for high resolution climate simulations, considering its high efficiency in parallel computation. Results from the first year of this experiment (1990) are discussed in detail in Hunke and Zhang (1997).

  9. Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

    Science.gov (United States)

    Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line; Delpeyroux, Francis

    2014-08-05

    between PV and CA17, we have developed a model of recombination, making it possible to rescue defective PV RNA genomes with a short deletion by cotransfecting cells with the defective PV genome and CA17 genomic RNA. Numerous recombinants were found, including homologous PV/CA17 recombinants, but mostly nonhomologous recombinants presenting duplications of parental sequences preferentially located in particular regions. Long duplications were excised by passages in cultured cells or in mice, generating diverse homologous recombinants. Recombination leading to nonhomologous recombinants, which evolve into homologous recombinants, may therefore be seen as a model of genetic plasticity in enteroviruses and, possibly, in other RNA viruses. Copyright © 2014 Holmblat et al.

  10. Decay Time Measurement for Different Energy Depositions of Plastic Scintillator Fabricated by High Temperature Polymerization Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Cheol Ho; Son, Jaebum; Lee, Sangmin; Kim, Tae Hoon; Kim, Yong-Kyun [Hanyang University, Seoul (Korea, Republic of)

    2016-10-15

    Plastic scintillators are based on organic fluorite. They have many advantages such as fast rise and decay time, high optical transmission, ease of manufacturing, low cost, and large available size. For these reasons they are widely used for particle identification. Also, protection of people against a variety of threats (such as nuclear, radiological, and explosive) represents a true challenge along with the continuing development of science and technology. The plastic scintillator is widely used in various devise, which serves for nuclear, photonics, quantum, and high-energy physics. The plastic scintillator is probably the most widely used organic detector, and polystyrene is one of the most widely used materials in the making of the plastic scintillator detector. Thus, a styrene monomer as a solvent was used to fabricate the plastic scintillator by using high temperature polymerization reaction, and then the emission wavelength and the decay times for different energy depositions were measured by using the fabricated plastic scintillator. A plastic scintillator was fabricated to measure decay time for different energy depositions using the high temperature polymerization. Emission wavelength was measured of 426.05 nm to confirm a scintillator property using the spectrophotometer. Four gamma-ray sources (Cs-137, Co-60, Na-22, and Ba-133) were used to evaluate effect for decay time of different energy depositions. The average decay time of the fabricated plastic scintillator was measured to approximately 4.72 ns slightly higher more than commercial plastic scintillator. In future, light output and linearity will be measured to evaluate other property compared with the commercial scintillator.

  11. Decay Time Measurement for Different Energy Depositions of Plastic Scintillator Fabricated by High Temperature Polymerization Reaction

    International Nuclear Information System (INIS)

    Lee, Cheol Ho; Son, Jaebum; Lee, Sangmin; Kim, Tae Hoon; Kim, Yong-Kyun

    2016-01-01

    Plastic scintillators are based on organic fluorite. They have many advantages such as fast rise and decay time, high optical transmission, ease of manufacturing, low cost, and large available size. For these reasons they are widely used for particle identification. Also, protection of people against a variety of threats (such as nuclear, radiological, and explosive) represents a true challenge along with the continuing development of science and technology. The plastic scintillator is widely used in various devise, which serves for nuclear, photonics, quantum, and high-energy physics. The plastic scintillator is probably the most widely used organic detector, and polystyrene is one of the most widely used materials in the making of the plastic scintillator detector. Thus, a styrene monomer as a solvent was used to fabricate the plastic scintillator by using high temperature polymerization reaction, and then the emission wavelength and the decay times for different energy depositions were measured by using the fabricated plastic scintillator. A plastic scintillator was fabricated to measure decay time for different energy depositions using the high temperature polymerization. Emission wavelength was measured of 426.05 nm to confirm a scintillator property using the spectrophotometer. Four gamma-ray sources (Cs-137, Co-60, Na-22, and Ba-133) were used to evaluate effect for decay time of different energy depositions. The average decay time of the fabricated plastic scintillator was measured to approximately 4.72 ns slightly higher more than commercial plastic scintillator. In future, light output and linearity will be measured to evaluate other property compared with the commercial scintillator

  12. High plasticity in epithelial morphogenesis during insect dorsal closure

    Directory of Open Access Journals (Sweden)

    Kristen A. Panfilio

    2013-09-01

    Insect embryos complete the outer form of the body via dorsal closure (DC of the epidermal flanks, replacing the transient extraembryonic (EE tissue. Cell shape changes and morphogenetic behavior are well characterized for DC in Drosophila, but these data represent a single species with a secondarily reduced EE component (the amnioserosa that is not representative across the insects. Here, we examine DC in the red flour beetle, Tribolium castaneum, providing the first detailed, functional analysis of DC in an insect with complete EE tissues (distinct amnion and serosa. Surprisingly, we find that differences between Drosophila and Tribolium DC are not restricted to the EE tissue, but also encompass the dorsal epidermis, which differs in cellular architecture and method of final closure (zippering. We then experimentally manipulated EE tissue complement via RNAi for Tc-zen1, allowing us to eliminate the serosa and still examine viable DC in a system with a single EE tissue (the amnion. We find that the EE domain is particularly plastic in morphogenetic behavior and tissue structure. In contrast, embryonic features and overall kinetics are robust to Tc-zen1RNAi manipulation in Tribolium and conserved with a more distantly related insect, but remain substantially different from Drosophila. Although correct DC is essential, plasticity and regulative, compensatory capacity have permitted DC to evolve within the insects. Thus, DC does not represent a strong developmental constraint on the nature of EE development, a property that may have contributed to the reduction of the EE component in the fly lineage.

  13. Grain dynamics and plastic properties of highly refined materials

    Energy Technology Data Exchange (ETDEWEB)

    Lagos, Miguel; Retamal, Cesar, E-mail: mlagos@utalca.c, E-mail: cretamal@utalca.c [Facultad de IngenierI a, Universidad de Talca, Campus Los Niches, Curico (Chile)

    2010-12-15

    It has been shown that a grain boundary may undergo two competing classes of elastic instability when the in-plane shear stress exceeds the proper critical values. It may buckle acquiring a sinusoidal shape or may develop a periodic series of fissures, separating bands with a sigmoidal profile. The two instabilities lead to grain sliding, but the corresponding expressions relating the relative velocity between adjacent grains with stress do differ. The plastic properties for small strains were calculated for the two force laws, which we called force models A and B. A comparison of the theoretical results with published experimental data shows that model A, while giving predictions within the experimental uncertainties for a series of superplastic aluminium and titanium alloys, fails for Avesta 2304 steel. However, excellent results are obtained when model B is applied for this steel.

  14. Grain dynamics and plastic properties of highly refined materials

    International Nuclear Information System (INIS)

    Lagos, Miguel; Retamal, Cesar

    2010-01-01

    It has been shown that a grain boundary may undergo two competing classes of elastic instability when the in-plane shear stress exceeds the proper critical values. It may buckle acquiring a sinusoidal shape or may develop a periodic series of fissures, separating bands with a sigmoidal profile. The two instabilities lead to grain sliding, but the corresponding expressions relating the relative velocity between adjacent grains with stress do differ. The plastic properties for small strains were calculated for the two force laws, which we called force models A and B. A comparison of the theoretical results with published experimental data shows that model A, while giving predictions within the experimental uncertainties for a series of superplastic aluminium and titanium alloys, fails for Avesta 2304 steel. However, excellent results are obtained when model B is applied for this steel.

  15. Grain dynamics and plastic properties of highly refined materials

    Science.gov (United States)

    Lagos, Miguel; Retamal, César

    2010-12-01

    It has been shown that a grain boundary may undergo two competing classes of elastic instability when the in-plane shear stress exceeds the proper critical values. It may buckle acquiring a sinusoidal shape or may develop a periodic series of fissures, separating bands with a sigmoidal profile. The two instabilities lead to grain sliding, but the corresponding expressions relating the relative velocity between adjacent grains with stress do differ. The plastic properties for small strains were calculated for the two force laws, which we called force models A and B. A comparison of the theoretical results with published experimental data shows that model A, while giving predictions within the experimental uncertainties for a series of superplastic aluminium and titanium alloys, fails for Avesta 2304 steel. However, excellent results are obtained when model B is applied for this steel.

  16. The genomic-level heritabilities of preparedness and plasticity in human life history: the strategic differentiation and integration of genetic transmissibilities

    Directory of Open Access Journals (Sweden)

    Michael Anthony Woodley of Menie

    2015-04-01

    Full Text Available The Continuous Parameter Estimation Model is applied to develop individual genomic-level heritabilities for the latent hierarchical structure and developmental dynamics of Life History (LH strategy LH strategies relate to the allocations of bioenergetic resources into different domains of fitness. LH has moderate to high population-level heritability in humans, both at the level of the high-order Super-K Factor and the lower-order factors, the K-Factor, Covitality Factor, and General Factor of Personality (GFP. Several important questions remain unexplored. We developed measures of genome-level heritabilities employing an American sample of 316 monozygotic (MZ and 274 dizygotic (DZ twin dyads and a Swedish sample of 863 MZ and 475 DZ twin dyads. This novel heritability index measures individual genetic transmissibility, therefore opening new avenues for analyzing complex interactions among heritable traits inaccessible to standard structural equations methods. For these samples: (1 moderate to high heritability of factor loadings of Super-K on its lower-order factors is demonstrated, evidencing biological preparedness, genetic accommodation, and the gene-culture coevolution of biased epigenetic rules of development; (2 moderate to high heritability of the magnitudes of the effect of the higher-order factors upon their loadings on their constituent factors, evidencing genetic constraints upon phenotypic plasticity; and (3 that heritability of the LH factors, of factor loadings, and of the magnitudes of the correlations among factors are weaker among those with slower LH speeds, demonstrating that inter-individual variation in transmissibility is a function of individual socioecological selection pressures.

  17. The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes.

    Science.gov (United States)

    Massart, R; Freyburger, M; Suderman, M; Paquet, J; El Helou, J; Belanger-Nelson, E; Rachalski, A; Koumar, O C; Carrier, J; Szyf, M; Mongrain, V

    2014-01-21

    Sleep is critical for normal brain function and mental health. However, the molecular mechanisms mediating the impact of sleep loss on both cognition and the sleep electroencephalogram remain mostly unknown. Acute sleep loss impacts brain gene expression broadly. These data contributed to current hypotheses regarding the role for sleep in metabolism, synaptic plasticity and neuroprotection. These changes in gene expression likely underlie increased sleep intensity following sleep deprivation (SD). Here we tested the hypothesis that epigenetic mechanisms coordinate the gene expression response driven by SD. We found that SD altered the cortical genome-wide distribution of two major epigenetic marks: DNA methylation and hydroxymethylation. DNA methylation differences were enriched in gene pathways involved in neuritogenesis and synaptic plasticity, whereas large changes (>4000 sites) in hydroxymethylation where observed in genes linked to cytoskeleton, signaling and neurotransmission, which closely matches SD-dependent changes in the transcriptome. Moreover, this epigenetic remodeling applied to elements previously linked to sleep need (for example, Arc and Egr1) and synaptic partners of Neuroligin-1 (Nlgn1; for example, Dlg4, Nrxn1 and Nlgn3), which we recently identified as a regulator of sleep intensity following SD. We show here that Nlgn1 mutant mice display an enhanced slow-wave slope during non-rapid eye movement sleep following SD but this mutation does not affect SD-dependent changes in gene expression, suggesting that the Nlgn pathway acts downstream to mechanisms triggering gene expression changes in SD. These data reveal that acute SD reprograms the epigenetic landscape, providing a unique molecular route by which sleep can impact brain function and health.

  18. The yak genome and adaptation to life at high altitude

    DEFF Research Database (Denmark)

    Qiu, Qiang; Zhang, Guojie; Ma, Tao

    2012-01-01

    . Here, we present the draft genome sequence of a female domestic yak generated using Illumina-based technology at 65-fold coverage. Genomic comparisons between yak and cattle identify an expansion in yak of gene families related to sensory perception and energy metabolism, as well as an enrichment...... important implications for understanding adaptation to high altitude in other animal species and for hypoxia-related diseases in humans....

  19. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  20. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

    Science.gov (United States)

    Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P

    2013-03-01

    Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.

  1. Dislocation-drag contribution to high-rate plastic deformation in shock-loaded tantalum

    International Nuclear Information System (INIS)

    Tonks, D.L.; Hixson, R.S.; Johnson, J.N.; Gray, G.T. III

    1994-01-01

    Time-resolved plastic waves in plate-impact experiments give information on the relationship between applied shear stress and plastic strain rate at low plastic strain. This information is essentially different from that obtained at intermediate strain rates using Hopkins on bar techniques, because in the former case the material deformation state is driven briefly into the regime dominated by dislocation drag rather than thermal activation. Two VISAR records of the particle velocity at the tantalum/sapphire (window) interface are obtained for symmetric impact producing peak in situ longitudinal stresses of approximately 75 kbar and 111 kbar. The risetimes of the plastic waves are about 100 ns and 60 ns, respectively, with peak strain rates of about 2x10 5 /s and 1x10 6 /s, respectively, as determined by weak-shock analysis [Wallace, Phys. Rev. B 22, 1487 (1980), and Tonks, Los Alamos DataShoP Report LA-12068-MS (1991)]. These data show a much stronger dependence of plastic strain rate on applied shear stress than previously predicted by linear viscous drag models in combination with thermal activation through a large Peierls barrier. The data also show complex evolution of the mobile dislocation density during early stages of high-rate plastic flow. This measurement and analysis aid significantly in establishing the fundamental picture of dynamic deformation of BCC metals and the evolution of the internal material state at early times following shock compression. copyright 1994 American Institute of Physics

  2. The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains

    DEFF Research Database (Denmark)

    Soares, Siomar C; Silva, Artur; Trost, Eva

    2013-01-01

    , Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic...

  3. A tailing genome walking method suitable for genomes with high local GC content.

    Science.gov (United States)

    Liu, Taian; Fang, Yongxiang; Yao, Wenjuan; Guan, Qisai; Bai, Gang; Jing, Zhizhong

    2013-10-15

    The tailing genome walking strategies are simple and efficient. However, they sometimes can be restricted due to the low stringency of homo-oligomeric primers. Here we modified their conventional tailing step by adding polythymidine and polyguanine to the target single-stranded DNA (ssDNA). The tailed ssDNA was then amplified exponentially with a specific primer in the known region and a primer comprising 5' polycytosine and 3' polyadenosine. The successful application of this novel method for identifying integration sites mediated by φC31 integrase in goat genome indicates that the method is more suitable for genomes with high complexity and local GC content. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.

    Science.gov (United States)

    Shen, Kai; Sayeed, Sameera; Antalis, Patricia; Gladitz, John; Ahmed, Azad; Dice, Bethany; Janto, Benjamin; Dopico, Richard; Keefe, Randy; Hayes, Jay; Johnson, Sandra; Yu, Sujun; Ehrlich, Nathan; Jocz, Jennifer; Kropp, Laura; Wong, Ray; Wadowsky, Robert M; Slifkin, Malcolm; Preston, Robert A; Erdos, Geza; Post, J Christopher; Ehrlich, Garth D; Hu, Fen Z

    2006-09-01

    The distributed genome hypothesis (DGH) states that each strain within a bacterial species receives a unique distribution of genes from a population-based supragenome that is many times larger than the genome of any given strain. The observations that natural infecting populations are often polyclonal and that most chronic bacterial pathogens have highly developed mechanisms for horizontal gene transfer suggested the DGH and provided the means and the mechanisms to explain how chronic infections persist in the face of a mammalian host's adaptive defense mechanisms. Having previously established the validity of the DGH for obligate pathogens, we wished to evaluate its applicability to an opportunistic bacterial pathogen. This was accomplished by construction and analysis of a highly redundant pooled genomic library containing approximately 216,000 functional clones that was constructed from 12 low-passage clinical isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other body sites. Sequence analysis of 3,214 randomly picked clones (mean insert size, approximately 1.4 kb) from this library demonstrated that 348 (10.8%) of the clones were unique with respect to all genomic sequences of the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the open reading frames within these unique sequences demonstrated protein homologies to a number of bacterial virulence factors and other proteins not previously identified in P. aeruginosa. PCR and reverse transcription-PCR-based assays were performed to analyze the distribution and expression patterns of a 70-open reading frame subset of these sequences among 11 of the clinical strains. These sequences were unevenly distributed among the clinical isolates, with nearly half (34/70) of the novel sequences being present in only one or two of the individual strains. Expression profiling revealed that a vast majority of these sequences are expressed, strongly suggesting they encode functional proteins.

  5. A Primer on High-Throughput Computing for Genomic Selection

    Directory of Open Access Journals (Sweden)

    Xiao-Lin eWu

    2011-02-01

    Full Text Available High-throughput computing (HTC uses computer clusters to solve advanced computational problems, with the goal of accomplishing high throughput over relatively long periods of time. In genomic selection, for example, a set of markers covering the entire genome is used to train a model based on known data, and the resulting model is used to predict the genetic merit of selection candidates. Sophisticated models are very computationally demanding and, with several traits to be evaluated sequentially, computing time is long and output is low. In this paper, we present scenarios and basic principles of how HTC can be used in genomic selection, implemented using various techniques from simple batch processing to pipelining in distributed computer clusters. Various scripting languages, such as shell scripting, Perl and R, are also very useful to devise pipelines. By pipelining, we can reduce total computing time and consequently increase throughput. In comparison to the traditional data processing pipeline residing on the central processors, performing general purpose computation on a graphics processing unit (GPU provide a new-generation approach to massive parallel computing in genomic selection. While the concept of HTC may still be new to many researchers in animal breeding, plant breeding, and genetics, HTC infrastructures have already been built in many institutions, such as the University of Wisconsin – Madison, which can be leveraged for genomic selection, in terms of central processing unit (CPU capacity, network connectivity, storage availability, and middleware connectivity. Exploring existing HTC infrastructures as well as general purpose computing environments will further expand our capability to meet increasing computing demands posed by unprecedented genomic data that we have today. We anticipate that HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of

  6. Quantitative high-resolution genomic analysis of single cancer cells.

    Science.gov (United States)

    Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

    2011-01-01

    During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

  7. Quantitative high-resolution genomic analysis of single cancer cells.

    Directory of Open Access Journals (Sweden)

    Juliane Hannemann

    Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

  8. Thermally induced processes in mixtures of aluminum with organic acids after plastic deformations under high pressure

    Science.gov (United States)

    Zhorin, V. A.; Kiselev, M. R.; Roldugin, V. I.

    2017-11-01

    DSC is used to measure the thermal effects of processes in mixtures of solid organic dibasic acids with powdered aluminum, subjected to plastic deformation under pressures in the range of 0.5-4.0 GPa using an anvil-type high-pressure setup. Analysis of thermograms obtained for the samples after plastic deformation suggests a correlation between the exothermal peaks observed around the temperatures of degradation of the acids and the thermally induced chemical reactions between products of acid degradation and freshly formed surfaces of aluminum particles. The release of heat in the mixtures begins at 30-40°C. The thermal effects in the mixtures of different acids change according to the order of acid reactivity in solutions. The extreme baric dependences of enthalpies of thermal effects are associated with the rearrangement of the electron subsystem of aluminum upon plastic deformation at high pressures.

  9. Fracture toughness evaluation of elastic-plastic J-integral for high temperature components of gas turbine in power plants

    International Nuclear Information System (INIS)

    Chung, Nam Yong; Kim, Moon Young; Kim, Jong Woo

    1999-01-01

    In the study, the analysis of elastic-plastic J-integral was performed in high temperature components for gas turbine based on elastic-plastic fracture mechanics. It had been operated on the range of about 700 deg C and degraded by high temperature. It was tested for material properties of used component because of material properties changing at high temperature condition. The elastic-plastic fracture mechanics parameter, J is obtained with finite element method. A method is suggested which determines J Ic applying analysis of elastic-plastic finite element method and results of experimental load-displacements with CT specimen. It is also investigated that J-integral is applied for the elastic-plastic analysis in high temperature components. The elastic-plastic fracture toughness. J Ic determined by finite element was obtained with high accuracy using the experimental method.=20

  10. High-performance flexible microwave passives on plastic

    Science.gov (United States)

    Ma, Zhenqiang; Seo, Jung-Hun; Cho, Sang June; Zhou, Weidong

    2014-06-01

    We report the demonstration of bendable inductors, capacitors and switches fabricated on a polyethylene terephthalate (PET) substrate that can operate at high microwave frequencies. By employing bendable dielectric and single crystalline semiconductor materials, spiral inductors and metal-insulator-metal (MIM) capacitors with high quality factors and high resonance frequencies and single-pole, single-throw (SPST) switches were archived. The effects of mechanical bending on the performance of inductors, capacitors and switches were also measured and analyzed. We further investigated the highest possible resonance frequencies and quality factors of inductors and capacitors and, high frequency responses and insertion loss. These demonstrations will lead to flexible radio-frequency and microwave systems in the future.

  11. High throughput platforms for structural genomics of integral membrane proteins.

    Science.gov (United States)

    Mancia, Filippo; Love, James

    2011-08-01

    Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts. Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy. Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Temperature-dependent plastic hysteresis in highly confined polycrystalline Nb films

    Science.gov (United States)

    Waheed, S.; Hao, R.; Zheng, Z.; Wheeler, J. M.; Michler, J.; Balint, D. S.; Giuliani, F.

    2018-02-01

    In this study, the effect of temperature on the cyclic deformation behaviour of a confined polycrystalline Nb film is investigated. Micropillars encapsulating a thin niobium interlayer are deformed under cyclic axial compression at different test temperatures. A distinct plastic hysteresis is observed for samples tested at elevated temperatures, whereas negligible plastic hysteresis is observed for samples tested at room temperature. These results are interpreted using planar discrete dislocation plasticity incorporating slip transmission across grain boundaries. The effect of temperature-dependent grain boundary energy and dislocation mobility on dislocation penetration and, consequently, the size of plastic hysteresis is simulated to correlate with the experimental results. It is found that the decrease in grain boundary energy barrier caused by the increase in temperature does not lead to any appreciable change in the cyclic response. However, dislocation mobility significantly affects the size of plastic hysteresis, with high mobilities leading to a larger hysteresis. Therefore, it is postulated that the experimental observations are predominantly caused by an increase in dislocation mobility as the temperature is increased above the critical temperature of body-centred cubic niobium.

  13. High-performance biodegradable polylactide composites fabricated using a novel plasticizer and functionalized eggshell powder.

    Science.gov (United States)

    Kong, Junjun; Li, Yi; Bai, Yungang; Li, Zonglin; Cao, Zengwen; Yu, Yancun; Han, Changyu; Dong, Lisong

    2018-06-01

    A novel polyester poly(diethylene glycol succinate) (PDEGS) was synthesized and evaluated as a plasticizer for polylactide (PLA) in this study. Meanwhile, an effective sustainable filler, functionalized eggshell powder (FES) with a surface layer of calcium phenyphosphonate was also prepared. Then, PLA biocomposites were prepared from FES and PDEGS using a facile melt blending process. The addition of 15 wt% PDEGS as plasticizer showed good miscibility with PLA macromolecules and increased the chain mobility of PLA. The crystallization kinetics of PLA composites revealed that the highly effective nucleating FES significantly improved the crystallization ability of PLA at both of non-isothermal and isothermal conditions. In addition, the effective plasticizer and well-dispersed FES increased the elongation at break from 6% of pure PLA to over 200% for all of the plasticized PLA composites. These biodegradable PLA biocomposites, coupled with excellent crystallization ability and tunable mechanical properties, demonstrate their potential as alternatives to traditional commodity plastics. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Plastic straw: future of high-speed signaling

    Science.gov (United States)

    Song, Ha Il; Jin, Huxian; Bae, Hyeon-Min

    2015-11-01

    The ever-increasing demand for bandwidth triggered by mobile and video Internet traffic requires advanced interconnect solutions satisfying functional and economic constraints. A new interconnect called E-TUBE is proposed as a cost-and-power-effective all-electrical-domain wideband waveguide solution for high-speed high-volume short-reach communication links. The E-TUBE achieves an unprecedented level of performance in terms of bandwidth-per-carrier frequency, power, and density without requiring a precision manufacturing process unlike conventional optical/waveguide solutions. The E-TUBE exhibits a frequency-independent loss-profile of 4 dB/m and has nearly 20-GHz bandwidth over the V band. A single-sideband signal transmission enabled by the inherent frequency response of the E-TUBE renders two-times data throughput without any physical overhead compared to conventional radio frequency communication technologies. This new interconnect scheme would be attractive to parties interested in high throughput links, including but not limited to, 100/400 Gbps chip-to-chip communications.

  15. Conversion of Mixed Plastic Wastes (High Density Polyethylene and Polypropylene) into Liquid Fuel

    International Nuclear Information System (INIS)

    Chaw Su Su Hmwe; Tint Tint Kywe; Moe Moe Kyaw

    2010-12-01

    In this study, mixed plastic wastes were converted into liquid fuels. Mixed plastic wastes used were high density polyethylene (HDPE) and polypropylene (PP). The pyrolysis of mixed plastic waste to liquid fuel was carried out with and without prepared zeolite catalyst.The catalyst was characterized by X-ray Diffraction (XRD). This catalyst was pre-treated for activation. The experiments were carried out at temperature range of 350-410C.Physical properties (density, kinematic, viscosity,refractive index)of prepared liquid fuel samples were measured. From this study, yields of liquid fuel and gas fuel were found to be 41-64% and 15-35% respectively. As for by products, char was obtained as the yield percentages from 9 to 14% and wax (yield% - 1 to 14) was formed during pyrolysis.

  16. Creep behavior of soil nail walls in high plasticity index (PI) soils : technical report.

    Science.gov (United States)

    2017-04-01

    An aspect of particular concern in the Geotechnical Engineering Circular No. 7: Soil Nail Walls (i.e., the soil : nail wall manual and construction guidelines) is the creep behavior of soil nail systems in high-plasticity : clays. This research proje...

  17. A primer on high-throughput computing for genomic selection.

    Science.gov (United States)

    Wu, Xiao-Lin; Beissinger, Timothy M; Bauck, Stewart; Woodward, Brent; Rosa, Guilherme J M; Weigel, Kent A; Gatti, Natalia de Leon; Gianola, Daniel

    2011-01-01

    High-throughput computing (HTC) uses computer clusters to solve advanced computational problems, with the goal of accomplishing high-throughput over relatively long periods of time. In genomic selection, for example, a set of markers covering the entire genome is used to train a model based on known data, and the resulting model is used to predict the genetic merit of selection candidates. Sophisticated models are very computationally demanding and, with several traits to be evaluated sequentially, computing time is long, and output is low. In this paper, we present scenarios and basic principles of how HTC can be used in genomic selection, implemented using various techniques from simple batch processing to pipelining in distributed computer clusters. Various scripting languages, such as shell scripting, Perl, and R, are also very useful to devise pipelines. By pipelining, we can reduce total computing time and consequently increase throughput. In comparison to the traditional data processing pipeline residing on the central processors, performing general-purpose computation on a graphics processing unit provide a new-generation approach to massive parallel computing in genomic selection. While the concept of HTC may still be new to many researchers in animal breeding, plant breeding, and genetics, HTC infrastructures have already been built in many institutions, such as the University of Wisconsin-Madison, which can be leveraged for genomic selection, in terms of central processing unit capacity, network connectivity, storage availability, and middleware connectivity. Exploring existing HTC infrastructures as well as general-purpose computing environments will further expand our capability to meet increasing computing demands posed by unprecedented genomic data that we have today. We anticipate that HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of marker panels to realized

  18. Comparison of plastic, high density carbon, and beryllium as indirect drive NIF ablators

    Science.gov (United States)

    Kritcher, A. L.; Clark, D.; Haan, S.; Yi, S. A.; Zylstra, A. B.; Callahan, D. A.; Hinkel, D. E.; Berzak Hopkins, L. F.; Hurricane, O. A.; Landen, O. L.; MacLaren, S. A.; Meezan, N. B.; Patel, P. K.; Ralph, J.; Thomas, C. A.; Town, R.; Edwards, M. J.

    2018-05-01

    Detailed radiation hydrodynamic simulations calibrated to experimental data have been used to compare the relative strengths and weaknesses of three candidate indirect drive ablator materials now tested at the NIF: plastic, high density carbon or diamond, and beryllium. We apply a common simulation methodology to several currently fielded ablator platforms to benchmark the model and extrapolate designs to the full NIF envelope to compare on a more equal footing. This paper focuses on modeling of the hohlraum energetics which accurately reproduced measured changes in symmetry when changes to the hohlraum environment were made within a given platform. Calculations suggest that all three ablator materials can achieve a symmetric implosion at a capsule outer radius of ˜1100 μm, a laser energy of 1.8 MJ, and a DT ice mass of 185 μg. However, there is more uncertainty in the symmetry predictions for the plastic and beryllium designs. Scaled diamond designs had the most calculated margin for achieving symmetry and the highest fuel absorbed energy at the same scale compared to plastic or beryllium. A comparison of the relative hydrodynamic stability was made using ultra-high resolution capsule simulations and the two dimensional radiation fluxes described in this work [Clark et al., Phys. Plasmas 25, 032703 (2018)]. These simulations, which include low and high mode perturbations, suggest that diamond is currently the most promising for achieving higher yields in the near future followed by plastic, and more data are required to understand beryllium.

  19. Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231.

    Science.gov (United States)

    Baptista, Rodrigo P; Reis-Cunha, Joao Luis; DeBarry, Jeremy D; Chiari, Egler; Kissinger, Jessica C; Bartholomeu, Daniella C; Macedo, Andrea M

    2018-02-14

    Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.

  20. Potential media influence on the high incidence of medical disputes from the perspective of plastic surgeons.

    Science.gov (United States)

    Chen, Chiehfeng; Lin, Ching-Feng; Chen, Cha-Chun; Chiu, Shih-Feng; Shih, Fuh-Yuan; Lyu, Shu-Yu; Lee, Ming-Been

    2017-08-01

    The main purpose of this study is to investigate the prevalence of medical disputes among plastic surgeons in Taiwan and to elucidate their perspectives regarding the influence of medical litigation media coverage on the physician-patient relationship. A self-administered questionnaire was distributed among plastic surgeons attending a series of continuing education training lectures organized by the Taiwan Society of Plastic Surgery in 2015. Of the 109 respondents, over a third (36.4%) had previously experienced a medical dispute. The vast majority of both physicians who had medical disputes (77.1%) and those who did not (72.1%) felt that the media tends to be supportive of patients in their reporting, and 37.1% of all plastic surgeons felt that the media always portrays the patient as a victim. Respondents who experienced medical disputes in this study felt that the top five leading causes of the high incidence of medical disputes were patient disappointment with procedure results (81.1%), insufficient patient psychological preparation or emotional instability (61.7%), inadequate risk communication on the part of the physician (64.9%), patient uneasiness with the procedure or perception of carelessness (60.6%), and insufficient physician training or incorrect medical evaluation (57.4%). Over a third of the respondents had previously experienced a medical dispute. This study highlights the perception among plastic surgeons that the media reporting of medical disputes and medical litigation is biased in favor of the patients, with 37.1% of the plastic surgeons surveyed opining that patients are always cast as victims. Copyright © 2017. Published by Elsevier B.V.

  1. Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates.

    Science.gov (United States)

    Storz, Jay F; Scott, Graham R; Cheviron, Zachary A

    2010-12-15

    High-altitude environments provide ideal testing grounds for investigations of mechanism and process in physiological adaptation. In vertebrates, much of our understanding of the acclimatization response to high-altitude hypoxia derives from studies of animal species that are native to lowland environments. Such studies can indicate whether phenotypic plasticity will generally facilitate or impede adaptation to high altitude. Here, we review general mechanisms of physiological acclimatization and genetic adaptation to high-altitude hypoxia in birds and mammals. We evaluate whether the acclimatization response to environmental hypoxia can be regarded generally as a mechanism of adaptive phenotypic plasticity, or whether it might sometimes represent a misdirected response that acts as a hindrance to genetic adaptation. In cases in which the acclimatization response to hypoxia is maladaptive, selection will favor an attenuation of the induced phenotypic change. This can result in a form of cryptic adaptive evolution in which phenotypic similarity between high- and low-altitude populations is attributable to directional selection on genetically based trait variation that offsets environmentally induced changes. The blunted erythropoietic and pulmonary vasoconstriction responses to hypoxia in Tibetan humans and numerous high-altitude birds and mammals provide possible examples of this phenomenon. When lowland animals colonize high-altitude environments, adaptive phenotypic plasticity can mitigate the costs of selection, thereby enhancing prospects for population establishment and persistence. By contrast, maladaptive plasticity has the opposite effect. Thus, insights into the acclimatization response of lowland animals to high-altitude hypoxia can provide a basis for predicting how altitudinal range limits might shift in response to climate change.

  2. Plastic Technology (Production). Industrial Arts, Senior High--Level II. North Dakota Senior High Industrial Arts Curriculum Guides.

    Science.gov (United States)

    Claus, Robert; And Others

    This course guide for a plastic technology course is one of four developed for the production area in the North Dakota senior high industrial arts education program. (Eight other guides are available for two other areas of Industrial Arts--energy/power and graphic communications.) Part 1 provides such introductory information as a definition and…

  3. High density polyethylene (HDPE-2) and polystyrene (PS-6) waste plastic mixture turns into valuable fuel energy

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, Moinuddin; Rashid, Mohammad Mamunor; Rahman, Md. Sadikur; Molla, Mohammed [Department of Research and Development, Natural State Research Inc, Stamford, (United States)

    2011-07-01

    Disposal of waste plastic is a serious concern in USA. Waste plastic generated from different cities and towns is a part of municipal solid waste. It is a matter of concern that disposal of waste plastic is causing many problems such as leaching impact on land and ground water, choking of drains, making land infertile, indiscriminate burning causes environmental hazards etc. Waste plastics being nonbiodegradable it can remain as a long period of landfill. Over 48 million tons of synthetic polymer material is produced in the United States every year. Plastic are made from limited resources such as petroleum. When waste plastic come in contact with light and starts photo degrading, it starts releasing harmful such as carbon, chlorine and sulfur causing the soil around them to decay, contributing many complications for cultivation. Waste plastics also end up in the ocean, where it becomes small particles due to the reaction caused by the sun ray and salt from the ocean. Million of ocean habitants die from consuming these small plastic particles when they mistake them for food. To solve this problem countries are resorting to dumping the waste plastics, which requires a lot of effort and money yet they are only able to recycle a fraction of waste plastics. This developed a new technology which will remove these waste plastics form landfill and ocean and convert them into useful liquid fuels. The fuels show high potential for commercialization due to the fact, its influence to the environment. Keywords: waste plastics, fuel, energy, polystyrene, high density polyethylene, thermal, environmental.

  4. High order curvilinear finite elements for elastic–plastic Lagrangian dynamics

    International Nuclear Information System (INIS)

    Dobrev, Veselin A.; Kolev, Tzanio V.; Rieben, Robert N.

    2014-01-01

    This paper presents a high-order finite element method for calculating elastic–plastic flow on moving curvilinear meshes and is an extension of our general high-order curvilinear finite element approach for solving the Euler equations of gas dynamics in a Lagrangian frame [1,2]. In order to handle transition to plastic flow, we formulate the stress–strain relation in rate (or incremental) form and augment our semi-discrete equations for Lagrangian hydrodynamics with an additional evolution equation for the deviatoric stress which is valid for arbitrary order spatial discretizations of the kinematic and thermodynamic variables. The semi-discrete equation for the deviatoric stress rate is developed for 2D planar, 2D axisymmetric and full 3D geometries. For each case, the strain rate is approximated via a collocation method at zone quadrature points while the deviatoric stress is approximated using an L 2 projection onto the thermodynamic basis. We apply high order, energy conserving, explicit time stepping methods to the semi-discrete equations to develop the fully discrete method. We conclude with numerical results from an extensive series of verification tests that demonstrate several practical advantages of using high-order finite elements for elastic–plastic flow

  5. An instrument for the high-statistics measurement of plastic scintillating fibers

    International Nuclear Information System (INIS)

    Buontempo, S.; Ereditato, A.; Marchetti-Stasi, F.; Riccardi, F.; Strolin, P.

    1994-01-01

    There is today widespread use of plastic scintillating fibers in particle physics, mainly for calorimetric and tracking applications. In the case of calorimeters, we have to cope with very massive detectors and a large quantity of scintillating fibers. The CHORUS Collaboration has built a new detector to search for ν μ -ν τ oscillations in the CERN neutrino beam. A crucial task of the detector is ruled by the high-energy resolution calorimeter. For its construction more than 400 000 scintillating plastic fibers have been used. In this paper we report on the design and performance of a new instrument for the high-statistics measurement of the fiber properties, in terms of light yield and light attenuation length. The instrument has been successfully used to test about 3% of the total number of fibers before the construction of the calorimeter. ((orig.))

  6. Experimental and numerical study of plastic shear instability under high-speed loading conditions

    International Nuclear Information System (INIS)

    Sokovikov, Mikhail; Chudinov, Vasiliy; Bilalov, Dmitry; Oborin, Vladimir; Uvarov, Sergey; Plekhov, Oleg; Terekhina, Alena; Naimark, Oleg

    2014-01-01

    The behavior of specimens dynamically loaded during the split Hopkinson (Kolsky) bar tests in a regime close to simple shear conditions was studied. The lateral surface of the specimens was investigated in a real-time mode with the aid of a high-speed infra-red camera CEDIP Silver 450M. The temperature field distribution obtained at different time made it possible to trace the evolution of plastic strain localization. The process of target perforation involving plug formation and ejection was examined using a high-speed infra-red camera and a VISAR velocity measurement system. The microstructure of tested specimens was analyzed using an optical interferometer-profilometer and a scanning electron microscope. The development of plastic shear instability regions has been simulated numerically

  7. High-voltage test and training of plastic streamer tubes for the DELPHI hadron calorimeter

    International Nuclear Information System (INIS)

    Alekseev, G.D.; Cellar, S.; Khomenko, B.A.; Korytov, A.V.; Kulinich, P.A.; Micelmacher, G.V.; Sedykh, Yu.V.; Toledo, R.

    1987-01-01

    The results of high-voltage test and training of plastic streamer tubes of the DELPHI hadron calorimeter are presented. The testing technique is considered in detail. The equipment for high-voltage training consists of a mini-computer, CAMAC-electronics, a controllable high-voltage supply and a digital ampermeter. The experimental results shows that high-voltage training of streamer tubes improves their characteristics. The value of dark current decreased up to 1 μA. The operational voltage range increased by a value more than 300 V

  8. Low-cost and high-capacity short-range optical interconnects using graded-index plastic optical fiber

    NARCIS (Netherlands)

    Tangdiongga, E.; Yang, H.; Lee, S.C.J.; Okonkwo, C.M.; Boom, van den H.P.A.; Randel, S.; Koonen, A.M.J.

    2010-01-01

    We demonstrate a transmission rate of 51.8 Gb/s over 100-meters of perfluorinated multimode graded-index plastic optical fiber using discrete multitone modulation. The results prove suitability of plastic fibers for low-cost high-capacity optical interconnects.

  9. Validation of a Crystal Plasticity Model Using High Energy Diffraction Microscopy

    Science.gov (United States)

    Beaudoin, A. J.; Obstalecki, M.; Storer, R.; Tayon, W.; Mach, J.; Kenesei, P.; Lienert, U.

    2012-01-01

    High energy diffraction microscopy is used to measure the crystallographic orientation and evolution of lattice strain in an Al Li alloy. The relative spatial arrangement of the several pancake-shaped grains in a tensile sample is determined through in situ and ex situ techniques. A model for crystal plasticity with continuity of lattice spin is posed, where grains are represented by layers in a finite element mesh following the arrangement indicated by experiment. Comparison is drawn between experiment and simulation.

  10. Experimental Study on the Utilization of Fine Steel Slag on Stabilizing High Plastic Subgrade Soil

    OpenAIRE

    Hussien Aldeeky; Omar Al Hattamleh

    2017-01-01

    The three major steel manufacturing factories in Jordan dump their byproduct, steel slag, randomly in open areas, which causes many environmental hazardous problems. This study intended to explore the effectiveness of using fine steel slag aggregate (FSSA) in improving the geotechnical properties of high plastic subgrade soil. First soil and fine steel slag mechanical and engineering properties were evaluating. Then 0%, 5%, 10%, 15%, 20%, and 25% dry weight of soil of fine steel slag (FSSA) w...

  11. A high granularity plastic scintillator tile hadronic calorimeter with APD readout for a linear collider detector

    Czech Academy of Sciences Publication Activity Database

    Andreev, V.; Cvach, Jaroslav; Danilov, M.; Devitsin, E.; Dodonov, V.; Eigen, G.; Garutti, E.; Gilitzky, Yu.; Groll, M.; Heuer, R.D.; Janata, Milan; Kacl, Ivan; Korbel, V.; Kozlov, V. Yu; Meyer, H.; Morgunov, V.; Němeček, Stanislav; Pöschl, R.; Polák, Ivo; Raspereza, A.; Reiche, S.; Rusinov, V.; Sefkow, F.; Smirnov, P.; Terkulov, A.; Valkár, Š.; Weichert, Jan; Zálešák, Jaroslav

    2006-01-01

    Roč. 564, - (2006), s. 144-154 ISSN 0168-9002 R&D Projects: GA MŠk(CZ) LC527; GA MŠk(CZ) 1P05LA259; GA ČR(CZ) GA202/05/0653 Institutional research plan: CEZ:AV0Z10100502 Keywords : hadronic calorimeter * plastic scintillator tile * APD readout * linear collider detector Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.185, year: 2006

  12. Telomerase activation by genomic rearrangements in high-risk neuroblastoma

    Science.gov (United States)

    Peifer, Martin; Hertwig, Falk; Roels, Frederik; Dreidax, Daniel; Gartlgruber, Moritz; Menon, Roopika; Krämer, Andrea; Roncaioli, Justin L.; Sand, Frederik; Heuckmann, Johannes M.; Ikram, Fakhera; Schmidt, Rene; Ackermann, Sandra; Engesser, Anne; Kahlert, Yvonne; Vogel, Wenzel; Altmüller, Janine; Nürnberg, Peter; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Mariappan, Aruljothi; Heynck, Stefanie; Mariotti, Erika; Henrich, Kai-Oliver; Glöckner, Christian; Bosco, Graziella; Leuschner, Ivo; Schweiger, Michal R.; Savelyeva, Larissa; Watkins, Simon C.; Shao, Chunxuan; Bell, Emma; Höfer, Thomas; Achter, Viktor; Lang, Ulrich; Theissen, Jessica; Volland, Ruth; Saadati, Maral; Eggert, Angelika; de Wilde, Bram; Berthold, Frank; Peng, Zhiyu; Zhao, Chen; Shi, Leming; Ortmann, Monika; Büttner, Reinhard; Perner, Sven; Hero, Barbara; Schramm, Alexander; Schulte, Johannes H.; Herrmann, Carl; O’Sullivan, Roderick J.; Westermann, Frank; Thomas, Roman K.; Fischer, Matthias

    2016-01-01

    Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system1. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive2–4. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type1,2,5. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours. PMID:26466568

  13. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization.

    Science.gov (United States)

    Song, B K; Pan, M Z; Lau, Y L; Wan, K L

    2014-07-29

    Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.

  14. Mechanical strength model for plastic bonded granular materials at high strain rates and large strains

    International Nuclear Information System (INIS)

    Browning, R.V.; Scammon, R.J.

    1998-01-01

    Modeling impact events on systems containing plastic bonded explosive materials requires accurate models for stress evolution at high strain rates out to large strains. For example, in the Steven test geometry reactions occur after strains of 0.5 or more are reached for PBX-9501. The morphology of this class of materials and properties of the constituents are briefly described. We then review the viscoelastic behavior observed at small strains for this class of material, and evaluate large strain models used for granular materials such as cap models. Dilatation under shearing deformations of the PBX is experimentally observed and is one of the key features modeled in cap style plasticity theories, together with bulk plastic flow at high pressures. We propose a model that combines viscoelastic behavior at small strains but adds intergranular stresses at larger strains. A procedure using numerical simulations and comparisons with results from flyer plate tests and low rate uniaxial stress tests is used to develop a rough set of constants for PBX-9501. Comparisons with the high rate flyer plate tests demonstrate that the observed characteristic behavior is captured by this viscoelastic based model. copyright 1998 American Institute of Physics

  15. Highly ordered nanowire arrays on plastic substrates for ultrasensitive flexible chemical sensors.

    Science.gov (United States)

    McAlpine, Michael C; Ahmad, Habib; Wang, Dunwei; Heath, James R

    2007-05-01

    The development of a robust method for integrating high-performance semiconductors on flexible plastics could enable exciting avenues in fundamental research and novel applications. One area of vital relevance is chemical and biological sensing, which if implemented on biocompatible substrates, could yield breakthroughs in implantable or wearable monitoring systems. Semiconducting nanowires (and nanotubes) are particularly sensitive chemical sensors because of their high surface-to-volume ratios. Here, we present a scalable and parallel process for transferring hundreds of pre-aligned silicon nanowires onto plastic to yield highly ordered films for low-power sensor chips. The nanowires are excellent field-effect transistors, and, as sensors, exhibit parts-per-billion sensitivity to NO2, a hazardous pollutant. We also use SiO2 surface chemistries to construct a 'nano-electronic nose' library, which can distinguish acetone and hexane vapours via distributed responses. The excellent sensing performance coupled with bendable plastic could open up opportunities in portable, wearable or even implantable sensors.

  16. Highly ordered nanowire arrays on plastic substrates for ultrasensitive flexible chemical sensors

    Science.gov (United States)

    McAlpine, Michael C.; Ahmad, Habib; Wang, Dunwei; Heath, James R.

    2007-05-01

    The development of a robust method for integrating high-performance semiconductors on flexible plastics could enable exciting avenues in fundamental research and novel applications. One area of vital relevance is chemical and biological sensing, which if implemented on biocompatible substrates, could yield breakthroughs in implantable or wearable monitoring systems. Semiconducting nanowires (and nanotubes) are particularly sensitive chemical sensors because of their high surface-to-volume ratios. Here, we present a scalable and parallel process for transferring hundreds of pre-aligned silicon nanowires onto plastic to yield highly ordered films for low-power sensor chips. The nanowires are excellent field-effect transistors, and, as sensors, exhibit parts-per-billion sensitivity to NO2, a hazardous pollutant. We also use SiO2 surface chemistries to construct a `nano-electronic nose' library, which can distinguish acetone and hexane vapours via distributed responses. The excellent sensing performance coupled with bendable plastic could open up opportunities in portable, wearable or even implantable sensors.

  17. Root-type-specific plasticity in response to localized high nitrate supply in maize (Zea mays).

    Science.gov (United States)

    Yu, Peng; Hochholdinger, Frank; Li, Chunjian

    2015-10-01

    Shoot-borne roots contribute to most of the nutrient uptake throughout the life cycle of maize (Zea mays). Compared with numerous studies with embryonic roots, detailed information on the phenotypic plasticity of shoot-borne roots in response to a heterogeneous nitrogen supply is scarce. The present study therefore provides a comprehensive profile of fine-scale plastic responses of distinct root types to localized high nitrate supply. Seedlings of the maize inbred line B73 were grown in split-root systems. The anatomy and morphological plasticity of the primary root and the roots initiated from the 2nd, 5th and 7th shoot nodes, and their lateral roots, were studied in response to local high nitrate supply to one side of the root system. In contrast to the insensitivity of axial roots, local high nitrate supply increased the length of 1st-order lateral roots on the primary root and the three whorls of shoot-borne roots at different growth stages, and increased the density of 1st-order lateral roots on the 7th shoot-borne root after silking. The length and density of 2nd-order lateral roots on the three whorls of shoot-borne roots displayed a more flexible response to local high nitrate than 1st-order lateral roots. Root diameter and number, and total area and diameter of metaxylem vessels increased from the primary root to early and then later developed shoot-borne roots, which showed a positive relationship with shoot growth and N accumulation. Maize axial roots and lateral roots responded differently to local high nitrate, and this was related to their function. The extent of morphological plasticity of lateral roots in response to local high nitrate depended on the initiation time of the shoot-borne roots on which the lateral roots developed. Morphological plasticity was higher on 2nd-order than on 1st-order lateral roots. The results suggest that higher order lateral root branching might be a potential target for genetic improvement in future maize breeding.

  18. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

    Science.gov (United States)

    Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2014-06-01

    To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

  19. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

    Directory of Open Access Journals (Sweden)

    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  20. High-fat diet prevents adaptive peripartum-associated adrenal gland plasticity and anxiolysis.

    Science.gov (United States)

    Perani, Clara V; Neumann, Inga D; Reber, Stefan O; Slattery, David A

    2015-10-07

    Maternal obesity is associated with lower basal plasma cortisol levels and increased risk of postpartum psychiatric disorders. Given that both obesity and the peripartum period are characterized by an imbalance between adrenocorticotropic hormone (ACTH) and cortisol, we hypothesized that the adrenal glands undergo peripartum-associated plasticity and that such changes would be prevented by a high-fat diet (HFD). Here, we demonstrate substantial peripartum adrenal gland plasticity in the pathways involved in cholesterol supply for steroidogenesis in female rats. In detail, the receptors involved in plasma lipid uptake, low density lipoprotein (LDL) receptor (LDLR) and scavenger receptor class B type 1 (SRB1), are elevated, intra-adrenal cholesterol stores are depleted, and a key enzyme in de novo cholesterol synthesis, hydroxymethylglutaryl coenzyme A reductase (HMGCR), is downregulated; particularly at mid-lactation. HFD prevented the lactation-associated anxiolysis, basal hypercorticism, and exaggerated the corticosterone response to ACTH. Moreover, we show that HFD prevented the downregulation of adrenal cholesterol stores and HMGCR expression, and LDLR upregulation at mid-lactation. These findings show that the adrenal gland is an important regulator of peripartum-associated HPA axis plasticity and that HFD has maladaptive consequences for the mother, partly by preventing these neuroendocrine and also behavioural changes.

  1. Genomic characterization of recurrent high-grade astroblastoma.

    Science.gov (United States)

    Bale, Tejus A; Abedalthagafi, Malak; Bi, Wenya Linda; Kang, Yun Jee; Merrill, Parker; Dunn, Ian F; Dubuc, Adrian; Charbonneau, Sarah K; Brown, Loreal; Ligon, Azra H; Ramkissoon, Shakti H; Ligon, Keith L

    2016-01-01

    Astroblastomas are rare primary brain tumors, diagnosed based on histologic features. Not currently assigned a WHO grade, they typically display indolent behavior, with occasional variants taking a more aggressive course. We characterized the immunohistochemical characteristics, copy number (high-resolution array comparative genomic hybridization, OncoCopy) and mutational profile (targeted next-generation exome sequencing, OncoPanel) of a cohort of seven biopsies from four patients to identify recurrent genomic events that may help distinguish astroblastomas from other more common high-grade gliomas. We found that tumor histology was variable across patients and between primary and recurrent tumor samples. No common molecular features were identified among the four tumors. Mutations commonly observed in astrocytic tumors (IDH1/2, TP53, ATRX, and PTEN) or ependymoma were not identified. However one case with rapid clinical progression displayed mutations more commonly associated with GBM (NF1(N1054H/K63)*, PIK3CA(R38H) and ERG(A403T)). Conversely, another case, originally classified as glioblastoma with nine-year survival before recurrence, lacked a GBM mutational profile. Other mutations frequently seen in lower grade gliomas (BCOR, BCORL1, ERBB3, MYB, ATM) were also present in several tumors. Copy number changes were variable across tumors. Our findings indicate that astroblastomas have variable growth patterns and morphologic features, posing significant challenges to accurate classification in the absence of diagnostically specific copy number alterations and molecular features. Their histopathologic overlap with glioblastoma will likely confound the observation of long-term GBM "survivors". Further genomic profiling is needed to determine whether these tumors represent a distinct entity and to guide management strategies. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Specific regions of genome plasticity and genetic diversity of the commensal Escherichia coli A0 34/86

    Czech Academy of Sciences Publication Activity Database

    Hejnová, Jana; Pages, Delphine; Rusniok, Ch.; Glaser, P.; Šebo, Peter; Buchrieser, C.

    2006-01-01

    Roč. 296, - (2006), s. 541-546 ISSN 1438-4221 Institutional research plan: CEZ:AV0Z50200510 Keywords : escherichia coli * commensal * genome comparison Subject RIV: EE - Microbiology, Virology Impact factor: 2.760, year: 2006

  3. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Directory of Open Access Journals (Sweden)

    Mark Ravinet

    2018-05-01

    Full Text Available Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus and the Japan Sea stickleback (G. nipponicus, which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  4. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Science.gov (United States)

    Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

    2018-05-01

    Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  5. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

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

  6. High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

    Science.gov (United States)

    Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

    2015-01-01

    Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

  7. Plastic nuclear track detectors as high x-ray and gamma dosimeters

    International Nuclear Information System (INIS)

    Chong Chon Sing

    1995-01-01

    A brief review of recent studies on the effects of high doses of x-ray and gamma ray on the track registration properties of several plastic track detectors is presented. The bulk etching rates and the etched track sizes have been found to increase with the dose in the range up to 100 Mrad. These results suggest that the changes in track registration characteristics can be employed as an index of the radiation dose in the megarad region. In particular, recent results on the effect of X-ray irradiation on two types of cellulose nitrate track detectors obtained in our laboratory are reported in this paper. (author)

  8. Tests of a Fast Plastic Scintillator for High-Precision Half-Life Measurements

    Science.gov (United States)

    Laffoley, A. T.; Dunlop, R.; Finlay, P.; Leach, K. G.; Michetti-Wilson, J.; Rand, E. T.; Svensson, C. E.; Grinyer, G. F.; Thomas, J. C.; Ball, G.; Garnsworthy, A. B.; Hackman, G.; Orce, J. N.; Triambak, S.; Williams, S. J.; Andreoiu, C.; Cross, D.

    2013-03-01

    A fast plastic scintillator detector is evaluated for possible use in an ongoing program of high-precision half-life measurements of short lived β emitters. Using data taken at TRI-UMF's Isotope Separator and Accelerator Facility with a radioactive 26Na beam, a detailed investigation of potential systematic effects with this new detector setup is being performed. The technique will then be applied to other β-decay half-life measurements including the superallowed Fermi β emitters 10C, 14O, and T = 1/2 decay of 15O.

  9. Deformation properties of highly plastic fissured Palaeogene clay - Lack of stress memory?

    DEFF Research Database (Denmark)

    Krogsbøll, Anette; Hededal, Ole; Foged, Niels Nielsen

    2012-01-01

    are evaluated based on the degree of debonding caused by natural processes insitu as compared to processes induced during severe loading and unloading in laboratory. A long term oedometer test on Lillebælt Clay with a series of loading and unloading cycles was carried out. The test results are used to evaluate......The geological preconsolidation of the Palaeogene clays in Denmark is estimated to 5-8 MPa or more, whereas laboratory and field experiences indicate values between 100 and 3000 kPa. Presumably, the high plasticity clay loses its memory of earlier preloads due to swelling, or as an effect...

  10. High-resolution characterization of a hepatocellular carcinoma genome.

    Science.gov (United States)

    Totoki, Yasushi; Tatsuno, Kenji; Yamamoto, Shogo; Arai, Yasuhito; Hosoda, Fumie; Ishikawa, Shumpei; Tsutsumi, Shuichi; Sonoda, Kohtaro; Totsuka, Hirohiko; Shirakihara, Takuya; Sakamoto, Hiromi; Wang, Linghua; Ojima, Hidenori; Shimada, Kazuaki; Kosuge, Tomoo; Okusaka, Takuji; Kato, Kazuto; Kusuda, Jun; Yoshida, Teruhiko; Aburatani, Hiroyuki; Shibata, Tatsuhiro

    2011-05-01

    Hepatocellular carcinoma, one of the most common virus-associated cancers, is the third most frequent cause of cancer-related death worldwide. By massively parallel sequencing of a primary hepatitis C virus-positive hepatocellular carcinoma (36× coverage) and matched lymphocytes (>28× coverage) from the same individual, we identified more than 11,000 somatic substitutions of the tumor genome that showed predominance of T>C/A>G transition and a decrease of the T>C substitution on the transcribed strand, suggesting preferential DNA repair. Gene annotation enrichment analysis of 63 validated non-synonymous substitutions revealed enrichment of phosphoproteins. We further validated 22 chromosomal rearrangements, generating four fusion transcripts that had altered transcriptional regulation (BCORL1-ELF4) or promoter activity. Whole-exome sequencing at a higher sequence depth (>76× coverage) revealed a TSC1 nonsense substitution in a subpopulation of the tumor cells. This first high-resolution characterization of a virus-associated cancer genome identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor.

  11. High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

    Directory of Open Access Journals (Sweden)

    Rodolphe François

    2006-08-01

    Full Text Available Abstract Background Comparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse. Results The bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes. Conclusion Analysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

  12. Effects of plastic mulches and high tunnel raspberry production systems on soil physicochemical quality indicators

    Science.gov (United States)

    Domagała-Świątkiewicz, Iwona; Siwek, Piotr

    2018-01-01

    In horticulture, degradable materials are desirable alternatives to plastic films. Our aim was to study the impact of soil plastic mulching on the soil properties in the high tunnel and open field production systems of raspberry. The raised beds were mulched with a polypropylene non-woven and two degradable mulches: polypropylene with a photodegradant and non-woven polylactide. The results indicated that the system of raspberry production, as well as the type of mulching had significant impact on soil organic carbon stock, moisture content and water stable aggregate amount. Soils taken from the open field system had a lower bulk density and water stability aggregation index, but higher organic carbon and capillary water content as compared to soils collected from high tunnel conditions. In comparison with the open field system, soil salinity was also found to be higher in high tunnel, as well as with higher P, Mg, Ca, S, Na and B content. Furthermore, mulch covered soils had more organic carbon amount than the bare soils. Soil mulching also enhanced the water capacity expressed as a volume of capillary water content. In addition, mulching improved the soil structure in relation to the bare soil, in particular, in open field conditions. The impact of the compared mulches on soil quality indicators was similar.

  13. The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes

    OpenAIRE

    Massart, R; Freyburger, M; Suderman, M; Paquet, J; El Helou, J; Belanger-Nelson, E; Rachalski, A; Koumar, O C; Carrier, J; Szyf, M; Mongrain, V

    2014-01-01

    Sleep is critical for normal brain function and mental health. However, the molecular mechanisms mediating the impact of sleep loss on both cognition and the sleep electroencephalogram remain mostly unknown. Acute sleep loss impacts brain gene expression broadly. These data contributed to current hypotheses regarding the role for sleep in metabolism, synaptic plasticity and neuroprotection. These changes in gene expression likely underlie increased sleep intensity following sleep deprivation ...

  14. Effects of thin high-Z layers on the hydrodynamics of laser-accelerated plastic targets

    International Nuclear Information System (INIS)

    Obenschain, S.P.; Colombant, D.G.; Karasik, M.; Pawley, C.J.; Serlin, V.; Schmitt, A.J.; Weaver, J.L.; Gardner, J.H.; Phillips, L.; Aglitskiy, Y.; Chan, Y.; Dahlburg, J.P.; Klapisch, M.

    2002-01-01

    Experimental results and simulations that study the effects of thin metallic layers with high atomic number (high-Z) on the hydrodynamics of laser accelerated plastic targets are presented. These experiments employ a laser pulse with a low-intensity foot that rises into a high-intensity main pulse. This pulse shape simulates the generic shape needed for high-gain fusion implosions. Imprint of laser nonuniformity during start up of the low intensity foot is a well-known seed for hydrodynamic instability. Large reductions are observed in hydrodynamic instability seeded by laser imprint when certain minimum thickness gold or palladium layers are applied to the laser-illuminated surface of the targets. The experiment indicates that the reduction in imprint is at least as large as that obtained by a 6 times improvement in the laser uniformity. Simulations supported by experiments are presented showing that during the low intensity foot the laser light can be nearly completely absorbed by the high-Z layer. X rays originating from the high-Z layer heat the underlying lower-Z plastic target material and cause large buffering plasma to form between the layer and the accelerated target. This long-scale plasma apparently isolates the target from laser nonuniformity and accounts for the observed large reduction in laser imprint. With onset of the higher intensity main pulse, the high-Z layer expands and the laser light is transmitted. This technique will be useful in reducing laser imprint in pellet implosions and thereby allow the design of more robust targets for high-gain laser fusion

  15. Elevated levels of ingested plastic in a high Arctic seabird, the northern fulmar (Fulmarus glacialis)

    NARCIS (Netherlands)

    Trevail, A.M.; Gabrielsen, G.W.; Kuhn, S.; Franeker, van J.A.

    2015-01-01

    Plastic pollution is of worldwide concern; however, increases in international commercial activity in the Arctic are occurring without the knowledge of the existing threat posed to the local marine environment by plastic litter. Here, we quantify plastic ingestion by northern fulmars, Fulmarus

  16. Improving the circular economy via hydrothermal processing of high-density waste plastics

    DEFF Research Database (Denmark)

    Pedersen, Thomas Helmer; Conti, Federica

    2017-01-01

    Rising environmental concerns on climate changes are causing an increasing attention on circular economies. The plastic economy, in particular, is in focus due to the accelerating consumption of plastics, mainly derived from virgin feedstock, combined with the lack of plastic recycling strategies...

  17. Determination of Polymer Additives-Antioxidants, Ultraviolet Stabilizers, Plasticizers and Photoinitiators in Plastic Food Package by Accelerated Solvent Extraction Coupled with High-Performance Liquid Chromatography.

    Science.gov (United States)

    Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying; Su, Qi-Zhi; Wu, Yu-Mei

    2015-07-01

    An analytical method for the quantitative determination of 4 antioxidants, 9 ultraviolet (UV) stabilizers, 12 phthalate plasticizers and 2 photoinitiators in plastic food package using accelerated solvent extraction (ASE) coupled with high-performance liquid chromatography-photodiode array detector (HPLC-PDA) has been developed. Parameters affecting the efficiency in the process such as extraction and chromatographic conditions were studied in order to determine operating conditions. The analytical method of ASE-HPLC showed good linearity with good correlation coefficients (R ≥ 0.9833). The limits of detection and quantification were between 0.03 and 0.30 µg mL(-1) and between 0.10 and 1.00 µg mL(-1) for 27 analytes. Average spiked recoveries for most analytes in samples were >70.4% at 10, 20 and 40 µg g(-1) spiked levels, except UV-9 and Irganox 1010 (58.6 and 64.0% spiked at 10 µg g(-1), respectively), the relative standard deviations were in the range from 0.4 to 15.4%. The methodology has been proposed for the analysis of 27 polymer additives in plastic food package. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Experimental Study on the Utilization of Fine Steel Slag on Stabilizing High Plastic Subgrade Soil

    Directory of Open Access Journals (Sweden)

    Hussien Aldeeky

    2017-01-01

    Full Text Available The three major steel manufacturing factories in Jordan dump their byproduct, steel slag, randomly in open areas, which causes many environmental hazardous problems. This study intended to explore the effectiveness of using fine steel slag aggregate (FSSA in improving the geotechnical properties of high plastic subgrade soil. First soil and fine steel slag mechanical and engineering properties were evaluating. Then 0%, 5%, 10%, 15%, 20%, and 25% dry weight of soil of fine steel slag (FSSA were added and mixed into the prepared soil samples. The effectiveness of the FSSA was judged by the improvement in consistency limits, compaction, free swell, unconfined compression strength, and California bearing ratio (CBR. From the test results, it is observed that 20% FSSA additives will reduce plasticity index and free swell by 26.3% and 58.3%, respectively. Furthermore, 20% FSSA additives will increase the unconfined compressive strength, maximum dry density, and CBR value by 100%, 6.9%, and 154%. By conclusion FSSA had a positive effect on the geotechnical properties of the soil and it can be used as admixture in proving geotechnical characteristics of subgrade soil, not only solving the waste disposal problem.

  19. Mechanical Properties of High Performance Concrete Containing Waste Plastic as Aggregate

    Directory of Open Access Journals (Sweden)

    Abdulkader Ismail Al-Hadithi

    2015-08-01

    Full Text Available The world's population growth and the increasing demand for new infrastructure facilities and buildings , present us with the vision of a higher resources consumption, specially in the form of more durable concrete such as High Performance Concrete (HPC . Moreover , the growth of the world pollution by plastic waste has been tremendous. The aim of this research is to investigate the change in mechanical properties of HPC with added waste plastics in concrete. For this purpose 2.5%, 5% and 7.5% in volume of natural fine aggregate in the HPC mixes were replaced by an equal volume of Polyethylene Terephthalate (PET waste , got by shredded PET bottles. The mechanical properties (compressive, splitting tensile, and flexural strength evaluated at the ages of (7 ,28, 56 and 91 days while the static modulus of elasticity tested at (28 and 91 days . The results indicated that HPC containing PET-aggregate presented lower compressive strength and static elasticity . The splitting strength displayed an arising trend at the initial stages, however, they have a tendency to decrease after a while. On the other hand, flexural strength results gave better modulus of rapture at all ages of curing , as compared with reference concrete specimens.

  20. Experimental study of Electro-Plastic Effect on Advanced High Strength Steels

    International Nuclear Information System (INIS)

    Liu, Xun; Lan, Shuhuai; Ni, Jun

    2013-01-01

    Application of Advanced High Strength Steels (AHSS) into vehicle structures calls for innovative manufacturing processes. In terms of reducing deformation resistance through external energy, Electro-Plastic Effect (EPE) provides a potential alternative to traditional thermal softening phenomenon. In this work, effectiveness of EPE on one group of AHSS, Transformation Induced Plasticity (TRIP) Steel, was evaluated. It was found that EPE cannot be effectively initiated until the current density reaches a threshold value between 7.4 A/mm 2 and 11.4 A/mm 2 . Besides, the softening phenomenon is more distinct at larger strains. Underlying mechanisms are explained from perspectives of dislocation multiplication, gliding and mechanical twinning. The inevitable Joule heating phenomenon associated with current was suppressed with forced air cooling and the temperature distribution inside the tensile specimen was numerically calculated with a coupled Finite Element Model. Effectiveness of EPE rather than thermal softening or expansion was further proved with the larger flow stress reduction under higher current density and shorter pulses at same temperature increase. Hollomon equation was adopted to model the observed stress strain relationships. Since material properties of TRIP steels are directly related to the phase transformation from retained austenite into martensite, volume fraction of retained austenite was quantitatively measured by X-ray Diffraction (XRD). It was found that the applied current retarded martensitic transformation process. Metallographic analysis was further performed and phenomena of change of grain structures and phase distribution were hardly observable

  1. Clinical dosimetry with plastic scintillators - Almost energy independent, direct absorbed dose reading with high resolution

    Energy Technology Data Exchange (ETDEWEB)

    Quast, U; Fluehs, D [Department of Radiotherapy, Essen (Germany). Div. of Clinical Radiation Physics; Fluehs, D; Kolanoski, H [Dortmund Univ. (Germany). Inst. fuer Physik

    1996-08-01

    Clinical dosimetry is still far behind the goal to measure any spatial or temporal distribution of absorbed dose fast and precise without disturbing the physical situation by the dosimetry procedure. NE 102A plastic scintillators overcome this border. These tissue substituting dosemeter probes open a wide range of new clinical applications of dosimetry. This versatile new dosimetry system enables fast measurement of the absorbed dose to water in water also in regions with a steep dose gradient, close to interfaces, or in partly shielded regions. It allows direct reading dosimetry in the energy range of all clinically used external photon and electron beams, or around all branchytherapy sources. Thin detector arrays permit fast and high resolution measurements in quality assurance, such as in-vivo dosimetry or even afterloading dose monitoring. A main field of application is the dosimetric treatment planning, the individual optimization of brachytherapy applicators. Thus, plastic scintillator dosemeters cover optimally all difficult fields of clinical dosimetry. An overview about its characteristics and applications is given here. 20 refs, 1 fig.

  2. High-pressure plastic scintillation detector for measuring radiogenic gases in flow systems

    CERN Document Server

    Schell, W R; Yoon, S R; Tobin, M J

    1999-01-01

    Radioactive gases are emitted into the atmosphere from nuclear electric power and nuclear fuel reprocessing plants, from hospitals discarding xenon used in diagnostic medicine, as well as from nuclear weapons tests. A high-pressure plastic scintillation detector was constructed to measure atmospheric levels of such radioactive gases by detecting the beta and internal conversion (IC) electron decays. Operational tests and calibrations were made that permit integration of the flow detectors into a portable Gas Analysis, Separation and Purification system (GASP). The equipment developed can be used for measuring fission gases released from nuclear reactor sources and/or as part of monitoring equipment for enforcing the Comprehensive Test Ban Treaty. The detector is being used routinely for in-line gas separation efficiency measurements, at the elevated operational pressures used for the high-pressure swing analysis system (2070 kPa) and at flow rates of 5-15 l/min . This paper presents the design features, opera...

  3. A complete life cycle assessment of high density polyethylene plastic bottle

    Science.gov (United States)

    Treenate, P.; Limphitakphong, N.; Chavalparit, O.

    2017-07-01

    This study was aimed to determine environmental performances of a lubricant oil bottle made from high density polyethylene and to develop potential measures for reducing its impacts. A complete life cycle assessment was carried out to understand a whole effect on the environment from acquiring, processing, using, and disposing the product. Two scenarios of disposal phase; recycle and incineration: were examined to quantify a lesser degree on environmental impact. The results illustrated that major impacts of the two scenarios were at the same categories with the highest contributor of raw material acquisition and pre-processing. However, all impacts in case of recycling provided a lower point than that in case of incineration, except mineral extraction. Finally, feasible measures for reducing the environmental impact of high density polyethylene plastic bottle were proposed in accordance with 3Rs concept.

  4. Wood plastic composites based on microfibrillar blends of high density polyethylene/poly(ethylene terephthalate).

    Science.gov (United States)

    Lei, Yong; Wu, Qinglin

    2010-05-01

    High-melting-temperature poly(ethylene terephthalate) (PET) was successfully introduced into wood plastic composites through a two-step reactive extrusion technology. Wood flour was added into pre-prepared PET/high density polyethylene (HDPE) microfibrillar blends (MFBs) in the second extrusion at the temperature for processing HDPE. Addition of 25% in situ formed PET microfibers obviously increased the mechanical properties of HDPE, and more significant enhancement by the in situ formed recycled PET microfibers was observed for the recycled HDPE. Adding 2% E-GMA improved the compatibility between matrix and microfibers in MFBs, resulting further enhanced mechanical properties. The subsequent addition of 40% wood flour did not influence the size and morphology of PET microfibers, and improved the comprehensive mechanical properties of MFBs. The wood flour increased the crystallinity level of HDPE in the compatibilized MFB in which PET phase did not crystallize. The storage modulus of MFB was greatly improved by wood flour. Published by Elsevier Ltd.

  5. Evolutionary growth process of highly conserved sequences in vertebrate genomes.

    Science.gov (United States)

    Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

    2012-08-01

    Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Microbial degradation of high impact polystyrene (HIPS), an e-plastic with decabromodiphenyl oxide and antimony trioxide

    International Nuclear Information System (INIS)

    Sekhar, Vini C.; Nampoothiri, K. Madhavan; Mohan, Arya J.; Nair, Nimisha R.; Bhaskar, Thallada; Pandey, Ashok

    2016-01-01

    Highlights: • Biodegradation of a high impact polystyrene e − plastic. • 12.4% (w/w) e plastic film lost using an isolate, Enterobacter sp. • Noted changes in the physico-chemical characteristics of degraded e-plastic film. • Polystyrene intermediates were detected in the degradation medium. • e-plastic degrading microbes displayed extracellular depolymerase activity. - Abstract: Accumulation of electronic waste has increased catastrophically and out of that various plastic resins constitute one of the leading thrown out materials in the electronic machinery. Enrichment medium, containing high impact polystyrene (HIPS) with decabromodiphenyl oxide and antimony trioxide as sole carbon source, was used to isolate microbial cultures. The viability of these cultures in the e-plastic containing mineral medium was further confirmed by triphenyl tetrazolium chloride (TTC) reduction test. Four cultures were identified by 16S rRNA sequencing as Enterobacter sp., Citrobacter sedlakii, Alcaligenes sp. and Brevundimonas diminuta. Biodegradation experiments were carried out in flask level and gelatin supplementation (0.1% w/v) along with HIPS had increased the degradation rate to a maximum of 12.4% (w/w) within 30 days. This is the first report for this kind of material. The comparison of FTIR, NMR, and TGA analysis of original and degraded e-plastic films revealed structural changes under microbial treatment. Polystyrene degradation intermediates in the culture supernatant were also detected using HPLC analysis. The gravity of biodegradation was validated by morphological changes under scanning electron microscope. All isolates displayed depolymerase activity to substantiate enzymatic degradation of e-plastic.

  7. Microbial degradation of high impact polystyrene (HIPS), an e-plastic with decabromodiphenyl oxide and antimony trioxide

    Energy Technology Data Exchange (ETDEWEB)

    Sekhar, Vini C. [Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695 019, Kerala (India); Nampoothiri, K. Madhavan, E-mail: madhavan85@hotmail.com [Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695 019, Kerala (India); Mohan, Arya J.; Nair, Nimisha R. [Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695 019, Kerala (India); Bhaskar, Thallada [Bio-Fuels Division (BFD), CSIR-Indian Institute of Petroleum (IIP), Dehradun, Uttarakhand 248005 (India); Pandey, Ashok [Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695 019, Kerala (India)

    2016-11-15

    Highlights: • Biodegradation of a high impact polystyrene e − plastic. • 12.4% (w/w) e plastic film lost using an isolate, Enterobacter sp. • Noted changes in the physico-chemical characteristics of degraded e-plastic film. • Polystyrene intermediates were detected in the degradation medium. • e-plastic degrading microbes displayed extracellular depolymerase activity. - Abstract: Accumulation of electronic waste has increased catastrophically and out of that various plastic resins constitute one of the leading thrown out materials in the electronic machinery. Enrichment medium, containing high impact polystyrene (HIPS) with decabromodiphenyl oxide and antimony trioxide as sole carbon source, was used to isolate microbial cultures. The viability of these cultures in the e-plastic containing mineral medium was further confirmed by triphenyl tetrazolium chloride (TTC) reduction test. Four cultures were identified by 16S rRNA sequencing as Enterobacter sp., Citrobacter sedlakii, Alcaligenes sp. and Brevundimonas diminuta. Biodegradation experiments were carried out in flask level and gelatin supplementation (0.1% w/v) along with HIPS had increased the degradation rate to a maximum of 12.4% (w/w) within 30 days. This is the first report for this kind of material. The comparison of FTIR, NMR, and TGA analysis of original and degraded e-plastic films revealed structural changes under microbial treatment. Polystyrene degradation intermediates in the culture supernatant were also detected using HPLC analysis. The gravity of biodegradation was validated by morphological changes under scanning electron microscope. All isolates displayed depolymerase activity to substantiate enzymatic degradation of e-plastic.

  8. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

    Directory of Open Access Journals (Sweden)

    Yandell Mark

    2010-07-01

    Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

  9. Liquid fuel obtain from polypropylene (PP-5) and high density polyethylene (HDPE-2) waste plastics mixture

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, Moinuddin; Rashid, Mohammad Mamunor; Rahman, Md. Sadikur; Molla, Mohammed [Department of Research and Development, Natural State Research Inc, Stamford, (United States)

    2011-07-01

    Plastics are made by combination of small based molecules to form monomers. The monomers are then joined together by chemical polymerization mechanism to form polymers also known as plastics. These plastics contain various elements such as carbon, hydrogen, oxygen, nitrogen, chlorine and sul fur. The use of plastics is vastly expanded and it is being used in every sector of the world. However, using plastics does have a negative aspect, after use they end up in our landfill as waste causing numerous health and environmental problems. Landfill waste plastics release harmful gases due to the presence of carbon, chlorine and sul fur in them into the atmosphere causing climates to change drastically, equivalent to the effects of greenhouse gases (GHG) emission. To overcome these environmental issues, scientists have already developed many methods to converting these waste plastics into energy and fuel . We developed one new methods thermal cracking conversion to convert these waste plastics into usable liquid fuel . Thermal cracking conversion is a process to shorten the long chain hydrocarbons to produce liquid fuel in the absence of a catalyst. The thermal degradation process of the waste plastics long chain hydrocarbon to makes short chain hydrocarbon fuel. The fuel produced has been analyzed and tested according to standard methods. Key words: fuel , hydrocarbon, waste plastic, thermal degradation, conversion, GC/MS.

  10. Liquid fuel obtain from polypropylene (PP-5) and high density polyethylene (HDPE-2) waste plastics mixture

    International Nuclear Information System (INIS)

    Sarker, Moinuddin; Rashid, Mohammad Mamunor; Rahman, Md. Sadikur; Molla, Mohammed

    2011-01-01

    Plastics are made by combination of small based molecules to form monomers. The monomers are then joined together by chemical polymerization mechanism to form polymers also known as plastics. These plastics contain various elements such as carbon, hydrogen, oxygen, nitrogen, chlorine and sul fur. The use of plastics is vastly expanded and it is being used in every sector of the world. However, using plastics does have a negative aspect, after use they end up in our landfill as waste causing numerous health and environmental problems. Landfill waste plastics release harmful gases due to the presence of carbon, chlorine and sul fur in them into the atmosphere causing climates to change drastically, equivalent to the effects of greenhouse gases (GHG) emission. To overcome these environmental issues, scientists have already developed many methods to converting these waste plastics into energy and fuel . We developed one new methods thermal cracking conversion to convert these waste plastics into usable liquid fuel . Thermal cracking conversion is a process to shorten the long chain hydrocarbons to produce liquid fuel in the absence of a catalyst. The thermal degradation process of the waste plastics long chain hydrocarbon to makes short chain hydrocarbon fuel. The fuel produced has been analyzed and tested according to standard methods. Key words: fuel , hydrocarbon, waste plastic, thermal degradation, conversion, GC/MS

  11. Get your high-quality low-cost genome sequence

    NARCIS (Netherlands)

    Faino, L.; Thomma, B.P.H.J.

    2014-01-01

    The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model

  12. Highly evolvable malaria vectors : The genomes of 16 Anopheles mosquitoes

    NARCIS (Netherlands)

    Neafsey, D. E.; Waterhouse, R. M.; Abai, M. R.; Aganezov, S. S.; Alekseyev, M. A.; Allen, J. E.; Amon, J.; Arca, B.; Arensburger, P.; Artemov, G.; Assour, L. A.; Basseri, H.; Berlin, A.; Birren, B. W.; Blandin, S. A.; Brockman, A. I.; Burkot, T. R.; Burt, A.; Chan, C. S.; Chauve, C.; Chiu, J. C.; Christensen, M.; Costantini, C.; Davidson, V. L. M.; Deligianni, E.; Dottorini, T.; Dritsou, V.; Gabriel, S. B.; Guelbeogo, W. M.; Hall, A. B.; Han, M. V.; Hlaing, T.; Hughes, D. S. T.; Jenkins, A. M.; Jiang, X.; Jungreis, I.; Kakani, E. G.; Kamali, M.; Kemppainen, P.; Kennedy, R. C.; Kirmitzoglou, I. K.; Koekemoer, L. L.; Laban, N.; Langridge, N.; Lawniczak, M. K. N.; Lirakis, M.; Lobo, N. F.; Lowy, E.; Maccallum, R. M.; Mao, C.; Maslen, G.; Mbogo, C.; Mccarthy, J.; Michel, K.; Mitchell, S. N.; Moore, W.; Murphy, K. A.; Naumenko, A. N.; Nolan, T.; Novoa, E. M.; O'loughlin, S.; Oringanje, C.; Oshaghi, M. A.; Pakpour, N.; Papathanos, P. A.; Peery, A. N.; Povelones, M.; Prakash, A.; Price, D. P.; Rajaraman, A.; Reimer, L. J.; Rinker, D. C.; Rokas, A.; Russell, T. L.; Sagnon, N.; Sharakhova, M. V.; Shea, T.; Simao, F. A.; Simard, F.; Slotman, M. A.; Somboon, P.; Stegniy, V.; Struchiner, C. J.; Thomas, G. W. C.; Tojo, M.; Topalis, P.; Tubio, J. M. C.; Unger, M. F.; Vontas, J.; Walton, C.; Wilding, C. S.; Willis, J. H.; Wu, Y.-c.; Yan, G.; Zdobnov, E. M.; Zhou, X.; Catteruccia, F.; Christophides, G. K.; Collins, F. H.; Cornman, R. S.; Crisanti, A.; Donnelly, M. J.; Emrich, S. J.; Fontaine, M. C.; Gelbart, W.; Hahn, M. W.; Hansen, I. A.; Howell, P. I.; Kafatos, F. C.; Kellis, M.; Lawson, D.; Louis, C.; Luckhart, S.; Muskavitch, M. A. T.; Ribeiro, J. M.; Riehle, M. A.; Sharakhov, I. V.; Tu, Z.; Zwiebel, L. J.; Besansky, N. J.

    2015-01-01

    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16

  13. Microstructure Evolution and Mechanical Behavior of a Hot-Rolled High-Manganese Dual-Phase Transformation-Induced Plasticity/Twinning-Induced Plasticity Steel

    Science.gov (United States)

    Fu, Liming; Shan, Mokun; Zhang, Daoda; Wang, Huanrong; Wang, Wei; Shan, Aidang

    2017-05-01

    The microstructures and deformation behavior were studied in a high-temperature annealed high-manganese dual-phase (28 vol pct δ-ferrite and 72 vol pct γ-austenite) transformation-induced plasticity/twinning-induced plasticity (TRIP/TWIP) steel. The results showed that the steel exhibits a special Lüders-like yielding phenomenon at room temperature (RT) and 348 K (75 °C), while it shows continuous yielding at 423 K, 573 K and 673 K (150 °C, 300 °C and 400 °C) deformation. A significant TRIP effect takes place during Lüders-like deformation at RT and 348 K (75 °C) temperatures. Semiquantitative analysis of the TRIP effect on the Lüders-like yield phenomenon proves that a softening effect of the strain energy consumption of strain-induced transformation is mainly responsible for this Lüders-like phenomenon. The TWIP mechanism dominates the 423 K (150 °C) deformation process, while the dislocation glide controls the plasticity at 573 K (300 °C) deformation. The delta-ferrite, as a hard phase in annealed dual-phase steel, greatly affects the mechanical stability of austenite due to the heterogeneous strain distribution between the two phases during deformation. A delta-ferrite-aided TRIP effect, i.e., martensite transformation induced by localized strain concentration of the hard delta-ferrite, is proposed to explain this kind of Lüders-like phenomenon. Moreover, the tensile curve at RT exhibits an upward curved behavior in the middle deformation stage, which is principally attributed to the deformation twinning of austenite retained after Lüders-like deformation. The combination of the TRIP effect during Lüders-like deformation and the subsequent TWIP effect greatly enhances the ductility in this annealed high-manganese dual-phase TRIP/TWIP steel.

  14. High prevalence of parental delivery of plastic debris in Cory's shearwaters (Calonectris diomedea).

    Science.gov (United States)

    Rodríguez, Airam; Rodríguez, Beneharo; Nazaret Carrasco, María

    2012-10-01

    Plastic ingestion by adult Procellariiformes has been widely recorded, but few studies have evaluated intergenerational transfer. We assessed the prevalence of plastic particles, as well as their basic characteristics, in the gut content of dead Cory's shearwater fledglings stranded by light pollution on Canary Islands. Eighty-three percent of birds were affected, containing on average 8.0 plastic pieces per bird. The average plastic weight per bird was low (2.97±3.97mg) compared with other petrel species. We found no relationships between plastic loads and body condition or body size, but negative effects may be hidden or delayed. We propose to use the fledglings stranded by light pollution to carry out more precise studies to understand the potential hidden costs of plastic ingestion; and to monitor in a long-term the marine debris to develop management actions for the control of pollution at the marine environment. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Preparation of plastic-cellulose compounds by high energy gamma radiation

    International Nuclear Information System (INIS)

    Rosa, M.C.F.

    1978-01-01

    The use of high intensity sources of ionizing radiation for inducing polymer cross-linking was studied and the feasibility of its application in making plastic and cellulose combined compounds, particularly plates formed by paper sheets aglutinated with polyester resin, was analyzed. Several types of paper capable of being used in the plate composition were tested. It was verified that with the preparation technique used in this work the ordinary filter paper gave the best results. By different material testing techniques it was found that the chemical and mechanical properties of plates cured with radiation doses of about 1.5 Mrad are favorably compared with those exhibited by plates of equal composition, cured by the classic method (adding chemical initiator and accelerator) [pt

  16. Collapse Scenarios of High-Rise Buildings Using Plastic Limit Analysis

    Directory of Open Access Journals (Sweden)

    G. Liu

    2009-01-01

    Full Text Available The Twin Towers of the World Trade Center (WTC in New York, USA collapsed on 11 September, 2001. The incident is regarded as the most severe disaster for high-rise buildings in history. Investigations into the collapse scenarios are still being conducted. Possible collapse scenarios assessed by local and international experts were reported. Another possible collapse scenario of the WTC based on two hypotheses was proposed in this paper, and the idea of plastic limit analysis was applied to evaluate the approximate limit load. According to the theory analysis and numerical calculations, a conclusion can be drawn that the large fires, aroused by the terrorist attack, play a significant role on the collapse of the WTC.

  17. Doped polymer electrodes for high performance ferroelectric capacitors on plastic substrates

    KAUST Repository

    Khan, M. A.

    2012-10-03

    Flexible ferroelectric capacitors with doped polymer electrodes have been fabricated on plastic substrates with performance as good as metal electrodes. The effect of doping on the morphology of polymer electrodes and its impact on device performance have been studied. Improved fatigue characteristics using doped and undoped poly (3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) electrodes versus metal electrodes are observed. It is shown that the polymer electrodes follow classical ferroelectric and dielectric responses, including series resistance effects. The improved device characteristics obtained using highly conducting doped PEDOT:PSS suggest that it may be used both as an electrode and as global interconnect for all-polymer transparent circuits on flexible substrates.

  18. Neutron scattering experiments of the ionic crystal deformed plastically with uniaxial compression under high temperature

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Yoshinori; Minakawa, Nobuaki; Aizawa, Kazuya; Ozawa, Kunio [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1996-04-01

    As an aim of huge growth of alkali halide (AH) single crystal, a mosaic structure of small size AH single crystal deformed plastically with uniaxial compression under high temperature was evaluated due to its neutron irradiation experiment. Using TAS-2 installed at JRR-3M guide hole of Japan Atomic Energy Research Institute, locking curve at a representative face factor of the specimen was measured to observe the mosaic structure accompanied with expansion of the crystal due to compression. As a result, though the specimen before compression could be supposed to be divided to some parts already, the locking curve under 10 sec. of compression time showed already some fracture to divisions to suppose finer degradation of the crystal, and division of the locking curve at 600 sec. of compression time could be observed onto its 220 face. And, every compressed specimens showed some changes of crystallization method from standard sample. (G.K.)

  19. A simple method for the investigation of the high temperature plasticity of metallic materials

    Energy Technology Data Exchange (ETDEWEB)

    Chinh, N.Q. (Inst. for General Physics, Lorand Eoetvoes Univ., Budapest (Hungary)); Juhasz, A. (Inst. for General Physics, Lorand Eoetvoes Univ., Budapest (Hungary)); Tasnadi, P. (Inst. for General Physics, Lorand Eoetvoes Univ., Budapest (Hungary)); Kovacs, I. (Inst. for General Physics, Lorand Eoetvoes Univ., Budapest (Hungary))

    1993-11-01

    The indentation creep test is a powerful and quick method for the investigation of the high temperature plasticity of various materials. During creep test a small cylindrical punch is pressed at constant loads into the surface of the sample and the penetration depth is registered as a function of testing time. On the basis of the creep curves taken at various temperatures and loads the strain rate sensitivity and the activation energy of the steady-state creep process can be determined. The main advantage of this test is that it needs only a small amount of testing material. In this paper the usefullness of this method illustrated by some results obtained on superplastic and non superplastic Al alloys. The indentation results are compared with tensile data obtained on the same materials. (orig.).

  20. Development of high-flexible triboelectric generators using plastic metal as electrodes

    Science.gov (United States)

    Yang, Sen-Yeu; Shih, Jian-Fu; Chang, Chih-Chieh; Yang, Chii-Rong

    2017-02-01

    A triboelectric generator is a device that harvests energy through the conversion of mechanical energy into electrical energy. In this work, two polymer materials (PDMS and PET) were selected as triboelectric layers in conjunction with plastic metal (PM) films as conductive layers to produce an electrode with high flexibility. The PDMS film was fabricated with a microstructural array to enhance friction. The proposed PM material was prepared by mixing gallium-indium liquid metal and a glaze powder with excellent coating ability, extensibility, and conductivity. Results demonstrate the superior characteristics of the PM flexible electrodes, including large bending angle (≥180°), small curvature radius (≤1 mm), and stable conductivity. This PM-based triboelectric generator can achieve average output voltage of 80 V and current of 37.2 μA. The proposed flexible electrode with a PM conductive layer could be expected to make a notable contribution to the development of wearable devices.

  1. Features micro plastic deformation auxetic beryllium irradiated with high-energy electrons

    International Nuclear Information System (INIS)

    Rarans'kij, M.D.; Olyijnich-Lisyuk, A.V.; Tashchuk, O.Yu.

    2016-01-01

    By low-frequency internal friction (LFIF) (1...3 Hz) method, the study of the behavior of the dynamic modulus of torsion (Gef) and by mathematical modeling of dislocation motion studied micro plastic deformation in naturally aged and irradiated with high-energy (18 MeV) electrons auxetic beryllium. With increasing doses of radiation found an increase in IF and speed of movement of dislocations in 2-3 times. Installed stage character micro strain auxetic Be. By mathematical modeling showed that in the irradiated material the deformation occurs due to the accelerated movement of the twin dislocations in the early stages, and anomalous dynamic deceleration of complete dislocations with an increase in the degree of deformation in the second stage. It is shown that theoretically estimated values are in good agreement with the experimentally determined.

  2. High quality reference genome of drumstick tree (Moringa oleifera Lam.), a potential perennial crop.

    Science.gov (United States)

    Tian, Yang; Zeng, Yan; Zhang, Jing; Yang, ChengGuang; Yan, Liang; Wang, XuanJun; Shi, ChongYing; Xie, Jing; Dai, TianYi; Peng, Lei; Zeng Huan, Yu; Xu, AnNi; Huang, YeWei; Zhang, JiaJin; Ma, Xiao; Dong, Yang; Hao, ShuMei; Sheng, Jun

    2015-07-01

    The drumstick tree (Moringa oleifera Lam.) is a perennial crop that has gained popularity in certain developing countries for its high-nutrition content and adaptability to arid and semi-arid environments. Here we report a high-quality draft genome sequence of M. oleifera. This assembly represents 91.78% of the estimated genome size and contains 19,465 protein-coding genes. Comparative genomic analysis between M. oleifera and related woody plant genomes helps clarify the general evolution of this species, while the identification of several species-specific gene families and positively selected genes in M. oleifera may help identify genes related to M. oleifera's high protein content, fast-growth, heat and stress tolerance. This reference genome greatly extends the basic research on M. oleifera, and may further promote applying genomics to enhanced breeding and improvement of M. oleifera.

  3. Plastic litter accumulation on high-water strandline of urban beaches in Mumbai, India.

    Science.gov (United States)

    Jayasiri, H B; Purushothaman, C S; Vennila, A

    2013-09-01

    Today, almost every beach on every coastline is threatened by human activities. The inadequate recycling and poor management of waste in developing countries has resulted in considerable quantities of plastic contaminating beaches. Though India has long coastline of 5,420 km along the mainland with 43 % of sandy beaches, data on litter accumulation, particularly the plastics, which are one of the most common and persistent pollutants in marine environment, are scanty. The abundance and distribution of plastic litter was quantitatively assessed in four sandy beaches in Mumbai, India, bimonthly from May 2011 to March 2012. Triplicates of 2 × 2 m (4 m(2)) quadrats were sampled in each beach with a total of 72 quadrats. Overall, average abundance of 11.6 items m(-2) (0.25-282.5 items m(-2)) and 3.24 g m(-2) (0.27-15.53 g m(-2)) plastic litter was recorded in Mumbai beaches. Plastic litter accumulation significantly varied temporally and spatially at p = 0.05. Significantly higher plastic litter accumulation was recorded in Juhu beach. Furthermore, the highest abundance by weight was recorded in November and May numerically. More than 80 % of plastic particles were within the size range of 5-100 mm both by number and weight. Moreover, coloured plastics were predominant with 67 % by number of items and 51 % by weight. Probably, the intense use of beaches for recreation, tourism, and religious activities has increased the potential for plastic contamination in urban beaches in Mumbai.

  4. High prevalence of parental delivery of plastic debris in Cory’s shearwaters (Calonectris diomedea)

    OpenAIRE

    Rodríguez, Airam; Rodríguez, Beneharo; Carrasco, María Nazaret

    2012-01-01

    Plastic ingestion by adult Procellariiformes has been widely recorded, but few studies have evaluated intergenerational transfer. We assessed the prevalence of plastic particles, as well as their basic character- istics, in the gut content of dead Cory’s shearwater fledglings stranded by light pollution on Canary Islands. Eighty-three percent of birds were affected, containing on average 8.0 plastic pieces per bird. The average plastic weight per bird was low (2.97 ± 3.97 mg) compared with ...

  5. Conflicts in Chemistry: The Case of Plastics, a Role-Playing Game for High School Chemistry Students

    Science.gov (United States)

    Cook, Deborah H.

    2014-01-01

    Conflicts in Chemistry: The Case of Plastics, an innovative role-playing activity for high school students, was developed by the Chemical Heritage Foundation to promote increased public understanding of chemistry. The pilot program included three high school teachers and their students at three different schools and documented implementation and…

  6. High-fat diet induces hepatic insulin resistance and impairment of synaptic plasticity.

    Directory of Open Access Journals (Sweden)

    Zhigang Liu

    Full Text Available High-fat diet (HFD-induced obesity is associated with insulin resistance, which may affect brain synaptic plasticity through impairment of insulin-sensitive processes underlying neuronal survival, learning, and memory. The experimental model consisted of 3 month-old C57BL/6J mice fed either a normal chow diet (control group or a HFD (60% of calorie from fat; HFD group for 12 weeks. This model was characterized as a function of time in terms of body weight, fasting blood glucose and insulin levels, HOMA-IR values, and plasma triglycerides. IRS-1/Akt pathway was assessed in primary hepatocytes and brain homogenates. The effect of HFD in brain was assessed by electrophysiology, input/output responses and long-term potentiation. HFD-fed mice exhibited a significant increase in body weight, higher fasting glucose- and insulin levels in plasma, lower glucose tolerance, and higher HOMA-IR values. In liver, HFD elicited (a a significant decrease of insulin receptor substrate (IRS-1 phosphorylation on Tyr608 and increase of Ser307 phosphorylation, indicative of IRS-1 inactivation; (b these changes were accompanied by inflammatory responses in terms of increases in the expression of NFκB and iNOS and activation of the MAP kinases p38 and JNK; (c primary hepatocytes from mice fed a HFD showed decreased cellular oxygen consumption rates (indicative of mitochondrial functional impairment; this can be ascribed partly to a decreased expression of PGC1α and mitochondrial biogenesis. In brain, HFD feeding elicited (a an inactivation of the IRS-1 and, consequentially, (b a decreased expression and plasma membrane localization of the insulin-sensitive neuronal glucose transporters GLUT3/GLUT4; (c a suppression of the ERK/CREB pathway, and (d a substantial decrease in long-term potentiation in the CA1 region of hippocampus (indicative of impaired synaptic plasticity. It may be surmised that 12 weeks fed with HFD induce a systemic insulin resistance that impacts

  7. Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium

    NARCIS (Netherlands)

    Frangeul, L.; Quillardet, P.; Castets, A.M.; Humbert, J.F.; Matthijs, H.C.P.; Cortez, D.; Tolonen, A.; Zhang, C.C.; Gribaldo, S.; Kehr, J.C.; Zilliges, Y.; Ziemert, N.; Becker, S.; Talla, E.; Latifi, A.; Billault, A.; Lepelletier, A.; Dittmann, E.; Bouchier, C.; Tandeau de Marsac, N.

    2008-01-01

    Background The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There

  8. Genome of Plant Maca (Lepidium meyenii) Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes.

    Science.gov (United States)

    Zhang, Jing; Tian, Yang; Yan, Liang; Zhang, Guanghui; Wang, Xiao; Zeng, Yan; Zhang, Jiajin; Ma, Xiao; Tan, Yuntao; Long, Ni; Wang, Yangzi; Ma, Yujin; He, Yuqi; Xue, Yu; Hao, Shumei; Yang, Shengchao; Wang, Wen; Zhang, Liangsheng; Dong, Yang; Chen, Wei; Sheng, Jun

    2016-07-06

    Maca (Lepidium meyenii Walp, 2n = 8x = 64), belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru (4000-4500 m). Considering that the rapid uplift of the central Andes occurred 5-10 million years ago (Ma), an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications (WGDs; ∼6.7 Ma) were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes (i.e., small leaf shape and self-fertility) in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation (i.e., LEAF CURLING RESPONSIVENESS) and abiotic stress response (i.e., GLYCINE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION 2) under positive selection. Collectively, the maca genome provides useful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Study on elastic-plastic fracture toughness test in high temperature water

    International Nuclear Information System (INIS)

    Miura, Yasufumi

    2016-01-01

    Structural integrity of internal components in light water reactors is important for the safety of operation and service lifetime. Fracture toughness is important parameter for structural integrity assessment of nuclear power plant. In general, fracture toughness of materials which compose the components in light water reactor is obtained with fracture toughness tests in air although some components are subjected to high temperature water because of the difficulty of fracture toughness test in high temperature water. However, the effects of high temperature water and hydrogen on fracture behavior of the structural materials in nuclear power plant such as low alloy steel, cast austenitic stainless steel, and Ni base alloy are concerned recently. In this study, elastic-plastic fracture toughness test of low alloy steel in simulated BWR water environment was studied. Fracture toughness test in high temperature water with original clip gage and normalization data reduction technique was established. The difference of fracture toughness J_Q tested in air between using elastic unload compliance method and normalization data reduction technique was also discussed. As a result, obtained value with normalization data reduction technique tended to be higher than the value with elastic unload compliance. (author)

  10. Development of radiophotometric dosemeters with high sensitivity using plastic scintillators as a light intensifier

    International Nuclear Information System (INIS)

    Mesquita, C.H. de; Hamada, M.M.

    1987-01-01

    Rectangular plates of plastic scintillators are developed and their effect as light converter evaluated, when used as film-holder in conventional photography dosemeters. In this dosemeter, the radiation that not interacts in the photographic film can be detected by light photons generation in the plastic scintillators, sensitizing the film. (C.G.C.) [pt

  11. Low-temperature internal friction in high-purity monocrystalline and impure polycrystalline niobium after plastic deformation

    International Nuclear Information System (INIS)

    Wasserbaech, W.; Thompson, E.

    2001-01-01

    The internal friction Q -1 of plastically deformed, high-purity monocrystalline and impure polycrystalline niobium specimens was measured in the temperature range between 65 mK and about 2 K. Plastic deformation has a pronounced effect on the internal friction Q -1 of the high-purity monocrystalline specimens, and the effect has been found to be almost temperature independent. By contrast, surprisingly, the internal friction Q -1 of the impure polycrystalline specimens was found to be almost independent of the extent of plastic deformation. Comparison of the experimental results with different models of a dynamic scattering of acoustic phonons by dislocations leads to the conclusion that the results cannot be explained with the two-level tunneling model. Instead it is suggested that a strong interaction between acoustic phonons and geometrical kinks in non-screw dislocations is responsible for the observed internal friction Q -1 . (orig.)

  12. Plastic deformation

    NARCIS (Netherlands)

    Sitter, de L.U.

    1937-01-01

    § 1. Plastic deformation of solid matter under high confining pressures has been insufficiently studied. Jeffreys 1) devotes a few paragraphs to deformation of solid matter as a preface to his chapter on the isostasy problem. He distinguishes two properties of solid matter with regard to its

  13. Nonhomologous Recombination between Defective Poliovirus and Coxsackievirus Genomes Suggests a New Model of Genetic Plasticity for Picornaviruses

    Science.gov (United States)

    Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line

    2014-01-01

    ABSTRACT Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3′ end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. PMID:25096874

  14. A High-Rate, Single-Crystal Model including Phase Transformations, Plastic Slip, and Twinning

    Energy Technology Data Exchange (ETDEWEB)

    Addessio, Francis L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Bronkhorst, Curt Allan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Bolme, Cynthia Anne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Explosive Science and Shock Physics Division; Brown, Donald William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Cerreta, Ellen Kathleen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Lebensohn, Ricardo A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Lookman, Turab [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Luscher, Darby Jon [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Mayeur, Jason Rhea [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Morrow, Benjamin M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Rigg, Paulo A. [Washington State Univ., Pullman, WA (United States). Dept. of Physics. Inst. for Shock Physics

    2016-08-09

    An anisotropic, rate-­dependent, single-­crystal approach for modeling materials under the conditions of high strain rates and pressures is provided. The model includes the effects of large deformations, nonlinear elasticity, phase transformations, and plastic slip and twinning. It is envisioned that the model may be used to examine these coupled effects on the local deformation of materials that are subjected to ballistic impact or explosive loading. The model is formulated using a multiplicative decomposition of the deformation gradient. A plate impact experiment on a multi-­crystal sample of titanium was conducted. The particle velocities at the back surface of three crystal orientations relative to the direction of impact were measured. Molecular dynamics simulations were conducted to investigate the details of the high-­rate deformation and pursue issues related to the phase transformation for titanium. Simulations using the single crystal model were conducted and compared to the high-­rate experimental data for the impact loaded single crystals. The model was found to capture the features of the experiments.

  15. High Genomic Instability Predicts Survival in Metastatic High-Risk Neuroblastoma

    Directory of Open Access Journals (Sweden)

    Sara Stigliani

    2012-09-01

    Full Text Available We aimed to identify novel molecular prognostic markers to better predict relapse risk estimate for children with high-risk (HR metastatic neuroblastoma (NB. We performed genome- and/or transcriptome-wide analyses of 129 stage 4 HR NBs. Children older than 1 year of age were categorized as “short survivors” (dead of disease within 5 years from diagnosis and “long survivors” (alive with an overall survival time ≥ 5 years. We reported that patients with less than three segmental copy number aberrations in their tumor represent a molecularly defined subgroup with a high survival probability within the current HR group of patients. The complex genomic pattern is a prognostic marker independent of NB-associated chromosomal aberrations, i.e., MYCN amplification, 1p and 11q losses, and 17q gain. Integrative analysis of genomic and expression signatures demonstrated that fatal outcome is mainly associated with loss of cell cycle control and deregulation of Rho guanosine triphosphates (GTPases functioning in neuritogenesis. Tumors with MYCN amplification show a lower chromosome instability compared to MYCN single-copy NBs (P = .0008, dominated by 17q gain and 1p loss. Moreover, our results suggest that the MYCN amplification mainly drives disruption of neuronal differentiation and reduction of cell adhesion process involved in tumor invasion and metastasis. Further validation studies are warranted to establish this as a risk stratification for patients.

  16. Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats.

    Science.gov (United States)

    Karadjian, Gregory; Hassanin, Alexandre; Saintpierre, Benjamin; Gembu Tungaluna, Guy-Crispin; Ariey, Frederic; Ayala, Francisco J; Landau, Irene; Duval, Linda

    2016-08-30

    Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria's agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity.

  17. Persistent and plastic effects of temperature on DNA methylation across the genome of threespine stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Metzger, David C H; Schulte, Patricia M

    2017-10-11

    Epigenetic mechanisms such as changes in DNA methylation have the potential to affect the resilience of species to climate change, but little is known about the response of the methylome to changes in environmental temperature in animals. Using reduced representation bisulfite sequencing, we assessed the effects of development temperature and adult acclimation temperature on DNA methylation levels in threespine stickleback ( Gasterosteus aculeatus ). Across all treatments, we identified 2130 differentially methylated cytosines distributed across the genome. Both increases and decreases in temperature during development and with thermal acclimation in adults increased global DNA methylation levels. Approximately 25% of the differentially methylated regions (DMRs) responded to both developmental temperature and adult thermal acclimation, and 50 DMRs were common to all treatments, demonstrating a core response of the epigenome to thermal change at multiple time scales. We also identified differentially methylated loci that were specific to a particular developmental or adult thermal response, which could facilitate the accumulation of epigenetic variation between natural populations that experience different thermal regimes. These data demonstrate that thermal history can have long-lasting effects on the epigenome, highlighting the role of epigenetic modifications in the response to temperature change across multiple time scales. © 2017 The Author(s).

  18. New developments of RNAi in Paracoccidioides brasiliensis: prospects for high-throughput, genome-wide, functional genomics.

    Directory of Open Access Journals (Sweden)

    Tercio Goes

    2014-10-01

    Full Text Available The Fungal Genome Initiative of the Broad Institute, in partnership with the Paracoccidioides research community, has recently sequenced the genome of representative isolates of this human-pathogen dimorphic fungus: Pb18 (S1, Pb03 (PS2 and Pb01. The accomplishment of future high-throughput, genome-wide, functional genomics will rely upon appropriate molecular tools and straightforward techniques to streamline the generation of stable loss-of-function phenotypes. In the past decades, RNAi has emerged as the most robust genetic technique to modulate or to suppress gene expression in diverse eukaryotes, including fungi. These molecular tools and techniques, adapted for RNAi, were up until now unavailable for P. brasiliensis.In this paper, we report Agrobacterium tumefaciens mediated transformation of yeast cells for high-throughput applications with which higher transformation frequencies of 150±24 yeast cell transformants per 1×106 viable yeast cells were obtained. Our approach is based on a bifunctional selective marker fusion protein consisted of the Streptoalloteichus hindustanus bleomycin-resistance gene (Shble and the intrinsically fluorescent monomeric protein mCherry which was codon-optimized for heterologous expression in P. brasiliensis. We also report successful GP43 gene knock-down through the expression of intron-containing hairpin RNA (ihpRNA from a Gateway-adapted cassette (cALf which was purpose-built for gene silencing in a high-throughput manner. Gp43 transcript levels were reduced by 73.1±22.9% with this approach.We have a firm conviction that the genetic transformation technique and the molecular tools herein described will have a relevant contribution in future Paracoccidioides spp. functional genomics research.

  19. High-pressure plastic scintillation detector for measuring radiogenic gases in flow systems

    International Nuclear Information System (INIS)

    Schell, W.R.; Tobin, M.J.; Vives-Batlle, J.; Yoon, S.R.

    1999-01-01

    Radioactive gases are emitted into the atmosphere from nuclear electric power and nuclear fuel reprocessing plants, from hospitals discarding xenon used in diagnostic medicine, as well as from nuclear weapons tests. A high-pressure plastic scintillation detector was constructed to measure atmospheric levels of such radioactive gases by detecting the beta and internal conversion (IC) electron decays. Operational tests and calibrations were made that permit integration of the flow detectors into a portable Gas Analysis, Separation and Purification system (GASP). The equipment developed can be used for measuring fission gases released from nuclear reactor sources and/or as part of monitoring equipment for enforcing the Comprehensive Test Ban Treaty. The detector is being used routinely for in-line gas separation efficiency measurements, at the elevated operational pressures used for the high-pressure swing analysis system (2070 kPa) and at flow rates of 5-15 l/min. This paper presents the design features, operational methods, calibration, and detector applications. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  20. High-pressure plastic scintillation detector for measuring radiogenic gases in flow systems

    Science.gov (United States)

    Schell, W. R.; Vives-Batlle, J.; Yoon, S. R.; Tobin, M. J.

    1999-02-01

    Radioactive gases are emitted into the atmosphere from nuclear electric power and nuclear fuel reprocessing plants, from hospitals discarding xenon used in diagnostic medicine, as well as from nuclear weapons tests. A high-pressure plastic scintillation detector was constructed to measure atmospheric levels of such radioactive gases by detecting the beta and internal conversion (IC) electron decays. Operational tests and calibrations were made that permit integration of the flow detectors into a portable Gas Analysis, Separation and Purification system (GASP). The equipment developed can be used for measuring fission gases released from nuclear reactor sources and/or as part of monitoring equipment for enforcing the Comprehensive Test Ban Treaty. The detector is being used routinely for in-line gas separation efficiency measurements, at the elevated operational pressures used for the high-pressure swing analysis system (2070 kPa) and at flow rates of 5-15 l/min [1, 2]. This paper presents the design features, operational methods, calibration, and detector applications.

  1. High-pressure plastic scintillation detector for measuring radiogenic gases in flow systems

    International Nuclear Information System (INIS)

    Schell, W.R.; Vives-Batlle, J.; Yoon, S.R; Tobin, M.J.

    1999-01-01

    Radioactive gases are emitted into the atmosphere from nuclear electric power and nuclear fuel reprocessing plants, from hospitals discarding xenon used in diagnostic medicine, as well as from nuclear weapons tests. A high-pressure plastic scintillation detector was constructed to measure atmospheric levels of such radioactive gases by detecting the beta and internal conversion (IC) electron decays. Operational tests and calibrations were made that permit integration of the flow detectors into a portable Gas Analysis, Separation and Purification system (GASP). The equipment developed can be used for measuring fission gases released from nuclear reactor sources and/or as part of monitoring equipment for enforcing the Comprehensive Test Ban Treaty. The detector is being used routinely for in-line gas separation efficiency measurements, at the elevated operational pressures used for the high-pressure swing analysis system (2070 kPa) and at flow rates of 5-15 l/min . This paper presents the design features, operational methods, calibration, and detector applications

  2. Morphology and mechanical properties of PA12/plasticized starch blends prepared by high-shear extrusion

    International Nuclear Information System (INIS)

    Teyssandier, F.; Cassagnau, P.; Gérard, J.F.; Mignard, N.; Mélis, F.

    2012-01-01

    Highlights: ► High shear rate processing was found to greatly impact PA12/starch blend morphologies. ► The morphology was observed to be stable under subsequent processing conditions. ► The mechanical properties of the blends under high-shear rate were greatly improved. ► Polymer blend preparation via high-shear processing has proved to be very effective. ► Finally, polymer blends with improved mechanical properties were obtained. - Abstract: PA12/plasticized starch blends (PA12/TPS) were prepared by high-shear twin screw extruder. The morphology development and the mechanical properties of the blends were investigated as a function of the apparent shear rate. High-shear processing has proved to be an efficient method to finely disperse thermoplastic starch in polyamide 12 matrix. Blends containing TPS domains with a size at the nano-scale (R n ∼ 150 nm) homogeneously dispersed in PA12 matrix were obtained. From a modeling point of view, the variation of the droplet radius is closer to the Wu's predictions compared to the Serpe's predictions. From the basic hypothesis of these models, it can be then assumed that compatibilization between both phases occurs during the blend processing. Furthermore, this morphology of the blends has been proved to be stable after a reprocessing step in an internal mixer most likely due to either strong hydrogen bonds between the hydroxyl groups of starch and amide groups of polyamide 12 or to potentially cross reactions between macroradicals accounting for in situ formation of graft copolymers with the potential function of compatibilizers. Mechanical properties of the blends were found to be strongly dependent on the shear rate parameter of blend processing as the mechanical properties increase with shear rate. In agreement to the blend morphology, the elongation at break of the blends was greatly improved attesting of a good adhesion between both phases.

  3. Plastic condoms.

    Science.gov (United States)

    1968-01-01

    mandrel. The condom is then ready for packaging, either on automatic equipment or manually into small envelopes of highly polished paper. Although their present design is based on a heat-sealed blank, it may be possible shortly to manufacture plastic condoms on the same principle as rubber ones. A dipping process would be used, but with less sophisticated technology and with higher outputs per increment of capital investment. The present equipment used to make plastic condoms cost about 3,000 for one stamping machine and 22 assembly and testing machines. On a three shift per day, 300-day working year, it is possible, with experienced workers, to make 100,000 gross of plastic condoms for each manufacturing unit annually. As the technology is refined, the output should improve significantly.

  4. Development of radiophotometric dosemeters of high sensitivity using plastic scintillators as light intensifiers

    International Nuclear Information System (INIS)

    Mesquita, C.H. de; Hamada, M.M.

    1987-01-01

    The use of rectangular plates of plastic scintillators as film holders in conventional photographic dosemeters is reported. The efficiency of their use as light converters for increase the sensitivity of these dosemeters are studied. (M.A.C.) [pt

  5. Using NIF to Test Theories of High-Pressure, High-Rate Plastic Flow in Metals

    Science.gov (United States)

    Rudd, Robert E.; Arsenlis, A.; Cavallo, R. M.; Huntington, C. M.; McNaney, J. M.; Park, H. S.; Powell, P.; Prisbrey, S. T.; Remington, B. A.; Swift, D.; Wehrenberg, C. E.; Yang, L.

    2017-10-01

    Precisely controlled plasmas are playing key roles both as pump and probe in experiments to understand the strength of solid metals at high energy density (HED) conditions. In concert with theoretical advances, these experiments have enabled a predictive capability to model material strength at Mbar pressures and high strain rates. Here we describe multiscale strength models developed for tantalum starting with atomic bonding and extending up through the mobility of individual dislocations, the evolution of dislocation networks and so on until the ultimate material response at the scale of an experiment. Experiments at the National Ignition Facility (NIF) probe strength in metals ramp compressed to 1-8 Mbar. The model is able to predict 1 Mbar experiments without adjustable parameters. The combination of experiment and theory has shown that solid metals can behave significantly differently at HED conditions. We also describe recent studies of lead compressed to 3-5 Mbar. Work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA273.

  6. Analysis of high-throughput sequencing and annotation strategies for phage genomes.

    Directory of Open Access Journals (Sweden)

    Matthew R Henn

    Full Text Available BACKGROUND: Bacterial viruses (phages play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage. METHODOLOGY/PRINCIPAL FINDINGS: To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles, and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL or of a whole genome shotgun library (WGSL, or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling. CONCLUSIONS/SIGNIFICANCE: These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.

  7. Functional outcomes following lesions in visual cortex: Implications for plasticity of high-level vision.

    Science.gov (United States)

    Liu, Tina T; Behrmann, Marlene

    2017-10-01

    Understanding the nature and extent of neural plasticity in humans remains a key challenge for neuroscience. Importantly, however, a precise characterization of plasticity and its underlying mechanism has the potential to enable new approaches for enhancing reorganization of cortical function. Investigations of the impairment and subsequent recovery of cognitive and perceptual functions following early-onset cortical lesions in humans provide a unique opportunity to elucidate how the brain changes, adapts, and reorganizes. Specifically, here, we focus on restitution of visual function, and we review the findings on plasticity and re-organization of the ventral occipital temporal cortex (VOTC) in published reports of 46 patients with a lesion to or resection of the visual cortex early in life. Findings reveal that a lesion to the VOTC results in a deficit that affects the visual recognition of more than one category of stimuli (faces, objects and words). In addition, the majority of pediatric patients show limited recovery over time, especially those in whom deficits in low-level vision also persist. Last, given that neither the equipotentiality nor the modularity view on plasticity was clearly supported, we suggest some intermediate possibilities in which some plasticity may be evident but that this might depend on the area that was affected, its maturational trajectory as well as its structural and functional connectivity constraints. Finally, we offer suggestions for future research that can elucidate plasticity further. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. High efficient plastic solar cells fabricated with a high-throughput gravure printing method

    Energy Technology Data Exchange (ETDEWEB)

    Kopola, P.; Jin, H.; Tuomikoski, M.; Maaninen, A.; Hast, J. [VTT, Kaitovaeylae 1, FIN-90571 Oulu (Finland); Aernouts, T. [IMEC, Organic PhotoVoltaics, Polymer and Molecular Electronics, Kapeldreef 75, B-3001 Leuven (Belgium); Guillerez, S. [CEA-INES RDI, 50 Avenue Du Lac Leman, 73370 Le Bourget Du Lac (France)

    2010-10-15

    We report on polymer-based solar cells prepared by the high-throughput roll-to-roll gravure printing method. The engravings of the printing plate, along with process parameters like printing speed and ink properties, are studied to optimise the printability of the photoactive as well as the hole transport layer. For the hole transport layer, the focus is on testing different formulations to produce thorough wetting of the indium-tin-oxide (ITO) substrate. The challenge for the photoactive layer is to form a uniform layer with optimal nanomorphology in the poly-3-hexylthiophene (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blend. This results in a power conversion efficiency of 2.8% under simulated AM1.5G solar illumination for a solar cell device with gravure-printed hole transport and a photoactive layer. (author)

  9. Al based ultra-fine eutectic with high room temperature plasticity and elevated temperature strength

    Energy Technology Data Exchange (ETDEWEB)

    Tiwary, C.S., E-mail: cst311@gmail.com [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012, Karnataka (India); Kashyap, S. [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012, Karnataka (India); Kim, D.H. [Center for Non-Crystalline Materials, Department of Metallurgical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Chattopadhyay, K. [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012, Karnataka (India)

    2015-07-15

    Developments of aluminum alloys that can retain strength at and above 250 °C present a significant challenge. In this paper we report an ultrafine scale Al–Fe–Ni eutectic alloy with less than 3.5 at% transition metals that exhibits room temperature ultimate tensile strength of ~400 MPa with a tensile ductility of 6–8%. The yield stress under compression at 300 °C was found to be 150 MPa. We attribute it to the refinement of the microstructure that is achieved by suction casting in copper mold. The characterization using scanning and transmission electron microscopy (SEM and TEM) reveals an unique composite structure that contains the Al–Al{sub 3}Ni rod eutectic with spacing of ~90 nm enveloped by a lamellar eutectic of Al–Al{sub 9}FeNi (~140 nm). Observation of subsurface deformation under Vickers indentation using bonded interface technique reveals the presence of extensive shear banding during deformation that is responsible for the origin of ductility. The dislocation configuration in Al–Al{sub 3}Ni eutectic colony indicates accommodation of plasticity in α-Al with dislocation accumulation at the α-Al/Al{sub 3}Ni interface boundaries. In contrast the dislocation activities in the intermetallic lamellae are limited and contain set of planner dislocations across the plates. We present a detailed analysis of the fracture surface to rationalize the origin of the high strength and ductility in this class of potentially promising cast alloy.

  10. Testing of molded high temperature plastic actuator road seals for use in advanced aircraft hydraulic systems

    Science.gov (United States)

    Waterman, A. W.; Huxford, R. L.; Nelson, W. G.

    1976-01-01

    Molded high temperature plastic first and second stage rod seal elements were evaluated in seal assemblies to determine performance characteristics. These characteristics were compared with the performance of machined seal elements. The 6.35 cm second stage Chevron seal assembly was tested using molded Chevrons fabricated from five molding materials. Impulse screening tests conducted over a range of 311 K to 478 K revealed thermal setting deficiencies in the aromatic polyimide molding materials. Seal elements fabricated from aromatic copolyester materials structurally failed during impulse cycle calibration. Endurance testing of 3.85 million cycles at 450 K using MIL-H-83283 fluid showed poorer seal performance with the unfilled aromatic polyimide material than had been attained with seals machined from Vespel SP-21 material. The 6.35 cm first stage step-cut compression loaded seal ring fabricated from copolyester injection molding material failed structurally during impulse cycle calibration. Molding of complex shape rod seals was shown to be a potentially controllable technique, but additional molding material property testing is recommended.

  11. Design and test of a high resolution plastic scintillating fiber detector with intensified CCD readout

    International Nuclear Information System (INIS)

    Rebourgeard, P.

    1991-01-01

    We present the design of a particle detector involving a coherent array of 100 000 plastic scintillating microfibers, with an individual core diameter around 50 micrometers, and an intensified bidimensional CCD array. We investigate both theoretically and experimentally the use of polystyrene based scintillators in optical multimodal fibers. The isotropic excitation of modes and the characteristics of energy transfers between the polystyrene matrix and the added fluorescent dyes are of particular interest. An experimental approach is proposed and applied to the development of a new binary scintillator. In order to study the transmission of the signal from the interaction area to the output face, we specify the loss factors, the resolution and the signal to noise ratio within the fiber array. The low light level at the output face of the detector leads us to use image intensifiers in photon counting mode. This requires a detailed analysis of resolutions, gain, noise and detectivity concepts. We propose to describe these strongly correlated notions by the moment generation formalism. Thus, a previous modelisation of the photoelectronic devices allows us to evaluate the performance of the readout chain. A complete detector has been assembled and tested on a high energy hadron beam; the measurements are in good agreement with the modelisation [fr

  12. High Morphologic Plasticity of Microglia/Macrophages Following Experimental Intracerebral Hemorrhage in Rats

    Directory of Open Access Journals (Sweden)

    Shu-Sheng Yang

    2016-07-01

    Full Text Available As current efforts have limited effects on the clinical outcome of intracerebral hemorrhage (ICH, the mechanisms including microglia/macrophages that involved inflammation need further investigation. Here, 0.4 units of collagenase VII were injected into the left caudate putamen (CPu to duplicate ICH rat models. In the brains of ICH rats, microglia/macrophages, the nearest cells to the hemorrhagic center, were observed as ameboid and Prussian-blue positive. Furthermore, the ameboid microglia/macrophages were differentiation (CD 68 and interleukin-1β (IL-1β positive, and neither CD206 nor chitinase3-like 3 (Ym1 positive, suggesting their strong abilities of phagocytosis and secretion of IL-1β. According to the distance to the hemorrhagic center, we selected four areas—I, II, III, and IV—to analyze the morphology of microglia/macrophages. The processes decreased successively from region I to region IV. Microglia/macrophages in region IV had no processes. The processes in region I were radially distributed, however, they showed obvious directivity towards the hemorrhagic center in regions II and III. Region III had the largest density of compactly arrayed microglia/macrophages. All these in vivo results present the high morphologic plasticity of microglia/macrophages and their functions in the pathogenesis of ICHs.

  13. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

    Science.gov (United States)

    Feehan, Joanna M; Scheibel, Katherine E; Bourras, Salim; Underwood, William; Keller, Beat; Somerville, Shauna C

    2017-03-31

    The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

  14. Pinus pinaster seedlings and their fungal symbionts show high plasticity in phosphorus acquisition in acidic soils.

    Science.gov (United States)

    Ali, M A; Louche, J; Legname, E; Duchemin, M; Plassard, C

    2009-12-01

    Young seedlings of maritime pine (Pinus pinaster Soland in Aït.) were grown in rhizoboxes using intact spodosol soil samples from the southwest of France, in Landes of Gascogne, presenting a large variation of phosphorus (P) availability. Soils were collected from a 93-year-old unfertilized stand and a 13-year-old P. pinaster stand with regular annual fertilization of either only P or P and nitrogen (N). After 6 months of culture in controlled conditions, different morphotypes of ectomycorrhiza (ECM) were used for the measurements of acid phosphatase activity and molecular identification of fungal species using amplification of the ITS region. Total biomass, N and P contents were measured in roots and shoots of plants. Bicarbonate- and NaOH-available inorganic P (Pi), organic P (Po) and ergosterol concentrations were measured in bulk and rhizosphere soil. The results showed that bulk soil from the 93-year-old forest stand presented the highest Po levels, but relatively higher bicarbonate-extractable Pi levels compared to 13-year-old unfertilized stand. Fertilizers significantly increased the concentrations of inorganic P fractions in bulk soil. Ergosterol contents in rhizosphere soil were increased by fertilizer application. The dominant fungal species was Rhizopogon luteolus forming 66.6% of analysed ECM tips. Acid phosphatase activity was highly variable and varied inversely with bicarbonate-extractable Pi levels in the rhizosphere soil. Total P or total N in plants was linearly correlated with total plant biomass, but the slope was steep only between total P and biomass in fertilized soil samples. In spite of high phosphatase activity in ECM tips, P availability remained a limiting nutrient in soil samples from unfertilized stands. Nevertheless young P. pinaster seedlings showed a high plasticity for biomass production at low P availability in soils.

  15. Plastic fish

    CERN Multimedia

    Antonella Del Rosso

    2015-01-01

    In terms of weight, the plastic pollution in the world’s oceans is estimated to be around 300,000 tonnes. This plastic comes from both land-based and ocean-based sources. A lecture at CERN by chemist Wolfgang Trettnak addressed this issue and highlighted the role of art in raising people’s awareness.   Artwork by Wolfgang Trettnak. Packaging materials, consumer goods (shoes, kids’ toys, etc.), leftovers from fishing and aquaculture activities… our oceans and beaches are full of plastic litter. Most of the debris from beaches is plastic bottles. “PET bottles have high durability and stability,” explains Wolfgang Trettnak, a chemist by education and artist from Austria, who gave a lecture on this topic organised by the Staff Association at CERN on 26 May. “PET degrades very slowly and the estimated lifetime of a bottle is 450 years.” In addition to the beach litter accumulated from human use, rivers bring several ki...

  16. Thermo-elastic-plastic analysis for elastic component under high temperature fatigue crack growth rate

    Science.gov (United States)

    Ali, Mohammed Ali Nasser

    The research project presents a fundamental understanding of the fatigue crack growth mechanisms of AISI 420 martensitic stainless steel, based on the comparison analysis between the theoretical and numerical modelling, incorporating research findings under isothermal fatigue loading for solid cylindrical specimen and the theoretical modelling with the numerical simulation for tubular specimen when subjected to cyclic mechanical loading superimposed by cyclic thermal shock.The experimental part of this research programme studied the fatigue stress-life data for three types of surface conditions specimen and the isothermal stress-controlled fatigue testing at 300 °C - 600 °C temperature range. It is observed that the highest strength is obtained for the polished specimen, while the machined specimen shows lower strength, and the lowest strength is the notched specimen due to the high effect of the stress concentration. The material behaviour at room and high temperatures shows an initial hardening, followed by slow extension until fully plastic saturation then followed by crack initiation and growth eventually reaching the failure of the specimen, resulting from the dynamic strain ageing occurred from the transformation of austenitic microstructure to martensite and also, the nucleation of precipitation at grain boundaries and the incremental temperature increase the fatigue crack growth rate with stress intensity factor however, the crack growth rate at 600 °C test temperature is less than 500 °C because of the creep-fatigue taking place.The theoretical modelling presents the crack growth analysis and stress and strain intensity factor approaches analysed in two case studies based on the addition of thermo-elastic-plastic stresses to the experimental fatigue applied loading. Case study one estimates the thermal stresses superimposed sinusoidal cyclic mechanical stress results in solid cylinder under isothermal fatigue simulation. Case study two estimates the

  17. Pyrolysis-catalysis of waste plastic using a nickel-stainless-steel mesh catalyst for high-value carbon products.

    Science.gov (United States)

    Zhang, Yeshui; Nahil, Mohamad A; Wu, Chunfei; Williams, Paul T

    2017-11-01

    A stainless-steel mesh loaded with nickel catalyst was produced and used for the pyrolysis-catalysis of waste high-density polyethylene with the aim of producing high-value carbon products, including carbon nanotubes (CNTs). The catalysis temperature and plastic-to-catalyst ratio were investigated to determine the influence on the formation of different types of carbon deposited on the nickel-stainless-steel mesh catalyst. Increasing temperature from 700 to 900°C resulted in an increase in the carbon deposited on the nickel-loaded stainless-steel mesh catalyst from 32.5 to 38.0 wt%. The increase in sample-to-catalyst ratio reduced the amount of carbon deposited on the mesh catalyst in terms of g carbon g -1 plastic. The carbons were found to be largely composed of filamentous carbons, with negligible disordered (amorphous) carbons. Transmission electron microscopy analysis of the filamentous carbons revealed them to be composed of a large proportion (estimated at ∼40%) multi-walled carbon nanotubes (MWCNTs). The optimum process conditions for CNT production, in terms of yield and graphitic nature, determined by Raman spectroscopy, was catalysis temperature of 800°C and plastic-to-catalyst ratio of 1:2, where a mass of 334 mg of filamentous/MWCNTs g -1 plastic was produced.

  18. Processing real-world waste plastics by pyrolysis-reforming for hydrogen and high-value carbon nanotubes.

    Science.gov (United States)

    Wu, Chunfei; Nahil, Mohamad A; Miskolczi, Norbert; Huang, Jun; Williams, Paul T

    2014-01-01

    Producing both hydrogen and high-value carbon nanotubes (CNTs) derived from waste plastics is reported here using a pyrolysis-reforming technology comprising a two-stage reaction system, in the presence of steam and a Ni-Mn-Al catalyst. The waste plastics consisted of plastics from a motor oil container (MOC), commercial waste high density polyethylene (HDPE) and regranulated HDPE waste containing polyvinyl chloride (PVC). The results show that hydrogen can be produced from the pyrolysis-reforming process, but also carbon nanotubes are formed on the catalyst. However, the content of 0.3 wt.% polyvinyl chloride in the waste HDPE (HDPE/PVC) has been shown to poison the catalyst and significantly reduce the quantity and purity of CNTs. The presence of sulfur has shown less influence on the production of CNTs in terms of quantity and CNT morphologies. Around 94.4 mmol H2 g(-1) plastic was obtained for the pyrolysis-reforming of HDPE waste in the presence of the Ni-Mn-Al catalyst and steam at a reforming temperature of 800 °C. The addition of steam in the process results in an increase of hydrogen production and reduction of carbon yield; in addition, the defects of CNTs, for example, edge dislocations were found to be increased with the introduction of steam (from Raman analysis).

  19. Structural and mechanical behaviour of severe plastically deformed high purity aluminium sheets processed by constrained groove pressing technique

    International Nuclear Information System (INIS)

    Satheesh Kumar, S.S.; Raghu, T.

    2014-01-01

    Highlights: • High purity aluminium sheets constrained groove pressed up to plastic strain of 5.8. • Microstructural evolution studied by TEM and X-ray diffraction profile analysis. • Ultrafine grained structure with grain size ∼900 nm achieved in sheets. • Yield strength increased by 5.3 times and tensile strength doubled after first pass. • Enhanced deformation homogeneity seen with increased accumulated plastic strain. - Abstract: High purity aluminium sheets (∼99.9%) are subjected to intense plastic straining by constrained groove pressing method successfully up to 5 passes thereby imparting an effective plastic strain of 5.8. Transmission electron microscopy studies of constrained groove pressed sheets divulged significant grain refinement and the average grain sizes obtained after five pass is estimated to be ∼0.9 μm. In addition to that, microstructural evolution of constrained groove pressed sheets is characterized by X-ray diffraction peak profile analysis employing Williamson–Hall method and the results obtained fairly concur with electron microscopy findings. The tensile behaviour evolution with increased straining indicates substantial improvement of yield strength by ∼5.3 times from 17 MPa to 90 MPa during first pass corroborated to grain refinement observed. Marginal increase in strengths is noticed during second pass followed by minor drop in strengths attributed to predominance of dislocation recovery is noticed in subsequent passes. Quantitative assessment of degree of deformation homogeneity using microhardness profiles reveal relatively better strain homogeneity at higher number of passes

  20. Plastic Surgery

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Plastic Surgery KidsHealth / For Teens / Plastic Surgery What's in ... her forehead lightened with a laser? What Is Plastic Surgery? Just because the name includes the word " ...

  1. High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

    Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

  2. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

    Science.gov (United States)

    Holden, Matthew T; Carter, Matthew C D; Wu, Cheng-Hsien; Wolfer, Jamison; Codner, Eric; Sussman, Michael R; Lynn, David M; Smith, Lloyd M

    2015-11-17

    The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

  3. A model for plasticity kinetics and its role in simulating the dynamic behavior of Fe at high strain rates

    Energy Technology Data Exchange (ETDEWEB)

    Colvin, J D; Minich, R W; Kalantar, D H

    2007-03-29

    The recent diagnostic capability of the Omega laser to study solid-solid phase transitions at pressures greater than 10 GPa and at strain rates exceeding 10{sup 7} s{sup -1} has also provided valuable information on the dynamic elastic-plastic behavior of materials. We have found, for example, that plasticity kinetics modifies the effective loading and thermodynamic paths of the material. In this paper we derive a kinetics equation for the time-dependent plastic response of the material to dynamic loading, and describe the model's implementation in a radiation-hydrodynamics computer code. This model for plasticity kinetics incorporates the Gilman model for dislocation multiplication and saturation. We discuss the application of this model to the simulation of experimental velocity interferometry data for experiments on Omega in which Fe was shock compressed to pressures beyond the {alpha}-to-{var_epsilon} phase transition pressure. The kinetics model is shown to fit the data reasonably well in this high strain rate regime and further allows quantification of the relative contributions of dislocation multiplication and drag. The sensitivity of the observed signatures to the kinetics model parameters is presented.

  4. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

    OpenAIRE

    Aljanabi, S M; Martinez, I

    1997-01-01

    A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

  5. Production of high-calorie energy briquettes from bark waste, plastic and oil

    Science.gov (United States)

    Suwinarti, W.; Amirta, R.; Yuliansyah

    2018-04-01

    Bark is the waste generated from the utilization of plantation timber, while plastics and oil waste are produced from daily human activity. These waste has the potential to be used as energy briquettes raw materials, especially for fuel in power plants. It would be worth very strategic for the environment and the welfare of society, considering that at this time we are not yet fully capable of well managing all three waste types. On the other hands most of the power plants that operate today still use diesel and coal as fuel. Therefore, the best composition of mixing bark, plastic and oil will be studied as well as its influence on the physical and chemical quality of the briquettes produced. The results show that the addition of the oil waste (70%) and used plastic (30%) as additive give effect to the performance of the briquette formation with the highest calorific value of 33.56 MJ/kg.

  6. Comparison of plastic, high-density carbon, and beryllium as NIF ablators

    Science.gov (United States)

    Kritcher, Andrea

    2017-10-01

    An effort is underway to compare the three principal ablators for National Ignition Facility (NIF) implosions: plastic (CH), High Density Carbon (HDC), and beryllium (Be). This presentation will summarize the comparison and discuss in more detail the issues pertaining to hohlraum performance and symmetry. Several aspects of the hohlraum design are affected by the ablator properties, as the ablator constrains the first shock and determines the overall pulse length. HDC targets can utilize shorter pulse lengths due to the thinner, higher density shell, and should be less susceptible to late time wall motion. However, HDC requires a larger picket energy to ensure adequate melt, leading to increased late time wall movement. Be is intermediate to CH and HDC in both these regards, and has more ablated material in the hohlraum. These tradeoffs as well as other design choices for currently fielded campaigns are assessed in this work. To assess consistently the radiation drive and symmetry, integrated postshot simulations of the hohlraum and capsule were done for each design using the same methodology. The simulation results are compared to experimental data. Using this post-shot model, we make a projection of the relative plausible performance that can be achieved, while maintaining adequate symmetry, using the full NIF laser, i.e. 1.8 MJ/500 TW Full NIF Equivalent (FNE). The hydrodynamic stability of the different ablators is also an important consideration and will be presented for the current platforms and projection to FNE. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  7. A new approach to film dosimetry for high-energy photon beams using organic plastic scintillators

    International Nuclear Information System (INIS)

    Yeo, I.J.; Wang, C.-K.C.; Burch, S.E.

    1999-01-01

    Successful radiotherapy relies on accurate dose measurement. Traditional dosimeters such as ion chambers, TLDs and diodes have disadvantages such as relatively long measurement time and poor spatial resolution. These drawbacks become more serious problems for dynamic beams (i.e. with the use of dynamic wedges or even the intensity modulation technique). X-ray film, an integrating dosimeter, may not be associated with the above disadvantages and problems. However, there are several major issues regarding use of x-ray film for routine dosimetry, including the over-response of the film to low-energy photons, variations in the dose response curve (nonlinearity), lack of reproducibility due to variation in processing, etc. This paper addresses the first problem. That is, x-ray film over-responds to low-energy photons (energies below 400 keV), and thus generates unacceptably inaccurate dosimetric data compared with ion-chamber data. To overcome the over-response problem of x-ray film in a phantom, a scintillation method has been investigated. In this method, a film is sandwiched by two plastic scintillation screens to enhance the film response to upstream electrons, and therefore minimize the over-response caused by low-energy photons. The sandwiched system was tested with a 4 MV linac beam. The result shows that, depending on the uniformity of the scintillation screens, the depth-dose distribution obtained from the sandwich system can be made to agree well with that obtained from ion chambers. However, the required high degree of uniformity remains a challenge for the scintillation screen manufacturers. (author)

  8. Biodegradability of Plastics

    Directory of Open Access Journals (Sweden)

    Yutaka Tokiwa

    2009-08-01

    Full Text Available Plastic is a broad name given to different polymers with high molecular weight, which can be degraded by various processes. However, considering their abundance in the environment and their specificity in attacking plastics, biodegradation of plastics by microorganisms and enzymes seems to be the most effective process. When plastics are used as substrates for microorganisms, evaluation of their biodegradability should not only be based on their chemical structure, but also on their physical properties (melting point, glass transition temperature, crystallinity, storage modulus etc.. In this review, microbial and enzymatic biodegradation of plastics and some factors that affect their biodegradability are discussed.

  9. Biodegradability of plastics.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P; Ugwu, Charles U; Aiba, Seiichi

    2009-08-26

    Plastic is a broad name given to different polymers with high molecular weight, which can be degraded by various processes. However, considering their abundance in the environment and their specificity in attacking plastics, biodegradation of plastics by microorganisms and enzymes seems to be the most effective process. When plastics are used as substrates for microorganisms, evaluation of their biodegradability should not only be based on their chemical structure, but also on their physical properties (melting point, glass transition temperature, crystallinity, storage modulus etc.). In this review, microbial and enzymatic biodegradation of plastics and some factors that affect their biodegradability are discussed.

  10. Fabrication of highly crystalline oxide thin films on plastics: Sol–gel transfer technique involving high temperature process

    Directory of Open Access Journals (Sweden)

    Hiromitsu Kozuka

    2016-09-01

    Full Text Available Si(100 substrates were coated with a polyimide (PI–polyvinylpyrrolidone (PVP mixture film, and an alkoxide-derived TiO2 gel film was deposited on it by spin-coating. The gel films were fired under various conditions with final annealing at 600–1000 °C. The PI–PVP layer was completely decomposed at such high temperatures while the TiO2 films survived on Si(100 substrates without any damages. When the final annealing temperature was raised, the crystalline phase changed from anatase to rutile, and the crystallite size and the refractive index of the films tended to increase. The TiO2 films thus fired on Si(100 substrates were transferred to polycarbonate (PC substrates by melting the surface of the plastic substrate either in a near-infrared image furnace or on a hot plate under a load. Cycles of deposition and firing were found to be effective in achieving successful transfer even for the films finally annealed at 1000 °C. X-ray photoelectron spectroscopic analyses on the film/Si(100 interface suggested that the residual carbon or carbides at the interface could be a possible factor, but not a necessary and decisive factor that allows the film transfer.

  11. The High Degree of Sequence Plasticity of the Arenavirus Noncoding Intergenic Region (IGR) Enables the Use of a Nonviral Universal Synthetic IGR To Attenuate Arenaviruses.

    Science.gov (United States)

    Iwasaki, Masaharu; Cubitt, Beatrice; Sullivan, Brian M; de la Torre, Juan C

    2016-01-06

    Hemorrhagic fever arenaviruses (HFAs) pose important public health problems in regions where they are endemic. Concerns about human-pathogenic arenaviruses are exacerbated because of the lack of FDA-licensed arenavirus vaccines and because current antiarenaviral therapy is limited to an off-label use of ribavirin that is only partially effective. We have recently shown that the noncoding intergenic region (IGR) present in each arenavirus genome segment, the S and L segments (S-IGR and L-IGR, respectively), plays important roles in the control of virus protein expression and that this knowledge could be harnessed for the development of live-attenuated vaccine strains to combat HFAs. In this study, we further investigated the sequence plasticity of the arenavirus IGR. We demonstrate that recombinants of the prototypic arenavirus lymphocytic choriomeningitis virus (rLCMVs), whose S-IGRs were replaced by the S-IGR of Lassa virus (LASV) or an entirely nonviral S-IGR-like sequence (Ssyn), are viable, indicating that the function of S-IGR tolerates a high degree of sequence plasticity. In addition, rLCMVs whose L-IGRs were replaced by Ssyn or S-IGRs of the very distantly related reptarenavirus Golden Gate virus (GGV) were viable and severely attenuated in vivo but able to elicit protective immunity against a lethal challenge with wild-type LCMV. Our findings indicate that replacement of L-IGR by a nonviral Ssyn could serve as a universal molecular determinant of arenavirus attenuation. Hemorrhagic fever arenaviruses (HFAs) cause high rates of morbidity and mortality and pose important public health problems in regions where they are endemic. Implementation of live-attenuated vaccines (LAVs) will represent a major step to combat HFAs. Here we document that the arenavirus noncoding intergenic region (IGR) has a high degree of plasticity compatible with virus viability. This observation led us to generate recombinant LCMVs containing nonviral synthetic IGRs. These r

  12. Recent advances in high performance poly(lactide: From green plasticization to super-tough materials via (reactive compounding

    Directory of Open Access Journals (Sweden)

    Georgio eKfoury

    2013-12-01

    Full Text Available Due to its origin from renewable resources, its biodegradability, and recently, its industrial implementation at low costs, poly(lactide (PLA is considered as one of the most promising ecological, bio-sourced and biodegradable plastic materials to potentially and increasingly replace traditional petroleum derived polymers in many commodity and engineering applications. Beside its relatively high rigidity (high tensile strength and modulus compared with many common thermoplastics such as poly(ethylene terephthalate (PET, high impact poly(styrene (HIPS and poly(propylene (PP, PLA suffers from an inherent brittleness, which can limit its applications especially where mechanical toughness such as plastic deformation at high impact rates or elongation is required. Therefore, the curve plotting stiffness vs. impact resistance and ductility must be shifted to higher values for PLA-based materials, while being preferably fully bio-based and biodegradable upon the application.This review aims to establish a state of the art focused on the recent progresses and preferably economically viable strategies developed in the literature for significantly improve the mechanical performances of PLA. A particular attention is given to plasticization as well as to impact resistance modification of PLA in the case of (reactive blending PLA-based systems.

  13. Recent advances in high performance poly(lactide): From ``green'' plasticization to super-tough materials via (reactive) compounding

    Science.gov (United States)

    Kfoury, Georgio; Raquez, Jean-Marie; Hassouna, Fatima; Odent, Jérémy; Toniazzo, Valérie; Ruch, David; Dubois, Philippe

    2013-12-01

    Due to its origin from renewable resources, its biodegradability, and recently, its industrial implementation at low costs, poly(lactide) (PLA) is considered as one of the most promising ecological, bio-sourced and biodegradable plastic materials to potentially and increasingly replace traditional petroleum derived polymers in many commodity and engineering applications. Beside its relatively high rigidity (high tensile strength and modulus compared with many common thermoplastics such as poly(ethylene terephthalate) (PET), high impact poly(styrene) (HIPS) and poly(propylene) (PP)), PLA suffers from an inherent brittleness, which can limit its applications especially where mechanical toughness such as plastic deformation at high impact rates or elongation is required. Therefore, the curve plotting stiffness vs. impact resistance and ductility must be shifted to higher values for PLA-based materials, while being preferably fully bio-based and biodegradable upon the application. This review aims to establish a state of the art focused on the recent progresses and preferably economically viable strategies developed in the literature for significantly improve the mechanical performances of PLA. A particular attention is given to plasticization as well as to impact resistance modification of PLA in the case of (reactive) blending PLA-based systems.

  14. Mechanisms of large strain, high strain rate plastic flow in the explosively driven collapse of Ni-Al laminate cylinders

    International Nuclear Information System (INIS)

    Olney, K L; Chiu, P H; Nesterenko, V F; Higgins, A; Serge, M; Weihs, T P; Fritz, G; Stover, A; Benson, D J

    2014-01-01

    Ni-Al laminates have shown promise as reactive materials due to their high energy release through intermetallic reaction. In addition to the traditional ignition methods, the reaction may be initiated in hot spots that can be created during mechanical loading. The explosively driven thick walled cylinder (TWC) technique was performed on two Ni-Al laminates composed of thin foil layers with different mesostructues: concentric and corrugated. These experiments were conducted to examine how these materials accommodate large plastic strain under high strain rates. Finite element simulations of these specimens with mesostuctures digitized from the experimental samples were conducted to provide insight into the mesoscale mechanisms of plastic flow. The dependence of dynamic behaviour on mesostructure may be used to tailor the hot spot formation and therefore the reactivity of the material system.

  15. Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses

    Directory of Open Access Journals (Sweden)

    Widad Dantoft

    2017-09-01

    Full Text Available Neonates and especially premature infants are highly susceptible to infection but still can have a remarkable resilience that is poorly understood. The view that neonates have an incomplete or deficient immune system is changing. Human neonatal studies are challenging, and elucidating host protective responses and underlying cognate pathway biology, in the context of viral infection in early life, remains to be fully explored. In both resource rich and poor settings, human cytomegalovirus (HCMV is the most common cause of congenital infection. By using unbiased systems analyses of transcriptomic resources for HCMV neonatal infection, we find the systemic response of a preterm congenital HCMV infection, involves a focused IFN regulatory response associated with dendritic cells. Further analysis of transcriptional-programming of neonatal dendritic cells in response to HCMV infection in culture revealed an early dominant IFN-chemokine regulatory subnetworks, and at later times the plasticity of pathways implicated in cell-cycle control and lipid metabolism. Further, we identify previously unknown suppressed networks associated with infection, including a select group of GPCRs. Functional siRNA viral growth screen targeting 516-GPCRs and subsequent validation identified novel GPCR-dependent antiviral (ADORA1 and proviral (GPR146, RGS16, PTAFR, SCTR, GPR84, GPR85, NMUR2, FZ10, RDS, CCL17, and SORT1 roles. By contrast a gene family cluster of protocadherins is significantly differentially induced in neonatal cells, suggestive of possible immunomodulatory roles. Unexpectedly, programming responses of adult and neonatal dendritic cells, upon HCMV infection, demonstrated comparable quantitative and qualitative responses showing that functionally, neonatal dendritic cell are not overly compromised. However, a delay in responses of neonatal cells for IFN subnetworks in comparison with adult-derived cells are notable, suggestive of subtle plasticity

  16. Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses.

    Science.gov (United States)

    Dantoft, Widad; Martínez-Vicente, Pablo; Jafali, James; Pérez-Martínez, Lara; Martin, Kim; Kotzamanis, Konstantinos; Craigon, Marie; Auer, Manfred; Young, Neil T; Walsh, Paul; Marchant, Arnaud; Angulo, Ana; Forster, Thorsten; Ghazal, Peter

    2017-01-01

    Neonates and especially premature infants are highly susceptible to infection but still can have a remarkable resilience that is poorly understood. The view that neonates have an incomplete or deficient immune system is changing. Human neonatal studies are challenging, and elucidating host protective responses and underlying cognate pathway biology, in the context of viral infection in early life, remains to be fully explored. In both resource rich and poor settings, human cytomegalovirus (HCMV) is the most common cause of congenital infection. By using unbiased systems analyses of transcriptomic resources for HCMV neonatal infection, we find the systemic response of a preterm congenital HCMV infection, involves a focused IFN regulatory response associated with dendritic cells. Further analysis of transcriptional-programming of neonatal dendritic cells in response to HCMV infection in culture revealed an early dominant IFN-chemokine regulatory subnetworks, and at later times the plasticity of pathways implicated in cell-cycle control and lipid metabolism. Further, we identify previously unknown suppressed networks associated with infection, including a select group of GPCRs. Functional siRNA viral growth screen targeting 516-GPCRs and subsequent validation identified novel GPCR-dependent antiviral (ADORA1) and proviral (GPR146, RGS16, PTAFR, SCTR, GPR84, GPR85, NMUR2, FZ10, RDS, CCL17, and SORT1) roles. By contrast a gene family cluster of protocadherins is significantly differentially induced in neonatal cells, suggestive of possible immunomodulatory roles. Unexpectedly, programming responses of adult and neonatal dendritic cells, upon HCMV infection, demonstrated comparable quantitative and qualitative responses showing that functionally, neonatal dendritic cell are not overly compromised. However, a delay in responses of neonatal cells for IFN subnetworks in comparison with adult-derived cells are notable, suggestive of subtle plasticity differences. These

  17. Calculation of efficiency of high-energy neutron detection by plastic scintillators

    International Nuclear Information System (INIS)

    Telegin, Yu.N.

    1977-01-01

    A computer was used to calculate neutron (5-30O MeV) registration effeciencies with plastic scintillators 2,5,10, 20,30,40 and 50 cm thick. The results are shown in the form of tables. The contributions to efficiency of various processes have been analysed. The calculation results may be used in planning experiments with neutron counters

  18. Techno-economic evaluation of high temperature pyrolysis processes for mixed plastic waste.

    NARCIS (Netherlands)

    Westerhout, R.W.J.; Westerhout, R.W.J.; van Koningsbruggen, M.P.; van der Ham, Aloysius G.J.; Kuipers, J.A.M.; van Swaaij, Willibrordus Petrus Maria

    1998-01-01

    Three pyrolysis processes for Mixed Plastic Waste (MPW) with different reactors (Bubbling Fluidized Bed, Circulating Fluidized Bed and Rotating Cone Reactor, respectively BFB, CFB and RCR) were designed and evaluated. The estimated fixed capital investment for a 50 kton/year MPW pyrolysis plant

  19. MATHEMATICAL FORMULATION OF PLASTIC CHARACTERISTICS OF WIRE OF STEEL 70 AT HIGH-SPEED WIRE DRAWING

    Directory of Open Access Journals (Sweden)

    Yu. L. Bobarikin

    2011-01-01

    Full Text Available The carried out numerical experiments subject to initial and boundary conditions indicate that mathematical model of elastic-plastic characteristics of steel 90 can be used for numerical calculations of wire drawing routes for this grade of steel.

  20. Growth plasticity of the southern Iberian barbel along longitudinal gradients in a highly regulated Mediterranean basin.

    Directory of Open Access Journals (Sweden)

    Ana Sánchez-Pérez

    2015-11-01

    At the present, studied parameters show that L. sclateri presents a great phenotypic plasticity to adapt to flow changes. This study offers a multi sites perspective of the relationships between barbel growth traits and hydrological variability, providing water resources managers with needed perspective about the effect of human induced alteration of flow magnitudes and regimes.

  1. Elastic-plastic analysis of high speed rotors with no plane of symmetry

    International Nuclear Information System (INIS)

    Anantha Ramu, S.

    1981-01-01

    A general method of analysis of elastic plastic shells has been developed. The material of the shell is assumed to obey von Mises yield condition and a stress strain law on the basis of deformation theory of plasticity. The method permits an easy iterative solution of the complete set of coupled nonlinear differential equations. The iterative procedure is essentially the solution of the elastic problem several times with different sets of loads. The solution finally yields among other things, the location of the elastic-plastic boundary in the shell wall. The second approach suggested is a three-dimensional hexahedral isoparametric solid element. The computer program developed is capable of modelling perfectly plastic, bilinear as well as nonlinear strain hardening behaviour of materials. As an example, a radial impeller is analysed by both the approaches by idealizing it as a rotating conical shell. The complete history of plastification of the shell wall as the speed increases is determined. The results of both approaches are found to be in good agreement with each other. (orig./HP)

  2. Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians.

    Directory of Open Access Journals (Sweden)

    Jinchuan Xing

    Full Text Available Deedu (DU Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR, neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1, as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG. Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1 shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.

  3. Plasticity theory

    CERN Document Server

    Lubliner, Jacob

    2008-01-01

    The aim of Plasticity Theory is to provide a comprehensive introduction to the contemporary state of knowledge in basic plasticity theory and to its applications. It treats several areas not commonly found between the covers of a single book: the physics of plasticity, constitutive theory, dynamic plasticity, large-deformation plasticity, and numerical methods, in addition to a representative survey of problems treated by classical methods, such as elastic-plastic problems, plane plastic flow, and limit analysis; the problem discussed come from areas of interest to mechanical, structural, and

  4. On the ability of some cyclic plasticity models to predict the evolution of stored energy in a type 304L stainless steel submitted to high cycle fatigue

    International Nuclear Information System (INIS)

    Vincent, L.

    2008-01-01

    Fatigue analyses of materials are generally based on a so-called stabilized cycle, on which plastic strain amplitude, plastic energy, maximum shear stress and so on are determined. The part of plastic energy which is dissipated in heat cannot be used to accumulate damage and it should be worthwhile extracting only the part of plastic energy which is stored in material microstructure in order to build a consistent damage model. In this paper, some cyclic plasticity models including a polycrystalline model are reformulated in the thermodynamic framework in order to test their capacity to predict both the stress-strain behaviour and the partition of plastic energy for a high cycle fatigue test on a type 304L stainless steel. For an equivalent description of stress-strain loops, the number of kinematic hardening variables chosen in a model may qualitatively alter the prediction of plastic energy partition due to the modification of the isotropic hardening variable. Measurements of the specimen temperature increase due to plastic dissipation is therefore proposed as a convenient complementary experimental data to identify the constitutive equation of the isotropic hardening variable of a cyclic plasticity model. (author)

  5. High-throughput sequencing of three Lemnoideae (duckweeds chloroplast genomes from total DNA.

    Directory of Open Access Journals (Sweden)

    Wenqin Wang

    Full Text Available BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power.

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

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

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

  7. Effects of Friction and Anvil Design on Plastic Deformation during the Compression Stage of High-Pressure Torsion

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yuepeng; Chen, Miaomiao; Xu, Baoyan; Guo, Jing; Xu, Lingfeng; Wang, Zheng [Mechanical and Electronic Engineering College, Tai’an (China); Gao, Dongsheng [Shandong Provincial Key Laboratory of Horticultural Machineries and Equipments, Tai’an (China); Kim, Hyoung Seop [Department of Materials Science and Engineering, Pohang (Korea, Republic of)

    2016-11-15

    Herein, we report the results of our investigation on the effect of friction and anvil design on the heterogeneous plastic-deformation characteristics of copper during the compressive stage of high-pressure torsion (HPT), using the finite element method. The results indicate that the friction and anvil geometry play important roles in the homogeneity of the deformation. These variables affect the heterogeneous level of strain in the HPT compressed disks, as well as the flash in the disk edge region. The heterogeneous plastic deformation of the disks becomes more severe with the increasing depth of the cavity, as anvil angle and friction coefficient increase. However, the homogeneity increases with increases in the wall angle. The length of flash and the area of the dead metal zone increase with the depth of the cavity, while they decrease at a wall angle of 180°.

  8. Plastic scintillators with {beta}-diketone Eu complexes for high ionizing radiation detection

    Energy Technology Data Exchange (ETDEWEB)

    Adadurov, A.F., E-mail: adadurov@isma.kharkov.ua [Institute for Scintillating Materials, NAN of Ukraine, Lenin Avenue 60, 61001 Kharkov (Ukraine); Zhmurin, P.N.; Lebedev, V.N.; Kovalenko, V.N. [Institute for Scintillating Materials, NAN of Ukraine, Lenin Avenue 60, 61001 Kharkov (Ukraine)

    2011-10-15

    Luminescent and scintillation properties of polystyrene-based plastic scintillators with {beta}-diketone Eu complexes are investigated. A scintillator with dibenzoylmethane Eu complex containing two phenyl groups demonstrates the maximum scintillating efficiency. It is shown that plastic scintillators efficiency is dramatically decreased if {beta}-diketone derivatives contain no phenyl groups as substituents. This fact can be explained by exciplex mechanism of energy transfer from a matrix to Eu complex. - Highlights: > Fluorescent properties of polystyrene scintillators with {beta}-diketone complexes of Eu were studied. > Scintillating efficiency is increased with the number of phenyl groups in Eu complex. > This is related to exciplex mechanism of energy transfer from a polymer matrix to Eu complex.

  9. Plastic scintillators with β-diketone Eu complexes for high ionizing radiation detection

    International Nuclear Information System (INIS)

    Adadurov, A.F.; Zhmurin, P.N.; Lebedev, V.N.; Kovalenko, V.N.

    2011-01-01

    Luminescent and scintillation properties of polystyrene-based plastic scintillators with β-diketone Eu complexes are investigated. A scintillator with dibenzoylmethane Eu complex containing two phenyl groups demonstrates the maximum scintillating efficiency. It is shown that plastic scintillators efficiency is dramatically decreased if β-diketone derivatives contain no phenyl groups as substituents. This fact can be explained by exciplex mechanism of energy transfer from a matrix to Eu complex. - Highlights: → Fluorescent properties of polystyrene scintillators with β-diketone complexes of Eu were studied. → Scintillating efficiency is increased with the number of phenyl groups in Eu complex. → This is related to exciplex mechanism of energy transfer from a polymer matrix to Eu complex.

  10. High flux operation of microstrip gas chambers on glass and plastic supports

    International Nuclear Information System (INIS)

    Bouclier, R.; Florent, J.J.; Gaudaen, J.; Millon, G.; Pasta, A.; Ropelewski, L.; Sauli, F.; Shekhtman, L.I.

    1992-01-01

    Recent observations on microstrip gas chambers realized on various glass and plastic supports are presented in this paper. Short term measurements indicate a rate capability up to and above 5x10 5 counts/s mm 2 . A long term exposure to radiation shows however gain modifications, dependent on the resistivity of the chamber substrate; a choice of low resistivity supports minimizes this effect. (orig.)

  11. A Conservative Formulation for Plasticity

    Science.gov (United States)

    1992-01-01

    concepts that apply to a broad class of macroscopic models: plastic deformation and plastic flow rule. CONSERVATIVE PLASTICITY 469 3a. Plastic Defrrnation...temperature. We illustrate these concepts with a model that has been used to describe high strain-rate plastic flow in metals [11, 31, 32]. In the case...JOURDREN, AND P. VEYSSEYRE. Un Modele ttyperelastique- Plastique Euldrien Applicable aux Grandes Dtformations: Que/ques R~sultats 1-D. preprint, 1991. 2. P

  12. Effect of steel fibers on plastic shrinkage cracking of normal and high strength concretes

    Directory of Open Access Journals (Sweden)

    Özgür Eren

    2010-06-01

    Full Text Available Naturally concrete shrinks when it is subjected to a drying environment. If this shrinkage is restrained, tensile stresses develop and concrete may crack. Plastic shrinkage cracks are especially harmful on slabs. One of the methods to reduce the adverse effects of shrinkage cracking of concrete is by reinforcing concrete with short randomly distributed fibers. The main objective of this study was to investigate the effect of fiber volume and aspect ratio of hooked steel fibers on plastic shrinkage cracking behavior together with some other properties of concrete. In this research two different compressive strength levels namely 56 and 73 MPa were studied. Concretes were produced by adding steel fibers of 3 different volumes of 3 different aspect ratios. From this research study, it is observed that steel fibers can significantly reduce plastic shrinkage cracking behavior of concretes. On the other hand, it was observed that these steel fibers can adversely affect some other properties of concrete during fresh and hardened states.

  13. Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

    International Nuclear Information System (INIS)

    Tak, Yu Kyung; Kim, Won Young; Kim, Min Jung; Han, Eunyoung; Han, Myun Soo; Kim, Jong Jin; Kim, Wook; Lee, Jong Eun; Song, Joon Myong

    2012-01-01

    Highlights: ► Genomic DNA quantification were performed using a quantum dot-labeled Alu sequence. ► This probe provided PCR-free determination of human genomic DNA. ► Qdot-labeled Alu probe-hybridized genomic DNAs had a 2.5-femtogram detection limit. ► Qdot-labeled Alu sequence was used to assess DNA samples for human identification. - Abstract: Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.

  14. High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge.

    Science.gov (United States)

    Cabrera-Bosquet, Llorenç; Crossa, José; von Zitzewitz, Jarislav; Serret, María Dolors; Araus, José Luis

    2012-05-01

    Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding community from both the public and private sectors world-wide. Both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Whereas high-throughput phenotyping may help to improve understanding of crop physiology, most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and comparable to genomic selection. Despite the fact that the two methodological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome), they both consider the targeted traits (e.g. grain yield, growth, phenology, plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e. physiological) putatively related to the target trait. Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology. This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield. © 2012 Institute of Botany, Chinese Academy of Sciences.

  15. Localization of plastic yield and fracture mechanism in high-strength niobium alloy with ultra-fine particles of non-metallic phase

    International Nuclear Information System (INIS)

    Tyumentsev, A.N.; Gonchikov, V.Ch.; Korotaev, A.D.; Pinzhin, Yu.P.; Tyumentseva, S.F.

    1989-01-01

    The regularities of localization of plastic flow in high-strength dispersion-strengthened niobium alloy are studied. On the basis of investigations of the microstructure of strain localization zones the mechanism of stability losses of plastic flow including, the processes of diffusion of nonequilibrium vacancies in fields of nonuniform stresses, is proposed. The role of diffuse strain mechanisms during reorientation of the crystalline lattice is discussed. The regularities of fracture of high-strength alloy under conditions of rotational-shift instability of plastic flow are investigated

  16. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

    Science.gov (United States)

    Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

    2017-11-16

    Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the

  17. Plastic deformation of FeSi at high pressures: implications for planetary cores

    Science.gov (United States)

    Kupenko, Ilya; Merkel, Sébastien; Achorner, Melissa; Plückthun, Christian; Liermann, Hanns-Peter; Sanchez-Valle, Carmen

    2017-04-01

    The cores of terrestrial planets is mostly comprised of a Fe-Ni alloy, but it should additionally contain some light element(s) in order to explain the observed core density. Silicon has long been considered as a likely candidate because of geochemical and cosmochemical arguments: the Mg/Si and Fe/Si ratios of the Earth does not match those of the chondrites. Since silicon preferentially partition into iron-nickel metal, having 'missing' silicon in the core would solve this problem. Moreover, the evidence of present (e.g. Mercury) or ancient (e.g. Mars) magnetic fields on the terrestrial planets is a good indicator of (at least partially) liquid cores. The estimated temperature profiles of these planets, however, lay below iron melting curve. The addition of light elements in their metal cores could allow reducing their core-alloy melting temperature and, hence, the generation of a magnetic field. Although the effect of light elements on the stability and elasticity of Fe-Ni alloys has been widely investigated, their effect on the plasticity of core materials remains largely unknown. Yet, this information is crucial for understanding how planetary cores deform. Here we investigate the plastic deformation of ɛ-FeSi up to 50 GPa at room temperature employing a technique of radial x-ray diffraction in diamond anvil cells. Stoichiometric FeSi endmember is a good first-order approximation of the Fe-FeSi system and a good starting material to develop new experimental perspectives. In this work, we focused on the low-pressure polymorph of FeSi that would be the stable phase in the cores of small terrestrial planets. We will present the analysis of measured data and discuss their potential application to constrain plastic deformation in planetary cores.

  18. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Directory of Open Access Journals (Sweden)

    Pengpeng Li

    Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  19. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  20. Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

  1. Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data.

    Science.gov (United States)

    Li, Shu-Fen; Gao, Wu-Jun; Zhao, Xin-Peng; Dong, Tian-Yu; Deng, Chuan-Liang; Lu, Long-Dou

    2014-01-01

    Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

  2. A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

    Science.gov (United States)

    Nowell, Reuben W; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J; Wheat, Christopher W; Saastamoinen, Marjo; Saccheri, Ilik J; Van't Hof, Arjen E; Wasik, Bethany R; Connahs, Heidi; Aslam, Muhammad L; Kumar, Sujai; Challis, Richard J; Monteiro, Antónia; Brakefield, Paul M; Blaxter, Mark

    2017-07-01

    The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). © The Authors 2017. Published by Oxford University Press.

  3. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

    Directory of Open Access Journals (Sweden)

    Walid Mottawea

    2018-05-01

    Full Text Available Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

  4. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

    Science.gov (United States)

    2011-01-01

    Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across

  5. Distinct genetic architectures for phenotype means and plasticities in Zea mays.

    Science.gov (United States)

    Kusmec, Aaron; Srinivasan, Srikant; Nettleton, Dan; Schnable, Patrick S

    2017-09-01

    Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.

  6. Optical design and development of a fiber coupled high-power diode laser system for laser transmission welding of plastics

    Science.gov (United States)

    Rodríguez-Vidal, Eva; Quintana, Iban; Etxarri, Jon; Azkorbebeitia, Urko; Otaduy, Deitze; González, Francisco; Moreno, Fernando

    2012-12-01

    Laser transmission welding (LTW) of thermoplastics is a direct bonding technique already used in different industrial applications sectors such as automobiles, microfluidics, electronics, and biomedicine. LTW evolves localized heating at the interface of two pieces of plastic to be joined. One of the plastic pieces needs to be optically transparent to the laser radiation whereas the other part has to be absorbent, being that the radiation produced by high power diode lasers is a good alternative for this process. As consequence, a tailored laser system has been designed and developed to obtain high quality weld seams with weld widths between 0.7 and 1.4 mm. The developed laser system consists of two diode laser bars (50 W per bar) coupled into an optical fiber using a nonimaging solution: equalization of the beam parameter product (BPP) in the slow and fast axes by a pair of step-mirrors. The power scaling was carried out by means of a multiplexing polarization technique. The analysis of energy balance and beam quality was performed considering ray tracing simulation (ZEMAX) and experimental validation. The welding experiments were conducted on acrylonitrile/butadiene/styrene (ABS), a thermoplastic frequently used in automotive, electronics and aircraft applications, doped with two different concentrations of carbon nanotubes (0.01% and 0.05% CNTs). Quality of the weld seams on ABS was analyzed in terms of the process parameters (welding speed, laser power and clamping pressure) by visual and optical microscope inspections. Mechanical properties of weld seams were analyzed by mechanical shear tests. High quality weld seams were produced in ABS, revealing the potential of the laser developed in this work for a wide range of plastic welding applications.

  7. Study by dislocation dynamics simulations of radiation effects on the plasticity of ferrite at high temperature

    International Nuclear Information System (INIS)

    Shi, Xiangjun

    2014-01-01

    This study is a contribution to the multi-scale modeling of hardening and embrittlement of the vessel steel in Pressurized Water Reactors (PWR) under irradiation conditions. Dislocation Dynamics simulations (DD) were conducted to describe the plasticity of irradiated iron at grain scale. Quantitative information about the pinning strength of radiation-induced loops was extracted and can be transferred at crystal plasticity scale. Elementary interactions between an edge dislocation and different types of loops were first analyzed. A new model of DD was identified and validated, both qualitatively in terms of interaction mechanisms and quantitatively in terms of critical stress, using Molecular Dynamics results available in the literature. The influence of the size of the loops and of the strain rate was particularly studied. Elementary simulations involving a screw dislocation and the same radiation-induced defects were conducted and carefully compared to available MD results, extending the range of validity of our model. Finally, a set of massive simulations involving an edge dislocation and a large number of loops was performed and allowed a first estimation of the obstacle strength for this type of defects (α≅0.26). This value is in a good agreement with previous experimental and numerical studies, and gives us confidence in future work based on this new DD model. (author) [fr

  8. Analysis of trophic interactions reveals highly plastic response to climate change in a tri-trophic High-Arctic ecosystem

    DEFF Research Database (Denmark)

    Mortensen, Lars O.; Schmidt, Niels Martin; Hoye, Toke T.

    2016-01-01

    As a response to current climate changes, individual species have changed various biological traits, illustrating an inherent phenotypic plasticity. However, as species are embedded in an ecological network characterised by multiple consumer-resource interactions, ecological mismatches are likely...... to arise when interacting species do not respond homogeneously. The approach of biological networks analysis calls for the use of structural equation modelling (SEM), a multidimensional analytical setup that has proven particularly useful for analysing multiple interactions across trophic levels. Here we...

  9. Comparative genome analysis of the high pathogenicity Salmonella Typhimurium strain UK-1.

    Directory of Open Access Journals (Sweden)

    Yingqin Luo

    Full Text Available Salmonella enterica serovar Typhimurium, a gram-negative facultative rod-shaped bacterium causing salmonellosis and foodborne disease, is one of the most common isolated Salmonella serovars in both developed and developing nations. Several S. Typhimurium genomes have been completed and many more genome-sequencing projects are underway. Comparative genome analysis of the multiple strains leads to a better understanding of the evolution of S. Typhimurium and its pathogenesis. S. Typhimurium strain UK-1 (belongs to phage type 1 is highly virulent when orally administered to mice and chickens and efficiently colonizes lymphoid tissues of these species. These characteristics make this strain a good choice for use in vaccine development. In fact, UK-1 has been used as the parent strain for a number of nonrecombinant and recombinant vaccine strains, including several commercial vaccines for poultry. In this study, we conducted a thorough comparative genome analysis of the UK-1 strain with other S. Typhimurium strains and examined the phenotypic impact of several genomic differences. Whole genomic comparison highlights an extremely close relationship between the UK-1 strain and other S. Typhimurium strains; however, many interesting genetic and genomic variations specific to UK-1 were explored. In particular, the deletion of a UK-1-specific gene that is highly similar to the gene encoding the T3SS effector protein NleC exhibited a significant decrease in oral virulence in BALB/c mice. The complete genetic complements in UK-1, especially those elements that contribute to virulence or aid in determining the diversity within bacterial species, provide key information in evaluating the functional characterization of important genetic determinants and for development of vaccines.

  10. Effects of exercise and diet change on cognition function and synaptic plasticity in high fat diet induced obese rats

    Science.gov (United States)

    2013-01-01

    Background Nutritional imbalance-induced obesity causes a variety of diseases and in particular is an important cause of cognitive function decline. This study was performed on Sprague Dawley (SD) rats with 13-weeks of high fat diet-induced obesity in connection to the effects of regular exercise and dietary control for 8 weeks on the synaptic plasticity and cognitive abilities of brain. Methods Four weeks-old SD rats were adopted classified into normal-normal diet-sedentary (NNS, n = 8), obesity-high fat diet-sedentary (OHS, n = 8), obesity-high fat diet-training (OHT, n = 8), obesity-normal diet-sedentary (ONS, n = 8) and obesity- normal diet-training (ONT, n = 8). The exercise program consisted of a treadmill exercise administered at a speed of 8 m/min for 1–4 weeks, and 14 m/min for 5–8 weeks. The Western blot method was used to measure the expression of NGF, BDNF, p38MAPK and p-p38MAPK proteins in hippocampus of the brain, and expressions of NGF, BDNF, TrkA, TrkB, CREB and synapsin1 mRNA were analyzed through qRT-PCR. Results The results suggest cognitive function-related protein levels and mRNA expression to be significantly decreased in the hippocampus of obese rats, and synaptic plasticity as well as cognitive function signaling sub-pathway factors were also significantly decreased. In addition, 8-weeks exercises and treatment by dietary change had induced significant increase of cognitive function-related protein levels and mRNA expression as well as synaptic plasticity and cognitive function signaling sub-pathway factors in obese rats. In particular, the combined treatment had presented even more positive effect. Conclusions Therefore, it was determined that the high fat diet-induced obesity decreases plasticity and cognitive function of the brain, but was identified as being improved by exercises and dietary changes. In particular, it is considered that regular exercise has positive effects on memory span and learning

  11. Mechanical energy losses in plastically deformed and electron plus neutron irradiated high purity single crystalline molybdenum at elevated temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Zelada, Griselda I. [Laboratorio de Materiales, Escuela de Ingenieria Electrica, Facultad de Ciencias Exactas, Ingenieria y Agrimensura, Universidad Nacional de Rosario, Avda. Pellegrini 250, 2000 Rosario (Argentina); Lambri, Osvaldo Agustin [Laboratorio de Materiales, Escuela de Ingenieria Electrica, Facultad de Ciencias Exactas, Ingenieria y Agrimensura, Universidad Nacional de Rosario, Avda. Pellegrini 250, 2000 Rosario (Argentina); Instituto de Fisica Rosario - CONICET, Member of the CONICET& #x27; s Research Staff, Avda. Pellegrini 250, 2000 Rosario (Argentina); Bozzano, Patricia B. [Laboratorio de Microscopia Electronica, Unidad de Actividad Materiales, Centro Atomico Constituyentes, Comision Nacional de Energia Atomica, Avda. Gral. Paz 1499, 1650 San Martin (Argentina); Garcia, Jose Angel [Departamento de Fisica Aplicada II, Facultad de Ciencias y Tecnologia, Universidad del Pais Vasco, Apdo. 644, 48080 Bilbao, Pais Vasco (Spain)

    2012-10-15

    Mechanical spectroscopy (MS) and transmission electron microscopy (TEM) studies have been performed in plastically deformed and electron plus neutron irradiated high purity single crystalline molybdenum, oriented for single slip, in order to study the dislocation dynamics in the temperature range within one third of the melting temperature. A damping peak related to the interaction of dislocation lines with both prismatic loops and tangles of dislocations was found. The peak temperature ranges between 900 and 1050 K, for an oscillating frequency of about 1 Hz. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Genomics approaches to unlock the high yield potential of cassava, a tropical model plant

    Directory of Open Access Journals (Sweden)

    Shengkui ZHANG,Ping'an MA,Haiyan WANG,Cheng LU,Xin CHEN,Zhiqiang XIA,Meiling ZOU,Xinchen ZHOU,Wenquan WANG

    2014-12-01

    Full Text Available Cassava, a tropical food, feed and biofuel crop, has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition, which makes it highly suitable as a model plant for tropical crops. However, the understanding of the metabolism and genomics of this important crop is limited. The recent breakthroughs in the genomics of cassava, including whole-genome sequencing and transcriptome analysis, as well as advances in the biology of photosynthesis, starch biosynthesis, adaptation to drought and high temperature, and resistance to virus and bacterial diseases, are reviewed here. Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars. Finally, the current challenges and future potential of cassava as a model plant are discussed.

  13. A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.

    Directory of Open Access Journals (Sweden)

    Anna V Protasio

    2012-01-01

    Full Text Available Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq from four time points in the parasite's life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has been reduced from 11,807 to 10,852. Using the new version of the genome, we identified trans-splicing events occurring in at least 11% of genes and identified clear cases where it is used to resolve polycistronic transcripts. We have produced a high-resolution map of temporal changes in expression for 9,535 genes, covering an unprecedented dynamic range for this organism. All of these data have been consolidated into a searchable format within the GeneDB (www.genedb.org and SchistoDB (www.schistodb.net databases. With further transcriptional profiling and genome sequencing increasingly accessible, the upgraded genome will form a fundamental dataset to underpin further advances in schistosome research.

  14. High affinity antigen recognition of the dual specific variants of herceptin is entropy-driven in spite of structural plasticity.

    Directory of Open Access Journals (Sweden)

    Jenny Bostrom

    Full Text Available The antigen-binding site of Herceptin, an anti-human Epidermal Growth Factor Receptor 2 (HER2 antibody, was engineered to add a second specificity toward Vascular Endothelial Growth Factor (VEGF to create a high affinity two-in-one antibody bH1. Crystal structures of bH1 in complex with either antigen showed that, in comparison to Herceptin, this antibody exhibited greater conformational variability, also called "structural plasticity". Here, we analyzed the biophysical and thermodynamic properties of the dual specific variants of Herceptin to understand how a single antibody binds two unrelated protein antigens. We showed that while bH1 and the affinity-improved bH1-44, in particular, maintained many properties of Herceptin including binding affinity, kinetics and the use of residues for antigen recognition, they differed in the binding thermodynamics. The interactions of bH1 and its variants with both antigens were characterized by large favorable entropy changes whereas the Herceptin/HER2 interaction involved a large favorable enthalpy change. By dissecting the total entropy change and the energy barrier for dual interaction, we determined that the significant structural plasticity of the bH1 antibodies demanded by the dual specificity did not translate into the expected increase of entropic penalty relative to Herceptin. Clearly, dual antigen recognition of the Herceptin variants involves divergent antibody conformations of nearly equivalent energetic states. Hence, increasing the structural plasticity of an antigen-binding site without increasing the entropic cost may play a role for antibodies to evolve multi-specificity. Our report represents the first comprehensive biophysical analysis of a high affinity dual specific antibody binding two unrelated protein antigens, furthering our understanding of the thermodynamics that drive the vast antigen recognition capacity of the antibody repertoire.

  15. Ultrathin film, high specific power InP solar cells on flexible plastic substrates

    International Nuclear Information System (INIS)

    Shiu, K.-T.; Zimmerman, Jeramy; Wang Hongyu; Forrest, Stephen R.

    2009-01-01

    We demonstrate ultrathin-film, single-crystal InP Schottky-type solar cells mounted on flexible plastic substrates. The lightly p-doped InP cell is grown epitaxially on an InP substrate via gas source molecular beam epitaxy. The InP substrate is removed via selective chemical wet-etching after the epitaxial layers are cold-welded to a 25 μm thick Kapton sheet, followed by the deposition of an indium tin oxide top contact that forms the Schottky barrier with InP. The power conversion efficiency under 1 sun is 10.2±1.0%, and its specific power is 2.0±0.2 kW/kg. The ultrathin-film solar cells can tolerate both tensile and compressive stress by bending over a <1 cm radius without damage.

  16. Muscle and plastic equivalent glass dosimeter for high-dose dosimetry

    International Nuclear Information System (INIS)

    Abdel-Rehim, F.; Maged, A.F.; Morsy, M.A.; Hashad, A.M.

    1990-01-01

    The alkali-silicate glass dosimeter is made up of 66.8% SiO 2 , 31.2% Li 2 O, 2% K 2 O. It is nearly colourless before irradiation and then takes on an amber colour with increasing doses of gamma radiation. This colouration is represented by the appearance of broad absorption bands at 405 nm and 600 nm wavelengths. The change in absorbance is linear with the absorbed dose in the range of 0.1-4.5 kGy, when measured at its 405 nm absorption band maximum. This glass dosimeter simulates low-z plastics and muscle tissue in terms of gamma-ray absorption properties over broad radiation spectra (0.1 MeV to 10 MeV). (author) 22 refs.; 4 figs.; 2 tabs

  17. Dislocation motion and high temperature plasticity of binary and ternary oxides

    International Nuclear Information System (INIS)

    Bretheau, T.; Castaing, J.; Rabier, J.; Veyssiere, P.

    1979-01-01

    Literature dealing with the plasticity of single crystal oxides deformed at elevated temperatures and the associated mobility of dislocations is reviewed. The experimental approach to the subject is examined critically by selecting oxides and deforming samples and by studying their specific mechanical behaviour, characterizing the deformation substructures and modelling the rate controlling processes. Since oxides with the simple rocksalt structure (Mg0, Ni0, Co0, Fe0,...) are not representative of all oxides, examples of other structures are also examined in detail, including Ti0 2 and Cu 2 0 oxides with fluorite (Zr0 2 , U0 2 ), with corundum (A1 2 0 3 ) and with spinel (MgA1 2 0 4 ternary) structures. Occasionally work on more exotic compounds like Y 2 0 3 or some with the garnet structure is included. (UK)

  18. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

    KAUST Repository

    Perdigão, João

    2014-11-18

    Background Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. Results In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM). The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation. Conclusions Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

  19. Catalytic co-pyrolysis of paper biomass and plastic mixtures (HDPE (high density polyethylene), PP (polypropylene) and PET (polyethylene terephthalate)) and product analysis

    International Nuclear Information System (INIS)

    Chattopadhyay, Jayeeta; Pathak, T.S.; Srivastava, R.; Singh, A.C.

    2016-01-01

    Catalytic co-pyrolysis of biomass and plastics (HDPE (high density polyethylene), PP (polypropylene) and PET (polyethylene terephthalate)) has been performed in a fixed-bed reactor in presence of cobalt based alumina, ceria and ceria-alumina catalysts to analyze the product distribution and selectivity. Catalysts are synthesized using co-precipitation method and characterized by BET (Brunauer–Emmett–Teller) surface area and XRD analysis. The effect of catalytic co-pyrolysis at different temperature with product distribution has been evaluated. The results have clearly shown the synergistic effect between biomass and plastics, the liquid products gradually increases forming with rise in the plastic content in the blend. Gaseous products have yielded most during pyrolysis of blend having biomass/plastics ratio of 5:1 with the presence of 40% Co/30% CeO_2/30% Al_2O_3 catalyst with hydrogen gas production touched its peak of 47 vol%. Catalytic performance enhanced with increase with the cobalt loading, with best performance attributing to 40% Co/30% CeO_2/30% Al_2O_3 catalyst. - Highlights: • Catalytic co-pyrolysis of biomass and plastics (HDPE, PP & PET) blends in fixed-bed reactor. • Strong synergistic effect evident between biomass and plastics. • Solid residue diminished with application of catalysts. • Aromatics and olefins production increases with higher plastic content. • More hydrogen production with application of catalysts with higher cobalt content.

  20. Plastic scintillator

    International Nuclear Information System (INIS)

    Andreeshchev, E.A.; Kilin, S.F.; Kavyrzina, K.A.

    1978-01-01

    A plastic scintillator for ionizing radiation detectors with high time resolution is suggested. To decrease the scintillation pulse width and to maintain a high light yield, the 4 1 , 4 5 -dibromo-2 1 , 2 5 , 5 1 , 5 5 -tetramethyl-n-quinquiphenyl (Br 2 Me 4 Ph) in combination with n-terphenyl (Ph 3 ) or 2, 5-diphenyloxadiazol-1, 3, 4 (PPD) is used as a luminescent addition. Taking into consideration the results of a special study, it is shown, that the following ratio of ingradients is the optimum one: 3-4 mass% Ph 3 or 4-7 mas% PPD + 2-5 mass% Br 2 Me 4 Ph + + polymeric base. The suggested scintillator on the basis of polystyrene has the light yield of 0.23-0.26 arbitrary units and the scintillation pulse duration at half-height is 0.74-0.84 ns

  1. Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product

    OpenAIRE

    Hammerl, J. A.; Lasch, P.; Nitsche, A.; Dabrowski, P. W.; Hahmann, H.; Wicke, A.; Kleta, S.; Dahouk, S. Al; Dieckmann, R.

    2015-01-01

    In 2013, contaminated liquid soap was detected by routine microbiological monitoring of consumer products through state health authorities. Because of its high load of Klebsiella oxytoca, the liquid soap was notified via the European Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled. Here, we present two draft genome sequences and a summary of their general features.

  2. Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome

    DEFF Research Database (Denmark)

    Wang, Zhigang C.; Birkbak, Nicolai Juul; Culhane, Aedín C.

    2012-01-01

    Purpose: High-grade serous cancer (HGSC) is the most common cancer of the ovary and is characterized by chromosomal instability. Defects in homologous recombination repair (HRR) are associated with genomic instability in HGSC, and are exploited by therapy targeting DNA repair. Defective HRR cause...

  3. Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome

    Science.gov (United States)

    2013-01-01

    Background Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families and their roles in plants have been characterized. However, there have been fewer studies of MITE families and their potential roles in evolution of the recently triplicated Brassica genome. Results We identified a new MITE family, BRAMI-1, belonging to the Stowaway super-family in the Brassica genome. In silico mapping revealed that 697 members are dispersed throughout the euchromatic regions of the B. rapa pseudo-chromosomes. Among them, 548 members (78.6%) are located in gene-rich regions, less than 3 kb from genes. In addition, we identified 516 and 15 members in the 470 Mb and 15 Mb genomic shotgun sequences currently available for B. oleracea and B. napus, respectively. The resulting estimated copy numbers for the entire genomes were 1440, 1464 and 2490 in B. rapa, B. oleracea and B. napus, respectively. Concurrently, only 70 members of the related Arabidopsis ATTIRTA-1 MITE family were identified in the Arabidopsis genome. Phylogenetic analysis revealed that BRAMI-1 elements proliferated in the Brassica genus after divergence from the Arabidopsis lineage. MITE insertion polymorphism (MIP) was inspected for 50 BRAMI-1 members, revealing high levels of insertion polymorphism between and within species of Brassica that clarify BRAMI-1 activation periods up to the present. Comparative analysis of the 71 genes harbouring the BRAMI-1 elements with their non-insertion paralogs (NIPs) showed that the BRAMI-1 insertions mainly reside in non-coding sequences and that the expression levels of genes with the elements differ from those of their NIPs. Conclusion A Stowaway family MITE, named as BRAMI-1, was gradually amplified and remained present in over than 1400 copies in each of three Brassica species. Overall, 78% of the members were identified in

  4. Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

    Science.gov (United States)

    Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

    2012-01-01

    Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference

  5. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

    Directory of Open Access Journals (Sweden)

    César D Petroli

    Full Text Available Diversity Arrays Technology (DArT provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for

  6. Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification

    Directory of Open Access Journals (Sweden)

    Ito Takashi

    2011-06-01

    Full Text Available Abstract Background We previously developed a simple method termed HpaII-McrBC PCR (HM-PCR to discriminate allelic methylation status of the genomic sites of interest, and successfully applied it to a comprehensive analysis of CpG islands (CGIs on human chromosome 21q. However, HM-PCR requires 200 ng of genomic DNA to examine one target site, thereby precluding its application to such samples that are limited in quantity. Findings We developed HpaII-McrBC whole-genome-amplification PCR (HM-WGA-PCR that uses whole-genome-amplified DNA as the template. HM-WGA-PCR uses only 1/100th the genomic template material required for HM-PCR. Indeed, we successfully analyzed 147 CGIs by HM-WGA-PCR using only ~300 ng of DNA, whereas previous HM-PCR study had required ~30 μg. Furthermore, we confirmed that allelic methylation status revealed by HM-WGA-PCR is identical to that by HM-PCR in every case of the 147 CGIs tested, proving high consistency between the two methods. Conclusions HM-WGA-PCR would serve as a reliable alternative to HM-PCR in the analysis of allelic methylation status when the quantity of DNA available is limited.

  7. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

    Science.gov (United States)

    Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

    2015-06-01

    Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. © 2014 CIRAD. New Phytologist © 2014 New Phytologist Trust.

  8. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

    Science.gov (United States)

    Chen, Eric C H; Morin, Emmanuelle; Beaudet, Denis; Noel, Jessica; Yildirir, Gokalp; Ndikumana, Steve; Charron, Philippe; St-Onge, Camille; Giorgi, John; Krüger, Manuela; Marton, Timea; Ropars, Jeanne; Grigoriev, Igor V; Hainaut, Matthieu; Henrissat, Bernard; Roux, Christophe; Martin, Francis; Corradi, Nicolas

    2018-01-22

    Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

  9. Highly lead-loaded red plastic scintillators as an X-ray imaging system for the laser Mega Joule

    International Nuclear Information System (INIS)

    Hamel, Matthieu; Normand, Stephane; Turk, Gregory; Darbon, Stephane

    2012-01-01

    The scope of this project intends to record spatially resolved images of core shape and size of a deuterium-tritium micro-balloon during inertial confinement fusion (ICF) experiments at Laser Mega Joule facility (LMJ). We need to develop an x-ray imaging system which can operate in the hard radiative background generated by an ignition shot of ICF. The scintillator is a part of the imaging system and has to gather a compromise of scintillating properties (scintillating efficiency, decay time, emission wavelength) so as to both operate in the hard radiative environment and to allow the acquisition of spatially resolved images. Inorganic scintillators cannot be used because no compromise can be found regarding the expected scintillating properties. Most of them are not fast enough and emit blue light. Organic scintillators are generally fast, but present low x-ray photoelectric absorption in the 10 to 40 keV range. This does not enable the acquisition of spatially resolved images. To this aim, we have developed highly lead-loaded and red-fluorescent fast plastic scintillators. Such a combination is not currently available via scintillator suppliers, since they propose only blue-fluorescent plastic scintillators doped with up to 12 wt% Pb. Thus, incorporation ratio up to 27 wt% Pb has been reached in our laboratory, which can afford a plastic scintillator with an outstanding Z(eff) close to 50. X-rays in the 10 to 40 keV range can thus interact with a higher probability of photoelectric effect than for classic organic scintillators, such as NE-102. The strong orange-red fluorescence can be filtered, so that we can eliminate residual Cerenkov light, generated by gamma-ray absorption in glass parts of the imaging system. Characteristic decay times of our scintillators evaluated under UV excitation were estimated to be in the range 10 to 13 ns. (authors)

  10. Impaired induction of long-term potentiation-like plasticity in patients with high-functioning autism and Asperger syndrome.

    Science.gov (United States)

    Jung, Nikolai H; Janzarik, Wibke G; Delvendahl, Igor; Münchau, Alexander; Biscaldi, Monica; Mainberger, Florian; Bäumer, Tobias; Rauh, Reinhold; Mall, Volker

    2013-01-01

    We aimed to investigate the induction of long-term potentiation (LTP)-like plasticity by paired associative stimulation (PAS) in patients with high-functioning autism and Asperger syndrome (HFA/AS). PAS with an interstimulus interval between electrical and transcranial magnetic stimulation of 25 ms (PAS(25)) was performed in patients with HFA/AS (n=9; eight males, one female; mean age 17 y 11 mo, SD 4 y 5 mo) and in typically developing age-matched volunteers (n=9; five males, four females; mean age 22 y 4 mo, SD 5 y 2 mo). The amplitude of motor-evoked potentials was measured before PAS(25), immediately after stimulation, and 30 minutes and 60 minutes later. A PAS protocol adapted to individual N20 latency (PAS(N20+2)) was performed in six additional patients with HFA/AS. Short-interval intracortical inhibition was measured using paired-pulse stimulation. In contrast to the typically developing participants, the patients with HFA/AS did not show a significant increase in motor-evoked potentials after PAS(25). This finding could also be demonstrated after adaptation for N20 latency. Short-interval intracortical inhibition of patients with HFA/AS was normal compared with the comparison group and did not correlate with PAS effect. Our results show a significant impairment of LTP-like plasticity induced by PAS in individuals with HFA/AS compared with typically developing participants. This finding is in accordance with results from animal studies as well as human studies. Impaired LTP-like plasticity in patients with HFA/AS points towards reduced excitatory synaptic connectivity and deficits in sensory-motor integration in these patients. © The Authors. Developmental Medicine & Child Neurology © 2012 Mac Keith Press.

  11. Insight into dynamic genome imaging: Canonical framework identification and high-throughput analysis.

    Science.gov (United States)

    Ronquist, Scott; Meixner, Walter; Rajapakse, Indika; Snyder, John

    2017-07-01

    The human genome is dynamic in structure, complicating researcher's attempts at fully understanding it. Time series "Fluorescent in situ Hybridization" (FISH) imaging has increased our ability to observe genome structure, but due to cell type and experimental variability this data is often noisy and difficult to analyze. Furthermore, computational analysis techniques are needed for homolog discrimination and canonical framework detection, in the case of time-series images. In this paper we introduce novel ideas for nucleus imaging analysis, present findings extracted using dynamic genome imaging, and propose an objective algorithm for high-throughput, time-series FISH imaging. While a canonical framework could not be detected beyond statistical significance in the analyzed dataset, a mathematical framework for detection has been outlined with extension to 3D image analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in Escherichia coli

    DEFF Research Database (Denmark)

    Liu, Yilan; Yang, Maohua; Yan, Daojiang

    2016-01-01

    Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double...... for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision...... of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli....

  13. High-density transcriptional initiation signals underline genomic islands in bacteria.

    Directory of Open Access Journals (Sweden)

    Qianli Huang

    Full Text Available Genomic islands (GIs, frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special

  14. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar

    Directory of Open Access Journals (Sweden)

    Jurman Irena

    2010-03-01

    Full Text Available Abstract Background Most of the grapevine (Vitis vinifera L. cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. Results We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. Conclusions We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.

  15. Museum genomics: low-cost and high-accuracy genetic data from historical specimens.

    Science.gov (United States)

    Rowe, Kevin C; Singhal, Sonal; Macmanes, Matthew D; Ayroles, Julien F; Morelli, Toni Lyn; Rubidge, Emily M; Bi, Ke; Moritz, Craig C

    2011-11-01

    Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome. © 2011 Blackwell Publishing Ltd.

  16. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

    Science.gov (United States)

    We report a chromosome-scale assembly and analysis of the Daucus carota genome, an important source of provitamin A in the human diet and the first sequenced genome among members of the Euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carro...

  17. Using texture analysis to improve per-pixel classification of very high resolution images for mapping plastic greenhouses

    Science.gov (United States)

    Agüera, Francisco; Aguilar, Fernando J.; Aguilar, Manuel A.

    The area occupied by plastic-covered greenhouses has undergone rapid growth in recent years, currently exceeding 500,000 ha worldwide. Due to the vast amount of input (water, fertilisers, fuel, etc.) required, and output of different agricultural wastes (vegetable, plastic, chemical, etc.), the environmental impact of this type of production system can be serious if not accompanied by sound and sustainable territorial planning. For this, the new generation of satellites which provide very high resolution imagery, such as QuickBird and IKONOS can be useful. In this study, one QuickBird and one IKONOS satellite image have been used to cover the same area under similar circumstances. The aim of this work was an exhaustive comparison of QuickBird vs. IKONOS images in land-cover detection. In terms of plastic greenhouse mapping, comparative tests were designed and implemented, each with separate objectives. Firstly, the Maximum Likelihood Classification (MLC) was applied using five different approaches combining R, G, B, NIR, and panchromatic bands. The combinations of the bands used, significantly influenced some of the indexes used to classify quality in this work. Furthermore, the quality classification of the QuickBird image was higher in all cases than that of the IKONOS image. Secondly, texture features derived from the panchromatic images at different window sizes and with different grey levels were added as a fifth band to the R, G, B, NIR images to carry out the MLC. The inclusion of texture information in the classification did not improve the classification quality. For classifications with texture information, the best accuracies were found in both images for mean and angular second moment texture parameters. The optimum window size in these texture parameters was 3×3 for IK images, while for QB images it depended on the quality index studied, but the optimum window size was around 15×15. With regard to the grey level, the optimum was 128. Thus, the

  18. High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

    Science.gov (United States)

    Greub, Gilbert; Kebbi-Beghdadi, Carole; Bertelli, Claire; Collyn, François; Riederer, Beat M; Yersin, Camille; Croxatto, Antony; Raoult, Didier

    2009-12-23

    With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

  19. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

    Directory of Open Access Journals (Sweden)

    Trout-Yakel Keri M

    2010-02-01

    Full Text Available Abstract Background A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. Results The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. Conclusions High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.

  20. Plasticity in the proteome of Emiliania huxleyi CCMP 1516 to extremes of light is highly targeted.

    Science.gov (United States)

    McKew, Boyd A; Lefebvre, Stephane C; Achterberg, Eric P; Metodieva, Gergana; Raines, Christine A; Metodiev, Metodi V; Geider, Richard J

    2013-10-01

    Optimality principles are often applied in theoretical studies of microalgal ecophysiology to predict changes in allocation of resources to different metabolic pathways, and optimal acclimation is likely to involve changes in the proteome, which typically accounts for > 50% of cellular nitrogen (N). We tested the hypothesis that acclimation of the microalga Emiliania huxleyi CCMP 1516 to suboptimal vs supraoptimal light involves large changes in the proteome as cells rebalance the capacities to absorb light, fix CO2 , perform biosynthesis and resist photooxidative stress. Emiliania huxleyi was grown in nutrient-replete continuous culture at 30 (LL) and 1000 μmol photons m(-2) s(-1) (HL), and changes in the proteome were assessed by LC-MS/MS shotgun proteomics. Changes were most evident in proteins involved in the light reactions of photosynthesis; the relative abundance of photosystem I (PSI) and PSII proteins was 70% greater in LL, light-harvesting fucoxanthin-chlorophyll proteins (Lhcfs) were up to 500% greater in LL and photoprotective LI818 proteins were 300% greater in HL. The marked changes in the abundances of Lhcfs and LI818s, together with the limited plasticity in the bulk of the E. huxleyi proteome, probably reflect evolutionary pressures to provide energy to maintain metabolic capabilities in stochastic light environments encountered by this species in nature. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  1. From plastic to elastic stress relaxation in highly mismatched SiGe/Si heterostructures

    International Nuclear Information System (INIS)

    Isa, Fabio; Salvalaglio, Marco; Dasilva, Yadira Arroyo Rojas; Jung, Arik; Isella, Giovanni; Erni, Rolf; Niedermann, Philippe; Gröning, Pierangelo; Montalenti, Francesco; Känel, Hans von

    2016-01-01

    We present a detailed experimental and theoretical analysis of the epitaxial stress relaxation process in micro-structured compositionally graded alloys. We focus on the pivotal SiGe/Si(001) system employing patterned Si substrates at the micrometre-size scale to address the distribution of threading and misfit dislocations within the heterostructures. SiGe alloys with linearly increasing Ge content were deposited by low energy plasma enhanced chemical vapour deposition resulting in isolated, tens of micrometre tall 3D crystals. We demonstrate that complete elastic relaxation is achieved by appropriate choice of the Ge compositional grading rate and Si pillar width. We investigate the nature and distribution of dislocations along the [001] growth direction in SiGe crystals by transmission electron microscopy, chemical defect etching and etch pit counting. We show that for 3 μm wide Si pillars and a Ge grading rate of 1.5% μm −1 , only misfit dislocations are present while their fraction is reduced for higher Ge grading rates and larger structures due to dislocation interactions. The experimental results are interpreted with the help of theoretical calculations based on linear elasticity theory describing the competition between purely elastic and plastic stress relaxation with increasing crystal width and Ge compositional grading rate.

  2. Expression of Glutamate and GABA during the Process of Rat Retinal Synaptic Plasticity Induced by Acute High Intraocular Pressure

    International Nuclear Information System (INIS)

    Zhou, Lihong; Huang, Jufang; Wang, Hui; Luo, Jia; Zeng, Leping; Xiong, Kun; Chen, Dan

    2013-01-01

    Acute high intraocular pressure (HIOP) can induce plastic changes of retinal synapses during which the expression of the presynaptic marker synaptophysin (SYN) has a distinct spatiotemporal pattern from the inner plexiform layer to the outer plexiform layer. We identified the types of neurotransmitters in the retina that participated in this process and determined the response of these neurotransmitters to HIOP induction. The model of acute HIOP was established by injecting normal saline into the anterior chamber of the rat eye. We found that the number of glutamate-positive cells increased successively from the inner part to the outer part of the retina (from the ganglion cell layer to the inner nuclear layer to the outer nuclear layer) after HIOP, which was similar to the spatiotemporal pattern of SYN expression (internally to externally) following HIOP. However, the distribution and intensity of GABA immunoreactivity in the retina did not change significantly at different survival time post injury and had no direct correlation with SYN expression. Our results suggested that the excitatory neurotransmitter glutamate might participate in the plastic process of retinal synapses following acute HIOP, but no evidence was found for the role of the inhibitory neurotransmitter GABA

  3. Experiment and Modeling of Simultaneous Creep, Plasticity and Transformation of High Temperature Shape Memory Alloys During Cyclic Actuation

    Science.gov (United States)

    Kumar, Parikshith K.; Desai, Uri; Chatzigeorgiou, George; Lagoudas, Dimitris C.; Monroe, James; Karaman, Ibrahim; Noebe, Ron; Bigelow, Glen

    2010-01-01

    The present work is focused on studying the cycling actuation behavior of HTSMAs undergoing simultaneous creep and transformation. For the thermomechanical testing, a high temperature test setup was assembled on a MTS frame with the capability to test up to temperatures of 600 C. Constant stress thermal cycling tests were conducted to establish the actuation characteristics and the phase diagram for the chosen HTSMA. Additionally, creep tests were conducted at constant stress levels at different test temperatures to characterize the creep behavior of the alloy over the operational range. A thermodynamic constitutive model is developed and extended to take into account a) the effect of multiple thermal cycling on the generation of plastic strains due to transformation (TRIP strains) and b) both primary and secondary creep effects. The model calibration is based on the test results. The creep tests and the uniaxial tests are used to identify the viscoplastic behavior of the material. The parameters for the SMA properties, regarding the transformation and transformation induced plastic strain evolutions, are obtained from the material phase diagram and the thermomechanical tests. The model is validated by predicting the material behavior at different thermomechanical test conditions.

  4. High efficiency algorithm for 3D transient thermo-elasto-plastic contact problem in reactor pressure vessel sealing system

    International Nuclear Information System (INIS)

    Xu Mingyu; Lin Tengjiao; Li Runfang; Du Xuesong; Li Shuian; Yang Yu

    2005-01-01

    There are some complex operating cases such as high temperature and high pressure during the operating process of nuclear reactor pressure vessel. It is necessary to carry out mechanical analysis and experimental investigation for its sealing ability. On the basis of the self-developed program for 3-D transient sealing analysis for nuclear reactor pressure vessel, some specific measures are presented to enhance the calculation efficiency in several aspects such as the non-linear solution of elasto-plastic problem, the mixed solution algorithm for contact problem as well as contract heat transfer problem and linear equation set solver. The 3-D transient sealing analysis program is amended and complemented, with which the sealing analysis result of the pressure vessel model can be obtained. The calculation results have good regularity and the calculation efficiency is twice more than before. (authors)

  5. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    Science.gov (United States)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  6. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

    Science.gov (United States)

    Sealfon, Rachel; Gire, Stephen; Ellis, Crystal; Calderwood, Stephen; Qadri, Firdausi; Hensley, Lisa; Kellis, Manolis; Ryan, Edward T; LaRocque, Regina C; Harris, Jason B; Sabeti, Pardis C

    2012-09-11

    Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

  7. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic

    Directory of Open Access Journals (Sweden)

    Sealfon Rachel

    2012-09-01

    Full Text Available Abstract Background Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x; four of the seven isolates were previously sequenced. Results Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961, 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Conclusions Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

  8. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim.

    Science.gov (United States)

    Feldman, Michal; Harbeck, Michaela; Keller, Marcel; Spyrou, Maria A; Rott, Andreas; Trautmann, Bernd; Scholz, Holger C; Päffgen, Bernd; Peters, Joris; McCormick, Michael; Bos, Kirsten; Herbig, Alexander; Krause, Johannes

    2016-11-01

    The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  9. glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.

    Science.gov (United States)

    Hutchins, Andrew Paul; Jauch, Ralf; Dyla, Mateusz; Miranda-Saavedra, Diego

    2014-01-01

    Genomic datasets and the tools to analyze them have proliferated at an astonishing rate. However, such tools are often poorly integrated with each other: each program typically produces its own custom output in a variety of non-standard file formats. Here we present glbase, a framework that uses a flexible set of descriptors that can quickly parse non-binary data files. glbase includes many functions to intersect two lists of data, including operations on genomic interval data and support for the efficient random access to huge genomic data files. Many glbase functions can produce graphical outputs, including scatter plots, heatmaps, boxplots and other common analytical displays of high-throughput data such as RNA-seq, ChIP-seq and microarray expression data. glbase is designed to rapidly bring biological data into a Python-based analytical environment to facilitate analysis and data processing. In summary, glbase is a flexible and multifunctional toolkit that allows the combination and analysis of high-throughput data (especially next-generation sequencing and genome-wide data), and which has been instrumental in the analysis of complex data sets. glbase is freely available at http://bitbucket.org/oaxiom/glbase/.

  10. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.

    Directory of Open Access Journals (Sweden)

    Kui Lin

    2014-01-01

    Full Text Available Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

  11. glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

    Directory of Open Access Journals (Sweden)

    Andrew Paul Hutchins

    2014-01-01

    Full Text Available Genomic datasets and the tools to analyze them have proliferated at an astonishing rate. However, such tools are often poorly integrated with each other: each program typically produces its own custom output in a variety of non-standard file formats. Here we present glbase, a framework that uses a flexible set of descriptors that can quickly parse non-binary data files. glbase includes many functions to intersect two lists of data, including operations on genomic interval data and support for the efficient random access to huge genomic data files. Many glbase functions can produce graphical outputs, including scatter plots, heatmaps, boxplots and other common analytical displays of high-throughput data such as RNA-seq, ChIP-seq and microarray expression data. glbase is designed to rapidly bring biological data into a Python-based analytical environment to facilitate analysis and data processing. In summary, glbase is a flexible and multifunctional toolkit that allows the combination and analysis of high-throughput data (especially next-generation sequencing and genome-wide data, and which has been instrumental in the analysis of complex data sets. glbase is freely available at http://bitbucket.org/oaxiom/glbase/.

  12. A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

    Science.gov (United States)

    Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

    2012-01-01

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits. PMID:22247776

  13. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

    Science.gov (United States)

    Gaynor, Kaitlyn M; Solomon, Joseph W; Siller, Stefanie; Jessell, Linnet; Duffy, J Emmett; Rubenstein, Dustin R

    2017-11-01

    Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes. © 2017 John Wiley & Sons Ltd.

  14. Mechanisms of plastic deformation in highly cross-linked UHMWPE for total hip components--the molecular physics viewpoint.

    Science.gov (United States)

    Takahashi, Yasuhito; Shishido, Takaaki; Yamamoto, Kengo; Masaoka, Toshinori; Kubo, Kosuke; Tateiwa, Toshiyuki; Pezzotti, Giuseppe

    2015-02-01

    Plastic deformation is an unavoidable event in biomedical polymeric implants for load-bearing application during long-term in-vivo service life, which involves a mass transfer process, irreversible chain motion, and molecular reorganization. Deformation-induced microstructural alterations greatly affect mechanical properties and durability of implant devices. The present research focused on evaluating, from a molecular physics viewpoint, the impact of externally applied strain (or stress) in ultra-high molecular weight polyethylene (UHMWPE) prostheses, subjected to radiation cross-linking and subsequent remelting for application in total hip arthroplasty (THA). Two different types of commercial acetabular liners, which belong to the first-generation highly cross-linked UHMWPE (HXLPE), were investigated by means of confocal/polarized Raman microprobe spectroscopy. The amount of crystalline region and the spatial distribution of molecular chain orientation were quantitatively analyzed according to a combined theory including Raman selection rules for the polyethylene orthorhombic structure and the orientation distribution function (ODF) statistical approach. The structurally important finding was that pronounced recrystallization and molecular reorientation increasingly appeared in the near-surface regions of HXLPE liners with increasing the amount of plastic (compressive) deformation stored in the microstructure. Such molecular rearrangements, occurred in response to external strains, locally increase surface cross-shear (CS) stresses, which in turn trigger microscopic wear processes in HXLPE acetabular liners. Thus, on the basis of the results obtained at the molecular scale, we emphasize here the importance of minimizing the development of irrecoverable deformation strain in order to retain the pristine and intrinsically high wear performance of HXLPE components. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

    Science.gov (United States)

    Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran

    2009-07-10

    A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.

  16. Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.

    Science.gov (United States)

    Versluis, Dennis; Nijsse, Bart; Naim, Mohd Azrul; Koehorst, Jasper J; Wiese, Jutta; Imhoff, Johannes F; Schaap, Peter J; van Passel, Mark W J; Smidt, Hauke; Sipkema, Detmer

    2018-01-01

    Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. The need for high-quality whole-genome sequence databases in microbial forensics.

    Science.gov (United States)

    Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

    2013-09-01

    Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

  18. Capsule physics comparison of National Ignition Facility implosion designs using plastic, high density carbon, and beryllium ablators

    Science.gov (United States)

    Clark, D. S.; Kritcher, A. L.; Yi, S. A.; Zylstra, A. B.; Haan, S. W.; Weber, C. R.

    2018-03-01

    Indirect drive implosion experiments on the National Ignition Facility (NIF) [E. I. Moses et al., Phys. Plasmas 16, 041006 (2009)] have now tested three different ablator materials: glow discharge polymer plastic, high density carbon, and beryllium. How do these different ablators compare in current and proposed implosion experiments on NIF? What are the relative advantages and disadvantages of each? This paper compares these different ablator options in capsule-only simulations of current NIF experiments and potential future designs. The simulations compare the impact of the capsule fill tube, support tent, and interface surface roughness for each case, as well as all perturbations in combination. According to the simulations, each ablator is impacted by the various perturbation sources differently, and each material poses unique challenges in the pursuit of ignition on NIF.

  19. Interstitial atoms enable joint twinning and transformation induced plasticity in strong and ductile high-entropy alloys.

    Science.gov (United States)

    Li, Zhiming; Tasan, Cemal Cem; Springer, Hauke; Gault, Baptiste; Raabe, Dierk

    2017-01-12

    High-entropy alloys (HEAs) consisting of multiple principle elements provide an avenue for realizing exceptional mechanical, physical and chemical properties. We report a novel strategy for designing a new class of HEAs incorporating the additional interstitial element carbon. This results in joint activation of twinning- and transformation-induced plasticity (TWIP and TRIP) by tuning the matrix phase's instability in a metastable TRIP-assisted dual-phase HEA. Besides TWIP and TRIP, such alloys benefit from massive substitutional and interstitial solid solution strengthening as well as from the composite effect associated with its dual-phase structure. Nanosize particle formation and grain size reduction are also utilized. The new interstitial TWIP-TRIP-HEA thus unifies all metallic strengthening mechanisms in one material, leading to twice the tensile strength compared to a single-phase HEA with similar composition, yet, at identical ductility.

  20. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library.

    Science.gov (United States)

    Hoffberg, Sandra L; Troendle, Nicholas J; Glenn, Travis C; Mahmud, Ousman; Louha, Swarnali; Chalopin, Domitille; Bennetzen, Jeffrey L; Mauricio, Rodney

    2018-04-27

    The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species. Copyright © 2018, G3: Genes, Genomes, Genetics.

  1. A high-coverage Neandertal genome from Vindija Cave in Croatia.

    Science.gov (United States)

    Prüfer, Kay; de Filippo, Cesare; Grote, Steffi; Mafessoni, Fabrizio; Korlević, Petra; Hajdinjak, Mateja; Vernot, Benjamin; Skov, Laurits; Hsieh, Pinghsun; Peyrégne, Stéphane; Reher, David; Hopfe, Charlotte; Nagel, Sarah; Maricic, Tomislav; Fu, Qiaomei; Theunert, Christoph; Rogers, Rebekah; Skoglund, Pontus; Chintalapati, Manjusha; Dannemann, Michael; Nelson, Bradley J; Key, Felix M; Rudan, Pavao; Kućan, Željko; Gušić, Ivan; Golovanova, Liubov V; Doronichev, Vladimir B; Patterson, Nick; Reich, David; Eichler, Evan E; Slatkin, Montgomery; Schierup, Mikkel H; Andrés, Aida M; Kelso, Janet; Meyer, Matthias; Pääbo, Svante

    2017-11-03

    To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  2. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

    Full Text Available Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb and 7 (1.1 Mb from an individual from the International HapMap Project (NA12872. We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

  3. Comparative genomic and proteomic analysis of high grade glioma primary cultures and matched tumor in situ.

    LENUS (Irish Health Repository)

    Howley, R

    2012-10-15

    Developing targeted therapies for high grade gliomas (HGG), the most common primary brain tumor in adults, relies largely on glioma cultures. However, it is unclear if HGG tumorigenic signaling pathways are retained under in-vitro conditions. Using array comparative genomic hybridization and immunohistochemical profiling, we contrasted the epidermal and platelet-derived growth factor receptor (EGFR\\/PDGFR) in-vitro pathway status of twenty-six primary HGG cultures with the pathway status of their original HGG biopsies. Genomic gains or amplifications were lost during culturing while genomic losses were more likely to be retained. Loss of EGFR amplification was further verified immunohistochemically when EGFR over expression was decreased in the majority of cultures. Conversely, PDGFRα and PDGFRβ were more abundantly expressed in primary cultures than in the original tumor (p<0.05). Despite these genomic and proteomic differences, primary HGG cultures retained key aspects of dysregulated tumorigenic signaling. Both in-vivo and in-vitro the presence of EGFR resulted in downstream activation of P70s6K while reduced downstream activation was associated with the presence of PDGFR and the tumor suppressor, PTEN. The preserved pathway dysregulation make this glioma model suitable for further studies of glioma tumorigenesis, however individual culture related differences must be taken into consideration when testing responsiveness to chemotherapeutic agents.

  4. Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

    Science.gov (United States)

    Neuer-Nitsche, B; Lu, X N; Werner, D

    1988-09-12

    The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

  5. Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.

    Science.gov (United States)

    Suzuki, Shino; Kuenen, J Gijs; Schipper, Kira; van der Velde, Suzanne; Ishii, Shun'ichi; Wu, Angela; Sorokin, Dimitry Y; Tenney, Aaron; Meng, XianYing; Morrill, Penny L; Kamagata, Yoichi; Muyzer, Gerard; Nealson, Kenneth H

    2014-05-21

    Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus 'Serpentinomonas'.

  6. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    DEFF Research Database (Denmark)

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes...... confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted...... of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential...

  7. Imaging mass spectrometry and genome mining reveal highly antifungal virulence factor of mushroom soft rot pathogen.

    Science.gov (United States)

    Graupner, Katharina; Scherlach, Kirstin; Bretschneider, Tom; Lackner, Gerald; Roth, Martin; Gross, Harald; Hertweck, Christian

    2012-12-21

    Caught in the act: imaging mass spectrometry of a button mushroom infected with the soft rot pathogen Janthinobacterium agaricidamnosum in conjunction with genome mining revealed jagaricin as a highly antifungal virulence factor that is not produced under standard cultivation conditions. The structure of jagaricin was rigorously elucidated by a combination of physicochemical analyses, chemical derivatization, and bioinformatics. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product.

    Science.gov (United States)

    Hammerl, J A; Lasch, P; Nitsche, A; Dabrowski, P W; Hahmann, H; Wicke, A; Kleta, S; Al Dahouk, S; Dieckmann, R

    2015-07-23

    In 2013, contaminated liquid soap was detected by routine microbiological monitoring of consumer products through state health authorities. Because of its high load of Klebsiella oxytoca, the liquid soap was notified via the European Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled. Here, we present two draft genome sequences and a summary of their general features. Copyright © 2015 Hammerl et al.

  9. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

    Directory of Open Access Journals (Sweden)

    Zhao Patrick X

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

  10. Filtering high-throughput protein-protein interaction data using a combination of genomic features

    Directory of Open Access Journals (Sweden)

    Patil Ashwini

    2005-04-01

    Full Text Available Abstract Background Protein-protein interaction data used in the creation or prediction of molecular networks is usually obtained from large scale or high-throughput experiments. This experimental data is liable to contain a large number of spurious interactions. Hence, there is a need to validate the interactions and filter out the incorrect data before using them in prediction studies. Results In this study, we use a combination of 3 genomic features – structurally known interacting Pfam domains, Gene Ontology annotations and sequence homology – as a means to assign reliability to the protein-protein interactions in Saccharomyces cerevisiae determined by high-throughput experiments. Using Bayesian network approaches, we show that protein-protein interactions from high-throughput data supported by one or more genomic features have a higher likelihood ratio and hence are more likely to be real interactions. Our method has a high sensitivity (90% and good specificity (63%. We show that 56% of the interactions from high-throughput experiments in Saccharomyces cerevisiae have high reliability. We use the method to estimate the number of true interactions in the high-throughput protein-protein interaction data sets in Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens to be 27%, 18% and 68% respectively. Our results are available for searching and downloading at http://helix.protein.osaka-u.ac.jp/htp/. Conclusion A combination of genomic features that include sequence, structure and annotation information is a good predictor of true interactions in large and noisy high-throughput data sets. The method has a very high sensitivity and good specificity and can be used to assign a likelihood ratio, corresponding to the reliability, to each interaction.

  11. An Integrative Genomic Island Affects the Adaptations of Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2016-11-01

    Full Text Available Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is thought to play an important role in the microbial adaptation to such an extreme environment. In this study, a 21.4-kb DNA fragment was identified as a genomic island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Pyrococcus yayanosii. According to the sequence alignment and functional annotation, the genes in PYG1 could tentatively be divided into five modules, with functions related to mobility, DNA repair, metabolic processes and the toxin-antitoxin system. Integrase can mediate the site-specific integration and excision of PYG1 in the chromosome of P. yayanosii A1. Gene replacement of PYG1 with a SimR cassette was successful. The growth of the mutant strain ∆PYG1 was compared with its parent strain P. yayanosii A2 under various stress conditions, including different pH, salinity, temperature and hydrostatic pressure. The ∆PYG1 mutant strain showed reduced growth when grown at 100 °C, while the biomass of ∆PYG1 increased significantly when cultured at 80 MPa. Differential expression of the genes in module Ⅲ of PYG1 was observed under different temperature and pressure conditions. This study demonstrates the first example of an archaeal integrative genomic island that could affect the adaptation of the hyperthermophilic piezophile P. yayanosii to high temperature and high hydrostatic pressure.

  12. Genomic prediction applied to high-biomass sorghum for bioenergy production.

    Science.gov (United States)

    de Oliveira, Amanda Avelar; Pastina, Maria Marta; de Souza, Vander Filipe; da Costa Parrella, Rafael Augusto; Noda, Roberto Willians; Simeone, Maria Lúcia Ferreira; Schaffert, Robert Eugene; de Magalhães, Jurandir Vieira; Damasceno, Cynthia Maria Borges; Margarido, Gabriel Rodrigues Alves

    2018-01-01

    The increasing cost of energy and finite oil and gas reserves have created a need to develop alternative fuels from renewable sources. Due to its abiotic stress tolerance and annual cultivation, high-biomass sorghum ( Sorghum bicolor L. Moench) shows potential as a bioenergy crop. Genomic selection is a useful tool for accelerating genetic gains and could restructure plant breeding programs by enabling early selection and reducing breeding cycle duration. This work aimed at predicting breeding values via genomic selection models for 200 sorghum genotypes comprising landrace accessions and breeding lines from biomass and saccharine groups. These genotypes were divided into two sub-panels, according to breeding purpose. We evaluated the following phenotypic biomass traits: days to flowering, plant height, fresh and dry matter yield, and fiber, cellulose, hemicellulose, and lignin proportions. Genotyping by sequencing yielded more than 258,000 single-nucleotide polymorphism markers, which revealed population structure between subpanels. We then fitted and compared genomic selection models BayesA, BayesB, BayesCπ, BayesLasso, Bayes Ridge Regression and random regression best linear unbiased predictor. The resulting predictive abilities varied little between the different models, but substantially between traits. Different scenarios of prediction showed the potential of using genomic selection results between sub-panels and years, although the genotype by environment interaction negatively affected accuracies. Functional enrichment analyses performed with the marker-predicted effects suggested several interesting associations, with potential for revealing biological processes relevant to the studied quantitative traits. This work shows that genomic selection can be successfully applied in biomass sorghum breeding programs.

  13. Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing.

    Science.gov (United States)

    Hu, Jiazhi; Meyers, Robin M; Dong, Junchao; Panchakshari, Rohit A; Alt, Frederick W; Frock, Richard L

    2016-05-01

    Unbiased, high-throughput assays for detecting and quantifying DNA double-stranded breaks (DSBs) across the genome in mammalian cells will facilitate basic studies of the mechanisms that generate and repair endogenous DSBs. They will also enable more applied studies, such as those to evaluate the on- and off-target activities of engineered nucleases. Here we describe a linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) method for the detection of genome-wide 'prey' DSBs via their translocation in cultured mammalian cells to a fixed 'bait' DSB. Bait-prey junctions are cloned directly from isolated genomic DNA using LAM-PCR and unidirectionally ligated to bridge adapters; subsequent PCR steps amplify the single-stranded DNA junction library in preparation for Illumina Miseq paired-end sequencing. A custom bioinformatics pipeline identifies prey sequences that contribute to junctions and maps them across the genome. LAM-HTGTS differs from related approaches because it detects a wide range of broken end structures with nucleotide-level resolution. Familiarity with nucleic acid methods and next-generation sequencing analysis is necessary for library generation and data interpretation. LAM-HTGTS assays are sensitive, reproducible, relatively inexpensive, scalable and straightforward to implement with a turnaround time of <1 week.

  14. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

    KAUST Repository

    Perdigã o, Joã o; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel

    2014-01-01

    Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

  15. Plastic dosimeter

    International Nuclear Information System (INIS)

    Nagai, Shiro; Matsuda, Kohji.

    1988-01-01

    The report outlines major features and applications of plastic dosimeters. Some plastic dosimeters, including the CTA and PVC types, detect the response of the plastic material itself to radiations while others, such as pigment-added plastic dosimeters, contain additives as radiation detecting material. Most of these dosimeters make use of color centers produced in the dosimeter by radiations. The PMMA dosimeter is widely used in the field of radiation sterilization of food, feed and medical apparatus. The blue cellophane dosimeter is easy to handle if calibrated appropriately. The rad-color dosimeter serves to determine whether products have been irradiated appropriately. The CTA dosimeter has better damp proofing properties than the blue cellophane type. The pigment-added plastic dosimeter consists of a resin such as nylon, CTA or PVC that contains a dye. Some other plastic dosimeters are also described briefly. Though having many advantages, these plastic dosimeter have disadvantages as well. Some of their major disadvantages, including fading as well as large dependence on dose, temperature, humidity and anviroment, are discussed. (Nogami, K.)

  16. High-performance flexible thin-film transistors fabricated using print-transferrable polycrystalline silicon membranes on a plastic substrate

    International Nuclear Information System (INIS)

    Qin, Guoxuan; Yuan, Hao-Chih; Ma, Zhenqiang; Yang, Hongjun; Zhou, Weidong

    2011-01-01

    Inexpensive polycrystalline Si (poly-Si) with large grain size is highly desirable for flexible electronics applications. However, it is very challenging to directly deposit high-quality poly-Si on plastic substrates due to processing constrictions, such as temperature tolerance and residual stress. In this paper, we present our study on poly-Si membranes that are stress free and most importantly, are transferrable to any substrate including a low-temperature polyethylene terephthalate (PET) substrate. We formed poly-Si-on-insulator by first depositing small-grain size poly-Si on an oxidized Si wafer. We then performed high-temperature annealing for recrystallization to obtain larger grain size. After selective doping on the poly-Si-on-insulator, buried oxide was etched away. By properly patterning the poly-Si layer, residual stress in the released poly-Si membranes was completely relaxed. The flat membrane topology allows the membranes to be print transferred to any substrates. High-performance TFTs were demonstrated on the transferred poly-Si membranes on a PET substrate

  17. All you can eat: high performance capacity and plasticity in the common big-eared bat, Micronycteris microtis (Chiroptera: Phyllostomidae).

    Science.gov (United States)

    Santana, Sharlene E; Geipel, Inga; Dumont, Elizabeth R; Kalka, Margareta B; Kalko, Elisabeth K V

    2011-01-01

    Ecological specialization and resource partitioning are expected to be particularly high in the species-rich communities of tropical vertebrates, yet many species have broader ecological niches than expected. In Neotropical ecosystems, Neotropical leaf-nosed bats (Phyllostomidae) are one of the most ecologically and functionally diverse vertebrate clades. Resource partitioning in phyllostomids might be achieved through differences in the ability to find and process food. We selected Micronycteris microtis, a very small (5-7 g) animalivorous phyllostomid, to explore whether broad resource use is associated with specific morphological, behavioral and performance traits within the phyllostomid radiation. We documented processing of natural prey and measured bite force in free-ranging M. microtis and other sympatric phyllostomids. We found that M. microtis had a remarkably broad diet for prey size and hardness. For the first time, we also report the consumption of vertebrates (lizards), which makes M. microtis the smallest carnivorous bat reported to date. Compared to other phyllostomids, M. microtis had the highest bite force for its size and cranial shape and high performance plasticity. Bite force and cranial shape appear to have evolved rapidly in the M. microtis lineage. High performance capacity and high efficiency in finding motionless prey might be key traits that allow M. microtis, and perhaps other species, to successfully co-exist with other gleaning bats.

  18. All you can eat: high performance capacity and plasticity in the common big-eared bat, Micronycteris microtis (Chiroptera: Phyllostomidae.

    Directory of Open Access Journals (Sweden)

    Sharlene E Santana

    Full Text Available Ecological specialization and resource partitioning are expected to be particularly high in the species-rich communities of tropical vertebrates, yet many species have broader ecological niches than expected. In Neotropical ecosystems, Neotropical leaf-nosed bats (Phyllostomidae are one of the most ecologically and functionally diverse vertebrate clades. Resource partitioning in phyllostomids might be achieved through differences in the ability to find and process food. We selected Micronycteris microtis, a very small (5-7 g animalivorous phyllostomid, to explore whether broad resource use is associated with specific morphological, behavioral and performance traits within the phyllostomid radiation. We documented processing of natural prey and measured bite force in free-ranging M. microtis and other sympatric phyllostomids. We found that M. microtis had a remarkably broad diet for prey size and hardness. For the first time, we also report the consumption of vertebrates (lizards, which makes M. microtis the smallest carnivorous bat reported to date. Compared to other phyllostomids, M. microtis had the highest bite force for its size and cranial shape and high performance plasticity. Bite force and cranial shape appear to have evolved rapidly in the M. microtis lineage. High performance capacity and high efficiency in finding motionless prey might be key traits that allow M. microtis, and perhaps other species, to successfully co-exist with other gleaning bats.

  19. Using neutrons to measure keV temperatures in highly compressed plastic at multi-Gbar pressures

    Science.gov (United States)

    Nilsen, J.; Bachmann, B.; Zimmerman, G. B.; Hatarik, R.; Döppner, T.; Swift, D.; Hawreliak, J.; Collins, G. W.; Falcone, R. W.; Glenzer, S. H.; Kraus, D.; Landen, O. L.; Kritcher, A. L.

    2016-12-01

    We have designed an experiment for the National Ignition Facility to measure the Hugoniot of materials such as plastic at extreme pressures. The design employs a strong spherically converging shock launched through a solid ball of material using a hohlraum radiation drive. The shock front conditions can be characterized using X-ray radiography until background from shock coalescence overtakes the backlit signal. Shock coalescence at the center is predicted to reach tens of Gbars and can be further characterized by measuring the X-ray self-emission and 2.45 MeV neutrons emitted from the shock flash region. In this simulation design work the standard plastic sphere is replaced with a deuterated polyethylene sphere, CD2, that reaches sufficiently high densities and temperatures in the central hot spot to produce neutrons from Deuterium-Deuterium (DD) fusion reactions that can be measured by a neutron time of flight spectrometer (nTOF) and act as a temperature diagnostic. This paper focuses on the design of these experiments, based on an extensive suite of radiation-hydrodynamics simulations, and the interpretation of the predicted DD neutron signals. The simulations predict mean temperatures of 1 keV in the central hot spot with mean densities of 33 g/cc and mean pressures of 25 Gbar. A preliminary comparison with early experimental results looks promising with an average ion temperature of 1.06 ± 0.15 keV in the central hot spot estimated from the nTOF spectral width and measured neutron yield of 7.0 (±0.5) × 109 DD neutrons.

  20. Quantification of the microstructures of high purity nickel subjected to dynamic plastic deformation

    DEFF Research Database (Denmark)

    Luo, Z.P.; Zhang, H.W.; Hansen, Niels

    2012-01-01

    and the misorientation angle across dislocation boundaries and high angle boundaries. These boundaries subdivide the structure on a finer and finer scale towards saturation at the highest strain. The structural evolution follows a hierarchical pattern from the formation of cells and cell blocks to a characteristic...... and high angle boundaries. Shear bands and twins have not been observed. In order to underpin the structural analysis, the mechanical properties as a function of strain have been determined by tensile and hardness tests. The flow stress is 850 MPa, showing that high strain rate deformation has potential...

  1. High-Temperature Structural Analysis of a Small-Scale Prototype of a Process Heat Exchanger (IV) - Macroscopic High-Temperature Elastic-Plastic Analysis -

    International Nuclear Information System (INIS)

    Song, Kee Nam; Hong, Sung Deok; Park, Hong Yoon

    2011-01-01

    A PHE (Process Heat Exchanger) is a key component required to transfer heat energy of 950 .deg. C generated in a VHTR (Very High Temperature Reactor) to a chemical reaction that yields a large quantity of hydrogen. A small-scale PHE prototype made of Hastelloy-X was scheduled for testing in a small-scale gas loop at the Korea Atomic Energy Research Institute. In this study, as a part of the evaluation of the high-temperature structural integrity of the PHE prototype, high-temperature structural analysis modeling, and macroscopic thermal and elastic-plastic structural analysis of the PHE prototype were carried out under the gas-loop test conditions as a preliminary qwer123$ study before carrying out the performance test in the gas loop. The results obtained in this study will be used to design the performance test setup for the modified PHE prototype

  2. Doped polymer electrodes for high performance ferroelectric capacitors on plastic substrates

    KAUST Repository

    Khan, M. A.; Bhansali, Unnat Sampatraj; Zhang, Xixiang; Saleh, Moussa M.; Odeh, Ihab; Alshareef, Husam N.

    2012-01-01

    classical ferroelectric and dielectric responses, including series resistance effects. The improved device characteristics obtained using highly conducting doped PEDOT:PSS suggest that it may be used both as an electrode and as global interconnect for all

  3. Effects of Thin High-z Layers on the Hydrodynamics of Laser-Accelerated Plastic Targets

    National Research Council Canada - National Science Library

    Obenschain, S. P; Colombant, D; Karasik, M; Pawley, C. J; Serlin, V; Schmitt, A. J; Gardner, J. H; Phillips, L; Aglitskly, Y; Chan, Y

    2002-01-01

    .... This pulse shape simulates the generic shape needed for high-gain fusion implosions. Imprint of laser nonuniformity during start up of the low intensity foot is a well-known seed for hydrodynamic instability...

  4. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    Science.gov (United States)

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species. PMID:27739446

  5. A protocol for generating a high-quality genome-scale metabolic reconstruction.

    Science.gov (United States)

    Thiele, Ines; Palsson, Bernhard Ø

    2010-01-01

    Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

  6. High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces.

    Science.gov (United States)

    Alexander, William G; Doering, Drew T; Hittinger, Chris Todd

    2014-11-01

    Current genome editing techniques available for Saccharomyces yeast species rely on auxotrophic markers, limiting their use in wild and industrial strains and species. Taking advantage of the ancient loss of thymidine kinase in the fungal kingdom, we have developed the herpes simplex virus thymidine kinase gene as a selectable and counterselectable marker that forms the core of novel genome engineering tools called the H: aploid E: ngineering and R: eplacement P: rotocol (HERP) cassettes. Here we show that these cassettes allow a researcher to rapidly generate heterogeneous populations of cells with thousands of independent chromosomal allele replacements using mixed PCR products. We further show that the high efficiency of this approach enables the simultaneous replacement of both alleles in diploid cells. Using these new techniques, many of the most powerful yeast genetic manipulation strategies are now available in wild, industrial, and other prototrophic strains from across the diverse Saccharomyces genus. Copyright © 2014 by the Genetics Society of America.

  7. Whole genome DNA methylation: beyond genes silencing

    OpenAIRE

    Tirado-Magallanes, Roberto; Rebbani, Khadija; Lim, Ricky; Pradhan, Sriharsa; Benoukraf, Touati

    2016-01-01

    The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the ...

  8. High survival of mouse embryos after rapid freezing and thawing inside plastic straws with 1-2 propanediol as cryoprotectant.

    Science.gov (United States)

    Renard, J P; Babinet, C

    1984-06-01

    A method for obtaining a high survival rate of frozen-thawed mouse embryos is presented. Eight-cell mouse embryos were frozen inside small plastic straws in the presence of 1-2 propanediol and stored at -196 C. After thawing, the embryos were diluted for only 5 min in a 1.0 M sucrose solution to remove the 1-2 propanediol from the cells. At high rate of thawing (is equivalent to 2500 C/min) more than 88% of the embryos survived in vitro to the blastocyst stage provided that the dilution of propanediol was performed rapidly during thawing. At a lower rate of thawing (is equivalent to 300 C/min), survival tended to be higher (94.7%) when dilution was done 5 min after thawing. When the frozen-thawed embryos were transferred to the oviducts of day 1 pseudopregnant recipients either directly after the dilution of 1-2 propanediol or after 24 or 48 hr of culture, a high proportion of them (65.9%) develop normally to viable fetuses.

  9. Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

    Directory of Open Access Journals (Sweden)

    Christian M. Tobias

    2008-11-01

    Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

  10. PLASTIC SURGERY

    African Journals Online (AJOL)

    Department of Plastic and Reconstructive Surgery Sefako Makgatho Health Science University, ... We report on a pilot study on the use of a circumareolar excision and the use of .... and 1 gynecomastia patient) requested reduction in NAC size.

  11. Screen Printing of Highly Loaded Silver Inks on Plastic Substrates Using Silicon Stencils.

    Science.gov (United States)

    Hyun, Woo Jin; Lim, Sooman; Ahn, Bok Yeop; Lewis, Jennifer A; Frisbie, C Daniel; Francis, Lorraine F

    2015-06-17

    Screen printing is a potential technique for mass-production of printed electronics; however, improvement in printing resolution is needed for high integration and performance. In this study, screen printing of highly loaded silver ink (77 wt %) on polyimide films is studied using fine-scale silicon stencils with openings ranging from 5 to 50 μm wide. This approach enables printing of high-resolution silver lines with widths as small as 22 μm. The printed silver lines on polyimide exhibit good electrical properties with a resistivity of 5.5×10(-6) Ω cm and excellent bending tolerance for bending radii greater than 5 mm (tensile strains less than 0.75%).

  12. Plastic Fishes

    CERN Multimedia

    Trettnak, Wolfgang

    2015-01-01

    In terms of weight, the plastic pollution in the world’s oceans is estimated to be around 300,000 tonnes. This plastic comes from both land-based and ocean-based sources. A lecture at CERN by chemist Wolfgang Trettnak addressed this issue and highlighted the role of art in raising people’s awareness. The slideshow below gives you a taste of the artworks by Wolfgang Trettnak and Margarita Cimadevila.

  13. Scintillating plastic optical fiber radiation detectors in high energy particle physics

    International Nuclear Information System (INIS)

    Bross, A.D.

    1991-01-01

    We describe the application of scintillating optical fiber in instrumentation for high energy particle physics. The basic physics of the scintillation process in polymers is discussed first and then we outline the fundamentals of scintillating fiber technology. Fiber performance, optimization, and characterization measurements are given. Detector applications in the areas of particle tracking and particle energy determination are then described. 13 refs., 12 figs

  14. High performance low voltage organic field effect transistors on plastic substrate for amplifier circuits

    NARCIS (Netherlands)

    Houin, G.J.R.; Duez, F.; Garcia, L.; Cantatore, E.; Torricelli, F.; Hirsch, L.; Belot, D.; Pellet, C.; Abbas, M.

    2016-01-01

    The high performance air stable organic semiconductor small molecule dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene (DNTT) was chosen as active layer for field effect transistors built to realize flexible amplifier circuits. Initial device on rigid Si/SiO2 substrate showed appreciable performance

  15. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  16. Use of high-molecular compounds in plastic lubricants for geological exploratory drilling

    Energy Technology Data Exchange (ETDEWEB)

    Smyk, Z.I.; Kuz' michev, S.P.; Mnishchenko, V.G.; Smertenko, M.I.

    1982-01-01

    The existing lubricants in the series KAVS (OST 81-4-70) do not correspond to the conditions of high-rotational diamond drilling for a number of operating properties. Results are presented of studying the hydrated calcium lubricants with high molecular additives (polyisobutylene KP-10, polyethylene of high density of low pressure and atactic propylene in a quantity of 1-6%) improving their operating properties. Selection of the additives is governed by their compatability with the base and the capacity to improve the adhesion-cohesion properties with relative constancy of other characteristics. As a result of the studies it was established that the use in the lubricant of polymers of the carbon-chain type of amorphous structure in a quantity of 1-2% depending on the molecular weight noticeably improves the stickiness, resistance to erosion by water, colloidal stability, and lubricant properties. When they are added in a large quantity, a sharp weakening of the lubricants is observed and in individual cases, formation of unstable systems. Polymers of the hetero-chain type because of the presence of polar groups are highly effective adhesives. Protective and packing lubricants are developed which contain rubbers. Alkyl-phenol-amine resins (octophor-N), the bottoms from the production of phenol formaldehyde resin, rosin and lignite wax introduced at the stage of cooling have a positive effect on the lubricant properties. The best operating properties with satisfactory other indicators (viscosity, colloidal stability, antiwear properties) are found in the samples containing polyisobutylene KP-10, lignite wax and rosin. Operating tests of an experimental batch of this lubricant under conditions of real drilling indicated that its use as compared to KEVS-45 makes it possible to increase the drilling rate by 40%, reduce the outlays of power to 50%, reduce the service time and the outlays of energy resources for applying the lubricant layer to the pipe surface.

  17. Highly-efficient, flexible piezoelectric PZT thin film nanogenerator on plastic substrates.

    Science.gov (United States)

    Park, Kwi-Il; Son, Jung Hwan; Hwang, Geon-Tae; Jeong, Chang Kyu; Ryu, Jungho; Koo, Min; Choi, Insung; Lee, Seung Hyun; Byun, Myunghwan; Wang, Zhong Lin; Lee, Keon Jae

    2014-04-23

    A highly-efficient, flexible piezoelectric PZT thin film nanogenerator is demonstrated using a laser lift-off (LLO) process. The PZT thin film nanogenerator harvests the highest output performance of ∼200 V and ∼150 μA·cm(-2) from regular bending motions. Furthermore, power sources generated from a PZT thin film nanogenerator, driven by slight human finger bending motions, successfully operate over 100 LEDs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Bekim Sadikovic

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

  19. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing

    Directory of Open Access Journals (Sweden)

    Plant Ramona N

    2006-08-01

    Full Text Available Abstract Background Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs or large scale (CGH array, FISH methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. Results All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Conclusion Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.

  20. [Simultaneous determination of six fluorescent whitening agents in plastic and paper packaging materials by high performance liquid chromatography].

    Science.gov (United States)

    Zhang, Juzhou; Ji, Shuilin; Cai, Huimei; Li, Jing; Wang, Yongxin; Wang, Jingqiu

    2017-11-08

    A novel analytical method was developed for the simultaneous determination of six fluorescent whitening agents (FWAs:FWA 135, FWA 184, FWA 185, FWA 199, FWA 378 and FWA 393) in paper and plastic food packaging materials by high performance liquid chromatography with fluorescence detection (HPLC-FLD). The sample was extracted with mixed solution of chloroform and acetonitrile (3:7, v/v), then cleaned up by HLB solid phase extraction column. Qualitative and quantitative analyses were carried out by HPLC. The sample was separated on a Phenomenex C18 column using acetonitrile and 5 mmol/L ammonium acetate aqueous solution as mobile phases. The results indicated that the linear range of FWA393 was 15-1500 μg/L and the linear ranges of the other five FWAs were 5-500 μg/L with correlation coefficients greater than 0.999. The recoveries in spiked samples were between 80.4% and 125.0% with RSDs ( n =6) of 1%-13%. Furthermore, this method was applied to analyze 12 samples in the market to verify the practicality of the method. The method showed the advantages of simplicity, high recovery and good precision, and is suitable for the detection of the six fluorescent whitening agents in food packaging materials.

  1. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity.

    Science.gov (United States)

    Granados-Cifuentes, Camila; Bellantuono, Anthony J; Ridgway, Tyrone; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

    2013-04-08

    Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

  2. Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.

    Science.gov (United States)

    Dos Santos, Renato Augusto Corrêa; Berretta, Andresa A; Barud, Hernane da Silva; Ribeiro, Sidney José Lima; González-García, Laura Natalia; Zucchi, Tiago Domingues; Goldman, Gustavo H; Riaño-Pachón, Diego M

    2014-07-24

    Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose. Copyright © 2014 dos Santos et al.

  3. A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

    Science.gov (United States)

    Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Davey Smith, G; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

    2016-08-01

    Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

  4. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library

    Directory of Open Access Journals (Sweden)

    Sandra L. Hoffberg

    2018-06-01

    Full Text Available The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.

  5. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Science.gov (United States)

    Bi, Yanwei; Sun, Le; Gao, Dandan; Ding, Chen; Li, Zhihua; Li, Yadong; Cun, Wei; Li, Qihan

    2014-05-01

    A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)) RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  6. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Directory of Open Access Journals (Sweden)

    Yanwei Bi

    2014-05-01

    Full Text Available A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR-associated (Cas RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ and homology-directed repair (HDR pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  7. The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.

    Science.gov (United States)

    Zeng, Xingquan; Long, Hai; Wang, Zhuo; Zhao, Shancen; Tang, Yawei; Huang, Zhiyong; Wang, Yulin; Xu, Qijun; Mao, Likai; Deng, Guangbing; Yao, Xiaoming; Li, Xiangfeng; Bai, Lijun; Yuan, Hongjun; Pan, Zhifen; Liu, Renjian; Chen, Xin; WangMu, QiMei; Chen, Ming; Yu, Lili; Liang, Junjun; DunZhu, DaWa; Zheng, Yuan; Yu, Shuiyang; LuoBu, ZhaXi; Guang, Xuanmin; Li, Jiang; Deng, Cao; Hu, Wushu; Chen, Chunhai; TaBa, XiongNu; Gao, Liyun; Lv, Xiaodan; Abu, Yuval Ben; Fang, Xiaodong; Nevo, Eviatar; Yu, Maoqun; Wang, Jun; Tashi, Nyima

    2015-01-27

    The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

  8. High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

    Directory of Open Access Journals (Sweden)

    Gilbert Greub

    Full Text Available BACKGROUND: With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. METHODS/PRINCIPAL FINDINGS: We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. CONCLUSIONS/SIGNIFICANCE: This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

  9. Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data.

    Science.gov (United States)

    Chiara, Matteo; Pavesi, Giulio

    2017-01-01

    Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science. Bioinformatic analysis of human resequencing data is one of the main factors limiting the effectiveness and general applicability of NGS for clinical studies. The requirement for multiple tools, to be combined in dedicated protocols in order to accommodate different types of data (gene panels, exomes, or whole genomes) and the high variability of the data makes difficult the establishment of a ultimate strategy of general use. While there already exist several studies comparing sensitivity and accuracy of bioinformatic pipelines for the identification of single nucleotide variants from resequencing data, little is known about the impact of quality assessment and reads pre-processing strategies. In this work we discuss major strengths and limitations of the various genome resequencing protocols are currently used in molecular diagnostics and for the discovery of novel disease-causing mutations. By taking advantage of publicly available data we devise and suggest a series of best practices for the pre-processing of the data that consistently improve the outcome of genotyping with minimal impacts on computational costs.

  10. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

    OpenAIRE

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-01-01

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gen...

  11. GREEN PLASTIC: A NEW PLASTIC FOR PACKAGING

    OpenAIRE

    Mr. Pankaj Kumar*, Sonia

    2016-01-01

    This paper gives a brief idea about a new type of plastic called as bio-plastic or green plastic. Plastic is used as a packaging material for various products, but this plastic is made up of non renewable raw materials. There are various disadvantages of using conventional plastic like littering, CO2 production, non-degradable in nature etc. To overcome these problems a new type of plastic is discovered called bio-plastic or green plastic. Bio-plastic is made from renewable resources and also...

  12. Whole genome DNA copy number changes identified by high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Huang Jing

    2004-05-01

    Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

  13. Plastic materials and Acome's use of high energy electron processing in France

    International Nuclear Information System (INIS)

    Goavec, P.G.

    1979-01-01

    Crosslinking is the way to improve the physical properties of polymer materials, particularly at high temperatures. Radiation crosslinking being the process most suited to achieve this target in the field of fine wire and cable, Acome built, for this application, an irradiation plant: the only one to date in that industry in France. The main piece of equipment in this plant is a Radiation Dynamics electron accelerator. Although simple in its principle, the process is delicate to operate owing to the complexity of the chemistry involved in the raw materials. The successful development of this process led Acome to a new generation of upgraded wires and cables for telecommunication, signal, automotive and special applications which are finding a growing market thanks to their increased reliability. (author)

  14. Recycling of packing plastics

    International Nuclear Information System (INIS)

    Gintenreiter-Koegl, S.

    2001-05-01

    The ordinance on the avoidance of packaging waste was a serious intervention in the public and private waste management in Austria. Above all the high expenses for an overall packaging waste collection and the recycling of packaging plastics were criticized. The landfill ordinance comes into force in 2004 and this means another major change in the Austrian waste management system. In the course of this change the overall collection and the recycling and recovery of waste streams, especially of the high caloric plastics waste, have to be discussed again. The goal of this work was on the one hand to develop and adapt the hydrocracking process for the recovery of mixed plastics waste and to show a possible application in Austria. On the other hand the work shows the technical, ecological and economical conditions for packaging plastics recycling and recovery in order to find optimum applications for the processes and to examine their contribution to a sustainable development. A hydrocracking test plant for the processing of mixed plastic wastes was built and had been running for about three years. The tests were carried out successfully and the suitability of the technology for the recovery of packaging plastics could be shown. Results show at least a 35 % yield of fuel. The hydrocracking technology is quite common in the oil industries and therefore an integration on a refinery site is suggested. (author)

  15. Boron content effect on the high-temperature plasticity of corrosion resistant low-carbon austenite type steels

    International Nuclear Information System (INIS)

    Gol'dshtejn, Ya.E.; Shmatko, M.N.; Chuvatina, S.N.

    1976-01-01

    With the concept that the state of grain and subgrain boundaries influences the hot plasticity of corrosion resistant steel as a starting point, the study was undertaken of the effect of boron microalloying up on the intergranular strength and of the action boron exerts upon the distribution (redistribution) of other phases present in austenitic 03Kh16N14M3 steels. An electron microscope study of the composition of redundant phases and that of the fine structure of steel have shown the effect of small additions of boron upon the hot plasticity of steel to be linked directly to its influence upon austenite disintegration and the precipitation along the boundaries of crystals of redundant phases in the course of hot plastic deformation. The action of boron upon the process plasticity of steel depends on the temperature and the rate of deformation which govern the kinetics of the precipitation of the redundant phases

  16. The Highly Divergent Mitochondrial Genomes Indicate That the Booklouse, Liposcelis bostrychophila (Psocoptera: Liposcelididae) Is a Cryptic Species.

    Science.gov (United States)

    Feng, Shiqian; Yang, Qianqian; Li, Hu; Song, Fan; Stejskal, Václav; Opit, George P; Cai, Wanzhi; Li, Zhihong; Shao, Renfu

    2018-03-02

    The booklouse, Liposcelis bostrychophila is an important storage pest worldwide. The mitochondrial (mt) genome of an asexual strain (Beibei, China) of the L. bostrychophila comprises two chromosomes; each chromosome contains approximate half of the 37 genes typically found in bilateral animals. The mt genomes of two sexual strains of L. bostrychophila , however, comprise five and seven chromosomes, respectively; each chromosome contains one to six genes. To understand mt genome evolution in L. bostrychophila , and whether L. bostrychophila is a cryptic species, we sequenced the mt genomes of six strains of asexual L. bostrychophila collected from different locations in China, Croatia, and the United States. The mt genomes of all six asexual strains of L. bostrychophila have two chromosomes. Phylogenetic analysis of mt genome sequences divided nine strains of L. bostrychophila into four groups. Each group has a distinct mt genome organization and substantial sequence divergence (48.7-87.4%) from other groups. Furthermore, the seven asexual strains of L. bostrychophila , including the published Beibei strain, are more closely related to two other species of booklice, L. paeta and L. sculptilimacula , than to the sexual strains of L. bostrychophila Our results revealed highly divergent mt genomes in the booklouse, L. bostrychophila , and indicate that L. bostrychophila is a cryptic species. Copyright © 2018 Feng et al.

  17. The Highly Divergent Mitochondrial Genomes Indicate That the Booklouse, Liposcelis bostrychophila (Psocoptera: Liposcelididae Is a Cryptic Species

    Directory of Open Access Journals (Sweden)

    Shiqian Feng

    2018-03-01

    Full Text Available The booklouse, Liposcelis bostrychophila is an important storage pest worldwide. The mitochondrial (mt genome of an asexual strain (Beibei, China of the L. bostrychophila comprises two chromosomes; each chromosome contains approximate half of the 37 genes typically found in bilateral animals. The mt genomes of two sexual strains of L. bostrychophila, however, comprise five and seven chromosomes, respectively; each chromosome contains one to six genes. To understand mt genome evolution in L. bostrychophila, and whether L. bostrychophila is a cryptic species, we sequenced the mt genomes of six strains of asexual L. bostrychophila collected from different locations in China, Croatia, and the United States. The mt genomes of all six asexual strains of L. bostrychophila have two chromosomes. Phylogenetic analysis of mt genome sequences divided nine strains of L. bostrychophila into four groups. Each group has a distinct mt genome organization and substantial sequence divergence (48.7–87.4% from other groups. Furthermore, the seven asexual strains of L. bostrychophila, including the published Beibei strain, are more closely related to two other species of booklice, L. paeta and L. sculptilimacula, than to the sexual strains of L. bostrychophila. Our results revealed highly divergent mt genomes in the booklouse, L. bostrychophila, and indicate that L. bostrychophila is a cryptic species.

  18. The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

    Science.gov (United States)

    Sakai, Hiroaki; Naito, Ken; Takahashi, Yu; Sato, Toshiyuki; Yamamoto, Toshiya; Muto, Isamu; Itoh, Takeshi; Tomooka, Norihiko

    2016-01-01

    The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Anomalous plastic flow of cerium near the isomorphic phase transformations under high hydrostatic pressure

    International Nuclear Information System (INIS)

    Witczak, Z.; Goncharova, V.A.

    1999-01-01

    Compression tests have been carried out on cerium specimens at room temperature (0.27 T m ) under high hydrostatic pressures up to 1.2 GPa. A strong increase of the yield strength was observed for both isomorphic γ and α phases at pressures approaching the γ ↔ α isomorphic phase transformations. That increase was in good agreement with the theory of dislocations when the dependence of elastic properties and a lattice parameter of cerium on pressure was applied to calculate the effect of pressure on the yield stress controlled by the edge dislocations. An anomalous strong decrease of the yield stress was observed in both γ and α phases in the vicinity of both γ ↔ α phase transformations. That phenomenon was explained as an effect of pressure induced new phase atoms through spreading the cores of edge dislocations. A complete disappearance of work hardening in both γ and α phases was also observed in the wide range of pressures. The influence of hydrostatic pressure on the energy of grain boundaries of both phases was considered to be responsible for that property. The ratio of the grain boundary energy to the Peierls energy is suggested to be a criterion of the work hardening ability of f.c.c. polycrystals

  20. Novel high-strength Fe-based composite materials with large plasticity

    Energy Technology Data Exchange (ETDEWEB)

    Werniewicz, Katarzna; Kuehn, Uta; Mattern, Norbert; Eckert, Juergen; Siegel, Uwe; Bartusch, Birgit; Schultz, Ludwig [IFW Dresden, P.O. Box 270116, D-01171 Dresden (Germany); Kulik, Tadeusz [Warsaw University of Technology, Faculty of Materials Science and Engineering (Poland)

    2007-07-01

    Among glass-forming alloy systems reported so far, Fe-based bulk metallic glasses play a special role. Compared to other amorphous alloys e.g. Zr-, Ti-based, such glasses show superior mechanical strength. However, due to the general brittleness their wider application as structural materials is strongly restricted. The alternative approach to overcome this defect is to design BMG composites. In this work we present a series of new Fe-Cr-Mo-Ga-(Si,C) composite materials derived from an Fe-Cr-Mo-Ga-C-P-B glassy alloy, with the aim to improve the ductility of this high-strength material. The effect of the composition and the phase formation on the resulting mechanical properties was investigated. It has been found that the formation of a complex microstructure, which essentially consists of soft Ga-rich dendrites embedded in a hard Cr- and Mo-rich matrix, leads to a material with excellent compressive mechanical properties. While the obtained values of true strength are comparable with data reported for Fe-Cr-Mo-Ga-C-P-B BMG, the values of true strain are greatly improved for investigated composites.

  1. Two efficient methods for isolation of high-quality genomic DNA from entomopathogenic fungi.

    Science.gov (United States)

    Serna-Domínguez, María G; Andrade-Michel, Gilda Y; Arredondo-Bernal, Hugo C; Gallou, Adrien

    2018-03-27

    Conventional and commercial methods for isolation of nucleic acids are available for fungal samples including entomopathogenic fungi (EPF). However, there is not a unique optimal method for all organisms. The cell wall structure and the wide range of secondary metabolites of EPF can broadly interfere with the efficiency of the DNA extraction protocol. This study compares three commercial protocols: DNeasy® Plant Mini Kit (Qiagen), Wizard® Genomic DNA Purification Kit (Promega), and Axygen™ Multisource Genomic DNA Miniprep Kit (Axygen) and three conventional methods based on different buffers: SDS, CTAB/PVPP, and CTAB/β-mercaptoethanol versus three cell lysis procedures: liquid nitrogen homogenization and two bead-beating materials (i.e., tungsten-carbide and stainless-steel) for four representative species of EPF (i.e., Beauveria bassiana, Hirsutella citriformis, Isaria javanica, and Metarhizium anisopliae). Liquid nitrogen homogenization combined with DNeasy® Plant Mini Kit (i.e., QN) or SDS buffer (i.e., SN) significantly improved the yield with a good purity (~1.8) and high integrity (>20,000 bp) of genomic DNA in contrast with other methods, also, these results were better when compared with the two bead-beating materials. The purified DNA was evaluated by PCR-based techniques: amplification of translation elongation factor 1-α (TEF) and two highly sensitive molecular markers (i.e., ISSR and AFLP) with reliable and reproducible results. Despite a variation in yield, purity, and integrity of extracted DNA across the four species of EPF with the different DNA extraction methods, the SN and QN protocols maintained a high-quality of DNA which is required for downstream molecular applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. [Determination of phthalate plasticizers in foods by high performance liquid chromatography with gel permeation chromatographic clean-up].

    Science.gov (United States)

    Zhang, Chunyu; Wang, Hui; Zhang, Xiaohui; Ma, Zhongqiang; Deng, Wanmei; Hu, Ke; Ding, Mingyu

    2011-12-01

    A method of gel permeation chromatography-high performance liquid chromatography (GPC-HPLC) was established for the simultaneous determination of 5 main phthalate plasticizers in foods (edible oil, instant noodles, fried pastries, Saqima, etc.). The samples were extracted with petroleum ether in an ultrasonator, purified by a GPC column, and analyzed by HPLC. The chromatographic separation was achieved on a Labtech-C18 column (250 mm x 4.6 mm, 5 microm) using acetonitrile and water mixture as the mobile phases in a gradient elution mode. The developed method exhibited a linear correlation coefficient of more than 0.997 and the detection limits of 3.25 - 13.4 microg/L. The spike recoveries were between 70.4% and 113.6% with the relative standard deviations (RSDs, n = 3) of 0.3% - 5.8% at the spiked level of 50 mg/L. This method is simple, rapid and practical, and can be used for the simultaneous determination of PAEs in grease food samples.

  3. Recovery and deformation substructures of zircaloy-4 in high temperature plasticity under stationary or non-stationary stress

    International Nuclear Information System (INIS)

    Bocek, M.; Armas, I.

    1982-01-01

    It was the aim of the present investigation to examine how the recovery rate in creep is influenced by a non-stationary stress. For purposes of phenomenological analysis it is postulated that, irrespective of whether the applied stress is stationary or not, for large strains the mean internal stress sigmasub(i) approaches a stationary value sigmasub(i,s). The stationary recovery rate Rsub(s) for constant load creep turns out be governed by the applied stress indicating that the recovery mechanism is dynamic in nature. For sigma-ramp loading, Rsub(s) is dependent on the stress rate sigma. In tensional stress cycling, Rsub(s) is governed by the maximum stress sigmasub(M) and is also dependent on the ratio of sigmasub(M) to the minimum stress sigma 0 . TEM examination of Zircaloy-4 specimens crept at 800 0 C at constant and cycling load respectively could not reveal any differences in the deformation substructure for the two loading types. Subgrain formation did not appear, individual dislocations were observed only rarely. However, typical networks were formed as well as pileups which perhaps are responsible for the back stress in high temperature plasticity (HTP). (orig.)

  4. Development of high radiation-resistant glass fiber reinforced plastics with cyanate-based resin for superconducting magnet systems

    Energy Technology Data Exchange (ETDEWEB)

    Idesaki, Akira, E-mail: idesaki.akira@qst.go.jp [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Watanuki 1233, Takasaki, Gunma 370-1292 (Japan); Nakamoto, Tatsushi [Cryogenic Science Center, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Yoshida, Makoto [Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shimada, Akihiko [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Watanuki 1233, Takasaki, Gunma 370-1292 (Japan); Iio, Masami; Sasaki, Kenichi; Sugano, Michinaka [Cryogenic Science Center, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Makida, Yasuhiro [Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Ogitsu, Toru [Cryogenic Science Center, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

    2016-11-15

    Highlights: • GFRPs for superconducting magnet systems were developed. • Cyanate-based resins were used for GFRPs as matrices. • Radiation resistance was evaluated based on gas evolution and mechanical properties. • GFRP with bismaleimide-triazine resin exhibited excellent radiation resistance. - Abstract: Glass fiber reinforced plastics (GFRPs) with cyanate ester resin/epoxy resin, bismaleimide resin/epoxy resin, and bismaleimide-triazine resin as matrices were developed for the superconducting magnet systems used in high intensity accelerators. The radiation resistance of these GFRPs was evaluated based on their gas evolution and changes in their mechanical properties after gamma-ray irradiation with dose of 100 MGy in vacuum at ambient temperature. After irradiation, a small amount of gas was evolved from all of the GFRPs, and a slight decrease in mechanical properties was observed compared with the conventional epoxy resin-GFRP, G10. Among the GFRPs, the smallest amount of gas (6 × 10{sup −5} mol/g) was evolved from the GFRP with the bismaleimide-triazine resin, which also retained more than 88% of its flexural strength after 100 MGy irradiation; this GFRP is thus considered the most promising material for superconducting magnet systems.

  5. The environmental plasticity of diverse body color caused by extremely long photoperiods and high temperature in Saccharosydne procerus (Homoptera: Delphacidae

    Directory of Open Access Journals (Sweden)

    Haichen Yin

    2016-09-01

    Full Text Available Melanization reflects not only body color variation but also environmental plasticity. It is a strategy that helps insects adapt to environmental change. Different color morphs may have distinct life history traits, e.g., development time, growth rate, and body weight. The green slender planthopper Saccharosydne procerus (Matsumura is the main pest of water bamboo (Zizania latifolia. This insect has two color morphs. The present study explored the influence of photoperiod and its interaction with temperature in nymph stage on adult melanism. Additionally, the longevity, fecundity, mating rate, and hatching rate of S. procerus were examined to determine whether the fitness of the insect was influenced by melanism under different temperature and photoperiod. The results showed that a greater number of melanic morphs occurred if the photoperiod was extremely long. A two-factor ANOVA showed that temperature and photoperiod both have a significant influence on melanism. The percentages of variation explained by these factors were 45.53% and 48.71%, respectively. Moreover, melanic morphs had greater advantages than non-melanic morphs under an environmental regime of high temperatures and a long photoperiod, whereas non-melanic morphs were better adapted to cold temperatures and a short photoperiod. These results cannot be explained by the thermal melanism hypothesis. Thus, it may be unavailable to seek to explain melanism in terms of only one hypothesis.

  6. Preparation and properties of thermoplastic poly(caprolactone) composites containing high amount of esterified starch without plasticizer.

    Science.gov (United States)

    Sun, Yujie; Hu, Qiongen; Qian, Jiangtao; Li, Ting; Ma, Piming; Shi, Dongjian; Dong, Weifu; Chen, Mingqing

    2016-03-30

    Based on stearyl chloride and native starch, esterified starch were prepared and the chemical structure was characterized by (1)H NMR and FTIR. It was found that stearyl chloride was an efficient agent to fabricate esterified starch with high degree of substitution (DS). During the melt blending of esterified starch (80 wt%) and poly(caprolactone) (PCL, 20 wt%), it was shown the torque of PCL/esterified starch was much lower than that of PCL/native starch without any plasticizer, and further decreased with increasing DS. Compared with PCL/native starch, the tensile properties of PCL/esterified starch composites were significantly enhanced. The tensile strength and elongation at break were increased from 2.7 MPa to 56% for PCL/native starch composites to 9.1 MPa and 626% for PCL/esterified starch ones with DS of 1.50, respectively. SEM observation revealed the esterified starch particles in matrix became smaller and more uniform. In addition, the water resistance and hydrophobic character of PCL/esterified starch composites were improved. PCL composites containing 80 wt% esterified starch with favorable mechanical properties would have great potential applications in broad areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. High-conductance low-voltage organic thin film transistor with locally rearranged poly(3-hexylthiophene) domain by current annealing on plastic substrate

    Science.gov (United States)

    Pei, Zingway; Tsai, Hsing-Wang; Lai, Hsin-Cheng

    2016-02-01

    The organic material based thin film transistors (TFTs) are attractive for flexible optoelectronics applications due to the ability of lager area fabrication by solution and low temperature process on plastic substrate. Recently, the research of organic TFT focus on low operation voltage and high output current to achieve a low power organic logic circuit for optoelectronic device,such as e-paper or OLED displayer. To obtain low voltage and high output current, high gate capacitance and high channel mobility are key factors. The well-arranged polymer chain by a high temperature postannealing, leading enhancement conductivity of polymer film was a general method. However, the thermal annealing applying heat for all device on the substrate and may not applicable to plastic substrate. Therefore, in this work, the low operation voltage and high output current of polymer TFTs was demonstrated by locally electrical bias annealing. The poly(styrene-comethyl methacrylate) (PS-r-PMMA) with ultra-thin thickness is used as gate dielectric that the thickness is controlled by thermal treatment after spin coated on organic electrode. In electrical bias-annealing process, the PS-r- PMMA is acted a heating layer. After electrical bias-annealing, the polymer TFTs obtain high channel mobility at low voltage that lead high output current by a locally annealing of P3HT film. In the future, the locally electrical biasannealing method could be applied on plastic substrate for flexible optoelectronic application.

  8. The mechanism of coking pressure generation I: Effect of high volatile matter coking coal, semi-anthracite and coke breeze on coking pressure and plastic coal layer permeability

    Energy Technology Data Exchange (ETDEWEB)

    Seiji Nomura; Merrick Mahoney; Koichi Fukuda; Kenji Kato; Anthony Le Bas; Sid McGuire [Nippon Steel Corporation, Chiba (Japan). Environment and Process Technology Center

    2010-07-15

    One of the most important aspects of the cokemaking process is to control and restrain the coking pressure since excessive coking pressure tends to lead to operational problems and oven wall damage. Therefore, in order to understand the mechanism of coking pressure generation, the permeability of the plastic coal layer and the coking pressure for the same single coal and the same blended coal were measured and the relationship between them was investigated. Then the 'inert' (pressure modifier) effect of organic additives such as high volatile matter coking coal, semi-anthracite and coke breeze was studied. The coking pressure peak for box charging with more uniform bulk density distribution was higher than that for top charging. It was found that the coking pressure peaks measured at different institutions (NSC and BHPBilliton) by box charging are nearly the same. The addition of high volatile matter coking coal, semi-anthracite and coke breeze to a low volatile matter, high coking pressure coal greatly increased the plastic layer permeability in laboratory experiments and correspondingly decreased the coking pressure. It was found that, high volatile matter coking coal decreases the coking pressure more than semi-anthracite at the same plastic coal layer permeability, which indicates that the coking pressure depends not only on plastic coal layer permeability but also on other factors. Coking pressure is also affected by the contraction behavior of the coke layer near the oven walls and a large contraction decreases the coal bulk density in the oven center and hence the internal gas pressure in the plastic layer. The effect of contraction on coking pressure needs to be investigated further. 33 refs., 18 figs., 5 tabs.

  9. Ebola virus genome plasticity as a marker of its passaging history: a comparison of in vitro passaging to non-human primate infection.

    Directory of Open Access Journals (Sweden)

    Jeffrey R Kugelman

    Full Text Available To identify polymorphic sites that could be used as biomarkers of Ebola virus passage history, we repeatedly amplified Ebola virus (Kikwit variant in vitro and in vivo and performed deep sequencing analysis of the complete genomes of the viral subpopulations. We then determined the sites undergoing selection during passage in Vero E6 cells. Four locations within the Ebola virus Kikwit genome were identified that together segregate cell culture-passaged virus and virus obtained from infected non-human primates. Three of the identified sites are located within the glycoprotein gene (GP sequence: the poly-U (RNA editing site at position 6925, as well as positions 6677, and 6179. One site was found in the VP24 gene at position 10833. In all cases, in vitro and in vivo, both populations (majority and minority variants were maintained in the viral swarm, with rapid selections occurring after a few passages or infections. This analysis approach will be useful to differentiate whether filovirus stocks with unknown history have been passaged in cell culture and may support filovirus stock standardization for medical countermeasure development.

  10. Abiotic degradation of plastic films

    Science.gov (United States)

    Ángeles-López, Y. G.; Gutiérrez-Mayen, A. M.; Velasco-Pérez, M.; Beltrán-Villavicencio, M.; Vázquez-Morillas, A.; Cano-Blanco, M.

    2017-01-01

    Degradable plastics have been promoted as an option to mitigate the environmental impacts of plastic waste. However, there is no certainty about its degradability under different environmental conditions. The effect of accelerated weathering (AW), natural weathering (NW) and thermal oxidation (TO) on different plastics (high density polyethylene, HDPE; oxodegradable high density polyethylene, HDPE-oxo; compostable plastic, Ecovio ® metalized polypropylene, PP; and oxodegradable metalized polypropylene, PP-oxo) was studied. Plastics films were exposed to AW per 110 hours; to NW per 90 days; and to TO per 30 days. Plastic films exposed to AW and NW showed a general loss on mechanical properties. The highest reduction in elongation at break on AW occurred to HDPE-oxo (from 400.4% to 20.9%) and was higher than 90% for HDPE, HDPE-oxo, Ecovio ® and PP-oxo in NW. No substantial evidence of degradation was found on plastics exposed to TO. Oxo-plastics showed higher degradation rates than their conventional counterparts, and the compostable plastic was resistant to degradation in the studied abiotic conditions. This study shows that degradation of plastics in real life conditions will vary depending in both, their composition and the environment.

  11. Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain

    Science.gov (United States)

    2013-01-01

    Background Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low direct mortality, EP is responsible for major economic losses in the pig industry. To identify the virulence-associated determinants of M. hyopneumoniae, we determined the whole genome sequence of M. hyopneumoniae strain 168 and its attenuated high-passage strain 168-L and carried out comparative genomic analyses. Results We performed the first comprehensive analysis of M. hyopneumoniae strain 168 and its attenuated strain and made a preliminary survey of coding sequences (CDSs) that may be related to virulence. The 168-L genome has a highly similar gene content and order to that of 168, but is 4,483 bp smaller because there are 60 insertions and 43 deletions in 168-L. Besides these indels, 227 single nucleotide variations (SNVs) were identified. We further investigated the variants that affected CDSs, and compared them to reported virulence determinants. Notably, almost all of the reported virulence determinants are included in these variants affected CDSs. In addition to variations previously described in mycoplasma adhesins (P97, P102, P146, P159, P216, and LppT), cell envelope proteins (P95), cell surface antigens (P36), secreted proteins and chaperone protein (DnaK), mutations in genes related to metabolism and growth may also contribute to the attenuated virulence in 168-L. Furthermore, many mutations were located in the previously described repeat motif, which may be of primary importance for virulence. Conclusions We studied the virulence attenuation mechanism of M. hyopneumoniae by comparative genomic analysis of virulent strain 168 and its attenuated high-passage strain 168-L. Our findings provide a preliminary survey of CDSs that may be related to virulence. While these include reported virulence-related genes, other novel virulence determinants were also detected. This new information will form

  12. Using Omega and NIF to Advance Theories of High-Pressure, High-Strain-Rate Tantalum Plastic Flow

    Science.gov (United States)

    Rudd, R. E.; Arsenlis, A.; Barton, N. R.; Cavallo, R. M.; Huntington, C. M.; McNaney, J. M.; Orlikowski, D. A.; Park, H.-S.; Prisbrey, S. T.; Remington, B. A.; Wehrenberg, C. E.

    2015-11-01

    Precisely controlled plasmas are playing an important role as both pump and probe in experiments to understand the strength of solid metals at high energy density (HED) conditions. In concert with theory, these experiments have enabled a predictive capability to model material strength at Mbar pressures and high strain rates. Here we describe multiscale strength models developed for tantalum and vanadium starting with atomic bonding and extending up through the mobility of individual dislocations, the evolution of dislocation networks and so on up to full scale. High-energy laser platforms such as the NIF and the Omega laser probe ramp-compressed strength to 1-5 Mbar. The predictions of the multiscale model agree well with the 1 Mbar experiments without tuning. The combination of experiment and theory has shown that solid metals can behave significantly differently at HED conditions; for example, the familiar strengthening of metals as the grain size is reduced has been shown not to occur in the high pressure experiments. Work performed under the auspices of the U.S. Dept. of Energy by Lawrence Livermore National Lab under contract DE-AC52-07NA273.

  13. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+".

    Directory of Open Access Journals (Sweden)

    Markus H Antwerpen

    Full Text Available The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  14. Insights from the genome of a high alkaline cellulase producing Aspergillus fumigatus strain obtained from Peruvian Amazon rainforest.

    Science.gov (United States)

    Paul, Sujay; Zhang, Angel; Ludeña, Yvette; Villena, Gretty K; Yu, Fengan; Sherman, David H; Gutiérrez-Correa, Marcel

    2017-06-10

    Here, we report the complete genome sequence of a high alkaline cellulase producing Aspergillus fumigatus strain LMB-35Aa isolated from soil of Peruvian Amazon rainforest. The genome is ∼27.5mb in size, comprises of 228 scaffolds with an average GC content of 50%, and is predicted to contain a total of 8660 protein-coding genes. Of which, 6156 are with known function; it codes for 607 putative CAZymes families potentially involved in carbohydrate metabolism. Several important cellulose degrading genes, such as endoglucanase A, endoglucanase B, endoglucanase D and beta-glucosidase, are also identified. The genome of A. fumigatus strain LMB-35Aa represents the first whole sequenced genome of non-clinical, high cellulase producing A. fumigatus strain isolated from forest soil. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

    Science.gov (United States)

    Sun, Fengming; Fan, Guangyi; Hu, Qiong; Zhou, Yongming; Guan, Mei; Tong, Chaobo; Li, Jiana; Du, Dezhi; Qi, Cunkou; Jiang, Liangcai; Liu, Weiqing; Huang, Shunmou; Chen, Wenbin; Yu, Jingyin; Mei, Desheng; Meng, Jinling; Zeng, Peng; Shi, Jiaqin; Liu, Kede; Wang, Xi; Wang, Xinfa; Long, Yan; Liang, Xinming; Hu, Zhiyong; Huang, Guodong; Dong, Caihua; Zhang, He; Li, Jun; Zhang, Yaolei; Li, Liangwei; Shi, Chengcheng; Wang, Jiahao; Lee, Simon Ming-Yuen; Guan, Chunyun; Xu, Xun; Liu, Shengyi; Liu, Xin; Chalhoub, Boulos; Hua, Wei; Wang, Hanzhong

    2017-11-01

    Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  16. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

    Directory of Open Access Journals (Sweden)

    Kevin A Wilkinson

    2008-04-01

    Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further

  17. Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.

    Science.gov (United States)

    Lin, Yu; Hu, Fei; Tang, Jijun; Moret, Bernard M E

    2013-01-01

    The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.

  18. High-voltage leak detection of a parenteral proteinaceous solution product packaged in form-fill-seal plastic laminate bags. Part 2. Method performance as a function of heat seal defects, product-package refrigeration, and package plastic laminate lot.

    Science.gov (United States)

    Rasmussen, Mats; Damgaard, Rasmus; Buus, Peter; Mulhall, Brian; Guazzo, Dana Morton

    2013-01-01

    Part 1 of this three-part research series detailed the development and validation of a high-voltage leak detection test (HVLD, also known as an electrical conductivity and capacitance test) for verifying the container-closure integrity of a small-volume laminate plastic bag containing an aqueous solution formulation of the rapid-acting insulin analogue, insulin aspart (NovoRapid®/NovoLog®) by Novo Nordisk A/S, Bagsværd, Denmark. Leak detection capability was verified using positive controls each with a single laser-drilled hole in the bag film face. In this Part 2, HVLD leak detection capability was further explored in four separate studies. Study 1 investigated the ability of HVLD to detect weaknesses and/or gaps in the bag heat seal. Study 2 checked the HVLD detection of bag holes in packages stored 4 days at ambient conditions followed by 17 days at refrigeration. Study 3 examined HVLD test results for packages tested when cold. Study 4 compared HVLD test results as a function of bag plastic film lots. The final Part 3 of this series will report the impact of HVLD exposure on product visual appearance and chemical stability. In Part 1 of this three-part series, a leak test method based on electrical conductivity and capacitance, also called high-voltage leak detection (HVLD), was used to find leaks in small plastic bags filled with a solution for injection of the rapid-acting insulin analogue, insulin aspart (NovoRapid®/NovoLog®) by Novo Nordisk A/S, Bagsværd, Denmark. In this Part 2, HVLD leak detection capability was further explored in four separate studies. Study 1 investigated the ability of HVLD to detect bag heat seal leaks. Study 2 checked HVLD's ability to detect bag holes after a total of 21 days at ambient plus refrigerated temperatures. Study 3 looked to see if HVLD results changed for packages tested when still cold. Study 4 compared HVLD results for multiple bag plastic film lots. The final Part 3 of this series will report any evidence of

  19. Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization.

    Science.gov (United States)

    Liao, Can; Fu, Fang; Yang, Xin; Sun, Yi-Min; Li, Dong-Zhi

    2011-06-01

    Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis. Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction. All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene. The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

  20. Comparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence.

    Science.gov (United States)

    Lu, Wei; Wise, Michael J; Tay, Chin Yen; Windsor, Helen M; Marshall, Barry J; Peacock, Christopher; Perkins, Tim

    2014-03-01

    Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (∼170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.

  1. Mixed plastics recycling technology

    CERN Document Server

    Hegberg, Bruce

    1995-01-01

    Presents an overview of mixed plastics recycling technology. In addition, it characterizes mixed plastics wastes and describes collection methods, costs, and markets for reprocessed plastics products.

  2. Pervasive plastic

    Science.gov (United States)

    2018-05-01

    Human manipulation of hydrocarbons — as fuel and raw materials for modern society — has changed our world and the indelible imprint we will leave in the rock record. Plastics alone have permeated our lives and every corner of our planet.

  3. Neurogenomic mechanisms of social plasticity.

    Science.gov (United States)

    Cardoso, Sara D; Teles, Magda C; Oliveira, Rui F

    2015-01-01

    Group-living animals must adjust the expression of their social behaviour to changes in their social environment and to transitions between life-history stages, and this social plasticity can be seen as an adaptive trait that can be under positive selection when changes in the environment outpace the rate of genetic evolutionary change. Here, we propose a conceptual framework for understanding the neuromolecular mechanisms of social plasticity. According to this framework, social plasticity is achieved by rewiring or by biochemically switching nodes of a neural network underlying social behaviour in response to perceived social information. Therefore, at the molecular level, it depends on the social regulation of gene expression, so that different genomic and epigenetic states of this brain network correspond to different behavioural states, and the switches between states are orchestrated by signalling pathways that interface the social environment and the genotype. Different types of social plasticity can be recognized based on the observed patterns of inter- versus intra-individual occurrence, time scale and reversibility. It is proposed that these different types of social plasticity rely on different proximate mechanisms at the physiological, neural and genomic level. © 2015. Published by The Company of Biologists Ltd.

  4. High-temperature plastic flow of a precipitation-hardened FeCoNiCr high entropy alloy

    Energy Technology Data Exchange (ETDEWEB)

    He, J.Y.; Wang, H.; Wu, Y.; Liu, X.J. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Nieh, T.G. [Department of Materials Science and Engineering, the University of Tennessee, Knoxville, TN 37996 (United States); Lu, Z.P., E-mail: luzhaoping@163.com [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China)

    2017-02-16

    In this work, we systematically investigated flow behavior of a high entropy alloy (HEA) strengthened by coherent γ′ precipitates in the temperature range of 1023–1173 K. In contrast to the single-phase FeCoNiCrMn HEA, this precipitate-hardened alloy, i.e., (FeCoNiCr){sub 94}Ti{sub 2}Al{sub 4}, exhibited large reduction of the steady-state strain rate (by ~2 orders of magnitude) or drastic enhancement in flow stress, indicating significant improvement in high-temperature properties. Our results showed that the deformation could be divided into two regimes. At temperatures below 1123 K, coherent γ′ precipitates effectively blocked the dislocation motion, thus resulted in a threshold stress effect. Above 1123 K, however, γ′ particles dissolved and the deformation was controlled by the ordinary dislocation climb mechanism. In addition, we conducted transmission electron microscopy to characterize dislocation-precipitate interaction to provide microstructural evidences to support our conclusion of the specific deformation mechanisms in the two temperature regimes.

  5. Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016.

    Science.gov (United States)

    Wang, Rui; Li, Liping; Huang, Yan; Luo, Fuguang; Liang, Wanwen; Gan, Xi; Huang, Ting; Lei, Aiying; Chen, Ming; Chen, Lianfu

    2015-11-04

    Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia. We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains. The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes. The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all

  6. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Science.gov (United States)

    Schuenemann, Verena J; Avanzi, Charlotte; Krause-Kyora, Ben; Seitz, Alexander; Herbig, Alexander; Inskip, Sarah; Bonazzi, Marion; Reiter, Ella; Urban, Christian; Dangvard Pedersen, Dorthe; Taylor, G Michael; Singh, Pushpendra; Stewart, Graham R; Velemínský, Petr; Likovsky, Jakub; Marcsik, Antónia; Molnár, Erika; Pálfi, György; Mariotti, Valentina; Riga, Alessandro; Belcastro, M Giovanna; Boldsen, Jesper L; Nebel, Almut; Mays, Simon; Donoghue, Helen D; Zakrzewski, Sonia; Benjak, Andrej; Nieselt, Kay; Cole, Stewart T; Krause, Johannes

    2018-05-01

    Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  7. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Directory of Open Access Journals (Sweden)

    Verena J Schuenemann

    2018-05-01

    Full Text Available Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  8. Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining.

    Directory of Open Access Journals (Sweden)

    Aurélie Kapusta

    2011-04-01

    Full Text Available During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs, each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs, which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5' overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ, are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi-mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5'-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3' ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a "cut-and-close" mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new

  9. Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining.

    Science.gov (United States)

    Kapusta, Aurélie; Matsuda, Atsushi; Marmignon, Antoine; Ku, Michael; Silve, Aude; Meyer, Eric; Forney, James D; Malinsky, Sophie; Bétermier, Mireille

    2011-04-01

    During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs), each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs), which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5' overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ), are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi-mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5'-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3' ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a "cut-and-close" mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new mechanisms

  10. High performance computation of landscape genomic models including local indicators of spatial association.

    Science.gov (United States)

    Stucki, S; Orozco-terWengel, P; Forester, B R; Duruz, S; Colli, L; Masembe, C; Negrini, R; Landguth, E; Jones, M R; Bruford, M W; Taberlet, P; Joost, S

    2017-09-01

    With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an F ST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  11. Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity

    KAUST Repository

    Orlando, Marta; Ravasenga, Tiziana; Petrini, Enrica Maria; Falqui, Andrea; Marotta, Roberto; Barberis, Andrea

    2017-01-01

    Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABAA Receptors (GABAARs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABAAR clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABAAR clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

  12. Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity

    KAUST Repository

    Orlando, Marta

    2017-10-17

    Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABAA Receptors (GABAARs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABAAR clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABAAR clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

  13. High Power Picosecond Laser Surface Micro-texturing of H13 Tool Steel and Pattern Replication onto ABS Plastics via Injection Moulding

    Science.gov (United States)

    Otanocha, Omonigho B.; Li, Lin; Zhong, Shan; Liu, Zhu

    2016-03-01

    H13 tool steels are often used as dies and moulds for injection moulding of plastic components. Certain injection moulded components require micro-patterns on their surfaces in order to modify the physical properties of the components or for better mould release to reduce mould contamination. With these applications it is necessary to study micro-patterning to moulds and to ensure effective pattern transfer and replication onto the plastic component during moulding. In this paper, we report an investigation into high average powered (100 W) picosecond laser interactions with H13 tool steel during surface micro-patterning (texturing) and the subsequent pattern replication on ABS plastic material through injection moulding. Design of experiments and statistical modelling were used to understand the influences of laser pulse repetition rate, laser fluence, scanning velocity, and number of scans on the depth of cut, kerf width and heat affected zones (HAZ) size. The characteristics of the surface patterns are analysed. The process parameter interactions and significance of process parameters on the processing quality and efficiency are characterised. An optimum operating window is recommended. The transferred geometry is compared with the patterns generated on the dies. A discussion is made to explain the characteristics of laser texturing and pattern replication on plastics.

  14. Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity.

    Science.gov (United States)

    Orlando, Marta; Ravasenga, Tiziana; Petrini, Enrica Maria; Falqui, Andrea; Marotta, Roberto; Barberis, Andrea

    2017-10-23

    Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABA A Receptors (GABA A Rs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABA A R clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABA A R clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

  15. Highly catalytic carbon nanotube counter electrode on plastic for dye solar cells utilizing cobalt-based redox mediator

    International Nuclear Information System (INIS)

    Aitola, Kerttu; Halme, Janne; Feldt, Sandra; Lohse, Peter; Borghei, Maryam; Kaskela, Antti; Nasibulin, Albert G.; Kauppinen, Esko I.; Lund, Peter D.; Boschloo, Gerrit; Hagfeldt, Anders

    2013-01-01

    A flexible, slightly transparent and metal-free random network of single-walled carbon nanotubes (SWCNTs) on plain polyethylene terephthalate (PET) plastic substrate outperformed platinum on conductive glass and on plastic as the counter electrode (CE) of a dye solar cell employing a Co(II/III)tris(2,2′-bipyridyl) complex redox mediator in 3-methoxypropionitrile solvent. The CE charge-transfer resistance of the SWCNT film was 0.60 Ω cm 2 , 4.0 Ω cm 2 for sputtered platinum on indium tin oxide-PET substrate and 1.7 Ω cm 2 for thermally deposited Pt on fluorine-doped tin oxide glass, respectively. The solar cell efficiencies were in the same range, thus proving that an entirely carbon-based SWCNT film on plastic is as good CE candidate for the Co electrolyte

  16. Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer.

    Science.gov (United States)

    Nordström, Tobias; Van Blarigan, Erin L; Ngo, Vy; Roy, Ritu; Weinberg, Vivian; Song, Xiaoling; Simko, Jeffry; Carroll, Peter R; Chan, June M; Paris, Pamela L

    2016-03-01

    Carotenoids are a class of nutrients with antioxidant properties that have been purported to protect against cancer. However, the reported associations between carotenoids and prostate cancer have been heterogeneous and lacking data on interactions with nucleotide sequence variations and genomic biomarkers. To examine the associations between carotenoid levels and the risk of high-grade prostate cancer, also considering antioxidant-related genes and tumor instability. We measured plasma levels of carotenoids and genotyped 20 single nucleotide polymorphisms (SNP) in SOD1, SOD2, SOD3, XRCC1, and OGG1 among 559 men with non-metastatic prostate cancer undergoing radical prostatectomy. We performed copy number analysis in a subset of these men (n = 67) to study tumor instability assessed as Fraction of the Genome Altered (FGA). We examined associations between carotenoids, genotypes, tumor instability and risk of high-grade prostate cancer (Gleason grade ≥ 4 + 3) using logistic and linear regression. Circulating carotenoid levels were inversely associated with the risk of high-grade prostate cancer; odds ratios (OR) and 95% confidence intervals (CI) comparing highest versus lowest quartiles were: 0.34 (95% CI: 0.18-0.66) for α-carotene, 0.31 (95% CI: 0.15-0.63) for β-carotene, 0.55 (0.28-1.08) for lycopene and 0.37 (0.18-0.75) for total carotenoids. SNPs rs25489 in XRCC1, rs699473 in SOD3 and rs1052133 in OGG1 modified these associations for α-carotene, β-carotene and lycopene, respectively (P ≤ 0.05). The proportion of men with a high degree of FGA increased with Gleason Score (P carotenoids at diagnosis, particularly among men carrying specific somatic variations, were inversely associated with risk of high-grade prostate cancer. In exploratory analyses, higher lycopene level was associated with less genomic instability among men with low-grade disease which is novel and supports the hypothesis that lycopene may inhibit progression of

  17. Direct liquefaction of plastics and coprocessing of coal with plastics

    Energy Technology Data Exchange (ETDEWEB)

    Huffman, G.P.; Feng, Z.; Mahajan, V. [Univ. of Kentucky, Lexington, KY (United States)

    1995-12-31

    The objectives of this work were to optimize reaction conditions for the direct liquefaction of waste plastics and the coprocessing of coal with waste plastics. In previous work, the direct liquefaction of medium and high density polyethylene (PE), polypropylene (PPE), poly(ethylene terephthalate) (PET), and a mixed plastic waste, and the coliquefaction of these plastics with coals of three different ranks was studied. The results established that a solid acid catalyst (HZSM-5 zeolite) was highly active for the liquefaction of the plastics alone, typically giving oil yields of 80-95% and total conversions of 90-100% at temperatures of 430-450 {degrees}C. In the coliquefaction experiments, 50:50 mixtures of plastic and coal were used with a tetralin solvent (tetralin:solid = 3:2). Using approximately 1% of the HZSM-5 catalyst and a nanoscale iron catalyst, oil yields of 50-70% and total conversion of 80-90% were typical. In the current year, further investigations were conducted of the liquefaction of PE, PPE, and a commingled waste plastic obtained from the American Plastics Council (APC), and the coprocessing of PE, PPE and the APC plastic with Black Thunder subbituminous coal. Several different catalysts were used in these studies.

  18. High-intensity Aerobic Exercise Blocks the Facilitation of iTBS-induced Plasticity in the Human Motor Cortex.

    Science.gov (United States)

    Smith, Ashleigh E; Goldsworthy, Mitchell R; Wood, Fiona M; Olds, Timothy S; Garside, Tessa; Ridding, Michael C

    2018-03-01

    Acute exercise studies using transcranial magnetic stimulation (TMS) can provide important insights into the mechanisms underpinning the positive relationship between regular engagement in physical activity and cortical neuroplasticity. Emerging evidence indicates that a single session of aerobic exercise can promote the response to an experimentally induced suppressive neuroplasticity paradigm; however, little is known about the neuroplasticity response to facilitatory paradigms, including intermittent theta burst stimulation (iTBS). To more fully characterize the effects of exercise on brain plasticity we investigated if a single 30 min bout of high-intensity cycling (80% predicted heart rate reserve) modulated the response to an iTBS paradigm compared to rest. In 18 participants (9 females; 25.5 ± 5.0 years, range: 18-35 years) iTBS was applied using standard repetitive transcranial magnetic stimulation techniques immediately following exercise or 30 min of rest. Motor evoked potentials (MEPs) were recorded from the right first dorsal interosseous muscle at baseline, after the exercise/rest period but before iTBS, and at 5 time points following iTBS (0, 5, 10, 20 and 30 min). Contrary to our hypothesis, MEPs were suppressed following iTBS after a single 30 min bout of lower limb aerobic exercise compared to rest. These results indicate that acute aerobic exercise may not always enhance the response to an experimentally induced neuroplasticity paradigm. Further investigation of the factors that influence the relationship between exercise and neuroplasticity is warranted. Copyright © 2018 IBRO. Published by Elsevier Ltd. All rights reserved.

  19. Genome architecture enables local adaptation of Atlantic cod despite high connectivity

    DEFF Research Database (Denmark)

    Barth, Julia M I; Berg, Paul R; Jonsson, Per R.

    2017-01-01

    Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species...... characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single......-nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless...

  20. Genome wide SSR high density genetic map construction from an interspecific cross of Gossypium hirsutum × Gossypium tomentosum

    Directory of Open Access Journals (Sweden)

    Muhammad Kashif Riaz eKhan

    2016-04-01

    Full Text Available A high density genetic map was constructed using F2 population derived from an interspecific cross of G. hirsutum x G. tomentosum. The map consisted of 3,093 marker loci distributed across all the 26 chromosomes and covered 4,365.3 cM of cotton genome with an average inter-marker distance of 1.48 cM. The maximum length of chromosome was 218.38 cM and the minimum was 122.09 cM with an average length of 167.90 cM. A sub-genome covers more genetic distance (2,189.01 cM with an average inter loci distance of 1.53 cM than D sub-genome which covers a length of 2,176.29 cM with an average distance of 1.43 cM. There were 716 distorted loci in the map accounting for 23.14% and most distorted loci were distributed on D sub-genome (25.06%, which were more than on A sub-genome (21.23%. In our map 49 segregation hotspots (SDR were distributed across the genome with more on D sub-genome as compared to A genome. Two post-polyploidization reciprocal translocations of A2/A3 and A4/A5 were suggested by 7 pairs of duplicate loci. The map constructed through these studies is one of the three densest genetic maps in cotton however; this is the first dense genome wide SSR interspecific genetic map between G. hirsutum and G. tomentosum.

  1. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

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

    Science.gov (United States)

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

    2007-08-01

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

  3. Identification of a High Affinity Nucleocapsid Protein Binding Element from The Bovine Leukemia Virus Genome

    Science.gov (United States)

    Yildiz, F. Zehra; Babalola, Kathleen; Summers, Michael F.

    2012-01-01

    Retroviral genome recognition is mediated by interactions between the nucleocapsid (NC) domain of the virally encoded Gag polyprotein and cognate RNA packaging elements that, for most retroviruses, appear to reside primarily within the 5′-untranslated region (5′-UTR) of the genome. Recent studies suggest that a major packaging determinant of Bovine Leukemia Virus (BLV), a member of the human T-cell leukemia virus (HTLV)/BLV family and a non-primate animal model for HTLV-induced leukemogenesis, resides within the gag open reading frame. We have prepared and purified the recombinant BLV NC protein and conducted electrophoretic mobility shift and isothermal titration calorimetry studies with RNA fragments corresponding to these proposed packaging elements. The gag-derived RNAs did not exhibit significant affinity for NC, suggesting an alternate role in packaging. However, an 83-nucleotide fragment of the 5′-UTR that resides just upstream of the gag start codon binds NC stoichiometrically and with high affinity (Kd = 136 ± 21 nM). These nucleotides were predicted to form tandem hairpin structures, and studies with smaller fragments indicate that the NC binding site resides exclusively within the distal hairpin (residues G369- U399, Kd = 67 ± 8 nM at physiological ionic strength). Unlike all other structurally characterized retroviral NC binding RNAs, this fragment is not expected to contain exposed guanosines, suggesting that RNA binding may be mediated by a previously uncharacterized mechanism. PMID:22846919

  4. Recent advances in high performance poly(lactide): from “green” plasticization to super-tough materials via (reactive) compounding

    Science.gov (United States)

    Kfoury, Georgio; Raquez, Jean-Marie; Hassouna, Fatima; Odent, Jérémy; Toniazzo, Valérie; Ruch, David; Dubois, Philippe

    2013-01-01

    Due to its origin from renewable resources, its biodegradability, and recently, its industrial implementation at low costs, poly(lactide) (PLA) is considered as one of the most promising ecological, bio-sourced and biodegradable plastic materials to potentially and increasingly replace traditional petroleum derived polymers in many commodity and engineering applications. Beside its relatively high rigidity [high tensile strength and modulus compared with many common thermoplastics such as poly(ethylene terephthalate) (PET), high impact poly(styrene) (HIPS) and poly(propylene) (PP)], PLA suffers from an inherent brittleness, which can limit its applications especially where mechanical toughness such as plastic deformation at high impact rates or elongation is required. Therefore, the curve plotting stiffness vs. impact resistance and ductility must be shifted to higher values for PLA-based materials, while being preferably fully bio-based and biodegradable upon the application. This review aims to establish a state of the art focused on the recent progresses and preferably economically viable strategies developed in the literature for significantly improve the mechanical performances of PLA. A particular attention is given to plasticization as well as to impact resistance modification of PLA in the case of (reactive) blending PLA-based systems. PMID:24790960

  5. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan

    2011-01-01

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  6. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  7. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  8. Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

    Science.gov (United States)

    Gifford, Miriam L.; Banta, Joshua A.; Katari, Manpreet S.; Hulsmans, Jo; Chen, Lisa; Ristova, Daniela; Tranchina, Daniel; Purugganan, Michael D.; Coruzzi, Gloria M.; Birnbaum, Kenneth D.

    2013-01-01

    Plant development is remarkably plastic but how precisely can the plant customize its form to specific environments? When the plant adjusts its development to different environments, related traits can change in a coordinated fashion, such that two traits co-vary across many genotypes. Alternatively, traits can vary independently, such that a change in one trait has little predictive value for the change in a second trait. To characterize such “tunability” in developmental plasticity, we carried out a detailed phenotypic characterization of complex root traits among 96 accessions of the model Arabidopsis thaliana in two nitrogen environments. The results revealed a surprising level of independence in the control of traits to environment – a highly tunable form of plasticity. We mapped genetic architecture of plasticity using genome-wide association studies and further used gene expression analysis to narrow down gene candidates in mapped regions. Mutants in genes implicated by association and expression analysis showed precise defects in the predicted traits in the predicted environment, corroborating the independent control of plasticity traits. The overall results suggest that there is a pool of genetic variability in plants that controls traits in specific environments, with opportunity to tune crop plants to a given environment. PMID:24039603

  9. plastic waste recycling

    African Journals Online (AJOL)

    Dr Ahmed

    incinerators is increasing around the world. Discarded plastic products ... Agency (EPA) estimated that the amount of plastics throw away is. 50 % greater in the ... The waste plastics were identified using the Society of the Plastic. Industry (SPI) ...

  10. Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator.

    Science.gov (United States)

    Lin, Y; Rajan, V; Moret, B M E

    2011-09-01

    The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current approaches are limited to small collections of genomes and low-resolution data (typically a few hundred syntenic blocks). Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis. We describe a fast and accurate algorithm for rearrangement analysis that scales up, in both time and accuracy, to modern high-resolution genomic data. We also describe a novel approach to estimate the robustness of results-an equivalent to the bootstrapping analysis used in sequence-based phylogenetic reconstruction. We present the results of extensive testing on both simulated and real data showing that our algorithm returns very accurate results, while scaling linearly with the size of the genomes and cubically with their number. We also present extensive experimental results showing that our approach to robustness testing provides excellent estimates of confidence, which, moreover, can be tuned to trade off thresholds between false positives and false negatives. Together, these two novel approaches enable us to attack heretofore intractable problems, such as phylogenetic inference for high-resolution vertebrate genomes, as we demonstrate on a set of six vertebrate genomes with 8,380 syntenic blocks. A copy of the software is available on demand.

  11. Influence of lubricant oil residual fraction on recycled high density polyethylene properties and plastic packaging reverse logistics proposal

    Directory of Open Access Journals (Sweden)

    Harley Moraes Martins

    2015-10-01

    Full Text Available Abstract To recycle post-consumer HDPE contaminated with waste lubricating oils, companies include prior washing and drying in the process. This consumes large amounts of water and energy, generates significant effluent requiring treatment. This study assesses lubricating oil influence on HDPE properties to evaluate the feasibility of its direct mechanical recycling without washing. The current lubricating oil packaging reverse logistics in Rio de Janeiro municipality is also analyzed. HDPE bottle samples were processed with seven oil contents ranging from 1.6-29.4 (wt%. The results indicated the possibility to reprocess the polymer with oily residue not exceeding 3.2%. At higher levels, the external oil lubricating action affects the plastic matrix processing in the extruder and injection, and the recycled material has a burnt oil odor and free oil on the surface. Small residual oil amounts retain the plastic properties comparable to the washed recycled polymer and exhibited benefits associated with the oil plasticizer action. However, oil presence above 7.7% significantly changes the properties and reduces the elasticity and flexural modulus and the plastic matrix crystallinity.

  12. Plastics control paraffin buildup

    Energy Technology Data Exchange (ETDEWEB)

    1965-06-01

    Paraffin buildup in producing oil wells has been virtually eliminated by the use of plastic-coated sucker rods. The payout of the plasticing process is generally reached in less than a year, and the paraffin buildup may be inhibited for 10 yr or longer. Most of the plants applying plastic coatings to sucker rods are now fully automated, though a few still offer the hand-sprayed coating that some operators prefer. The several steps involved are described. The ideal plastic for the job is resistant to chemicals at high and low temperatures, flexible, has good adhesion, abrasion resistance, impact resistance, and a smooth glossy finish. The phenol aldehyde and epoxy resins presently offered by the industry fulfill these specifications very well; the multicoating and multibaking techniques improve their performance. Due to wide variations in the severity of the paraffin problem from one oil field to another, there is no general rule to estimate the possible savings from using plastic-coated sucker rods. The process, however, does appear to do a remarkable job in controlling paraffin buildup wherever it is a problem in producing oil by pump.

  13. Intratumoural evolutionary landscape of high-risk prostate cancer: The PROGENY study of genomic and immune parameters

    DEFF Research Database (Denmark)

    Linch, M.; Goh, G.; Hiley, C.

    2017-01-01

    Background: Intratumoural heterogeneity (ITH) is well recognised in prostate cancer (PC), but its role in high-risk disease is uncertain. A prospective, single-arm, translational study using targeted multiregion prostate biopsies was carried out to study genomic and T-cell ITH in clinically high-...

  14. A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica for Functional Genomics Analyses

    Directory of Open Access Journals (Sweden)

    LEE MEISEL

    2005-01-01

    Full Text Available Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica. Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

  15. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

    Science.gov (United States)

    Gao, Song; Sung, Wing-Kin; Nagarajan, Niranjan

    2011-11-01

    Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).

  16. Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

    Science.gov (United States)

    Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

    2013-01-01

    The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine. PMID:24386196

  17. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Directory of Open Access Journals (Sweden)

    Chiao-Ling Lo

    2016-08-01

    Full Text Available Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP. This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross resulted in small haplotype blocks (HB with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS, were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50% of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284 and intronic regions (169 with the least in exon's (4, suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a, excitatory receptors (Grin2a, Gria3, Grip1, neurotransmitters (Pomc, and synapses (Snap29. This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  18. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  19. Distinct evolutionary mechanisms for genomic imbalances in high-risk and low-risk neuroblastomas

    Directory of Open Access Journals (Sweden)

    Gisselsson David

    2007-09-01

    Full Text Available Abstract Background Neuroblastoma (NB is the most common extracranial solid tumour of childhood. Several genomic imbalances correlate to prognosis in NB, with structural rearrangements, including gene amplification, in a near-diploid setting typically signifying high-risk tumours and numerical changes in a near-triploid setting signifying low-risk tumours. Little is known about the temporal sequence in which these imbalances occur during the carcinogenic process. Methods We have reconstructed the appearance of cytogenetic imbalances in 270 NBs by first grouping tumours and imbalances through principal component analysis and then using the number of imbalances in each tumour as an indicator of evolutionary progression. Results Tumours clustered in four sub-groups, dominated respectively by (1 gene amplification in double minute chromosomes and few other aberrations, (2 gene amplification and loss of 1p sequences, (3 loss of 1p and other structural aberrations including gain of 17q, and (4 whole-chromosome gains and losses. Temporal analysis showed that the structural changes in groups 1–3 were acquired in a step-wise fashion, with loss of 1p sequences and the emergence of double minute chromosomes as the earliest cytogenetic events. In contrast, the gains and losses of whole chromosomes in group 4 occurred through multiple simultaneous events leading to a near-triploid chromosome number. Conclusion The finding of different temporal patterns for the acquisition of genomic imbalances in high-risk and low-risk NBs lends strong support to the hypothesis that these tumours are biologically diverse entities, evolving through distinct genetic mechanisms.

  20. Plastic flashtube chambers

    International Nuclear Information System (INIS)

    Frisken, W.R.

    1977-01-01

    A brief discussion is given of the use and operation of plastic flashtube chambers. Gas leaks, electric pulsing, the glow discharge, and readout methods are considered. Three distinct problems with high rate applications deal with resolving time, dead time, and polarization/neutralization of the chamber

  1. New plastic recycling technology

    Science.gov (United States)

    Greater than 60% of the total plastic content of municipal solid waste is comprised of polyolefins (high-density, low-density, and linear polyethylene and polypropylene. Polyethylene (PE) is the largest-volume component but presents a challenge due to the absence of low-energy de...

  2. Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.

    Science.gov (United States)

    Barrero, Roberto A; Guerrero, Felix D; Black, Michael; McCooke, John; Chapman, Brett; Schilkey, Faye; Pérez de León, Adalberto A; Miller, Robert J; Bruns, Sara; Dobry, Jason; Mikhaylenko, Galina; Stormo, Keith; Bell, Callum; Tao, Quanzhou; Bogden, Robert; Moolhuijzen, Paula M; Hunter, Adam; Bellgard, Matthew I

    2017-08-01

    The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats. We identified 38,827 putative R. microplus gene loci, of which 24,758 were protein coding genes (≥100 amino acids). OrthoMCL comparative analysis against 11 selected species including insects and vertebrates identified 10,835 and 3,423 protein coding gene loci that are unique to R. microplus or common to both R. microplus and Ixodes scapularis ticks, respectively. We identified 191 microRNA loci, of which 168 have similarity to known miRNAs and 23 represent novel miRNA families. We identified the genomic loci of several highly divergent R. microplus esterases with sequence similarity to acetylcholinesterase. Additionally we report the finding of a novel cytochrome P450 CYP41 homolog that shows similar protein folding structures to known CYP41 proteins known to be involved in acaricide resistance. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  3. Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.

    Science.gov (United States)

    Terpolilli, Jason; Hill, Yvette; Tian, Rui; Howieson, John; Bräu, Lambert; Goodwin, Lynne; Han, James; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2013-12-20

    Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022 is highly effective at fixing nitrogen with M. truncatula and other annual species such as M. tornata and M. littoralis and is also highly effective with the perennial M. sativa (alfalfa or lucerne). In common with other characterized E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha and M. sphaerocarpos and does not nodulate M. murex. Here we describe the features of E. meliloti WSM1022, together with genome sequence information and its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121 scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

  4. Microstructure and High Temperature Plastic Deformation Behavior of Al-12Si Based Alloy Fabricated by an Electromagnetic Casting and Stirring Process

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, Kyung-Soo; Roh, Heung-Ryeol; Kim, Mok-Soon [Inha University, Incheon (Korea, Republic of); Kim, Jong-Ho; Park, Joon-Pyo [Research Institute of Industrial Science and Technology, Pohang (Korea, Republic of)

    2017-06-15

    An as-received EMC/S (electromagnetic casting and stirring)-processed Al-12Si based alloy billet was homogenized to examine its microstructure and high temperature plastic deformation behavior, using compressive tests over the temperature range from 623 to 743 K and a strain rate range from 1.0×10{sup -3} to 1.0×10{sup 0}s{sup -1}. The results were compared with samples processed by the direct chill casting (DC) method. The fraction of equiaxed structure for the as-received EMC/S billet(41%) was much higher than that of the as-received DC billet(6 %). All true stress – true strain curves acquired from the compressive tests exhibited a peak stress at the initial stage of plastic deformation. Flow stress showed a steady state region after the appearance of peak stress with increasing strain. The peak stress decreased with increasing temperature at a given strain rate and a decreasing strain rate at a given temperature. A constitutive equation was made for each alloy, which could be used to predict the peak stress. A recrystallized grain structure was observed in all the deformed specimens, indicating that dynamic recrystallization is the predominant mechanism during high temperature plastic deformation of both the homogenized EMC/S and DC-processed Al-12Si based alloys.

  5. Low temperature fabrication of ZnO compact layer for high performance plastic dye-sensitized ZnO solar cells

    International Nuclear Information System (INIS)

    Hu Fangyi; Xia Yujing; Guan Zisheng; Yin Xiong; He Tao

    2012-01-01

    Highlights: ► ZnO compact layer is prepared via simple electrochemical method at low temperature. ► Compact layer can effectively block electron transfer from TCO to electrolyte. ► DSC PCE is improved by 17% when ZnO compact layer is introduced. ► Plastic DSCs with ZnO compact layer show a PCE of 3.29% under AM1.5 100 mW cm −2 . ► The above efficiency is comparable to that with high temperature sintering step. - Abstract: ZnO compact layer has been fabricated on transparent conducting oxide glass and plastic polymer substrates at low temperature via electrodeposition. The results of dark current and cyclic voltammetric measurements demonstrate that the compact layer can effectively reduce the short circuit from transparent conducting oxide to electrolyte in dye-sensitized ZnO solar cells, leading to an increase of open-circuit photovoltage and fill factor of the devices and, thereby, the power conversion efficiency. The resultant plastic dye-sensitized ZnO solar cell presents an efficiency of 3.29% under illumination of 100 mW cm −2 , AM 1.5G. This indicates that electrodeposition is a viable method to fabricate ZnO compact layer for high performance flexible devices.

  6. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

    Science.gov (United States)

    Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

    2005-06-01

    Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

  7. High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01

    OpenAIRE

    Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

    2014-01-01

    Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales , class Bacilli and phylum Firmicutes . The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genom...

  8. A performance test of a new high-surface-quality and high-sensitivity CR-39 plastic nuclear track detector – TechnoTrak

    Energy Technology Data Exchange (ETDEWEB)

    Kodaira, S., E-mail: kodaira.satoshi@qst.go.jp [Radiation Measurement Research Team, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba (Japan); Morishige, K. [Research Institute for Science and Engineering, Waseda University, Tokyo (Japan); Kawashima, H.; Kitamura, H.; Kurano, M. [Radiation Measurement Research Team, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba (Japan); Hasebe, N. [Research Institute for Science and Engineering, Waseda University, Tokyo (Japan); Koguchi, Y.; Shinozaki, W. [Oarai Research Center, Chiyoda Technol Corporation, Ibaraki (Japan); Ogura, K. [College of Industrial Technology, Nihon University, Chiba (Japan)

    2016-09-15

    We have studied the performance of a newly-commercialized CR-39 plastic nuclear track detector (PNTD), “TechnoTrak”, in energetic heavy ion measurements. The advantages of TechnoTrak are derived from its use of a purified CR-39 monomer to improve surface quality combined with an antioxidant to improve sensitivity to low-linear-energy-transfer (LET) particles. We irradiated these detectors with various heavy ions (from protons to krypton) with various energies (30–500 MeV/u) at the heavy ion accelerator facilities in the National Institute of Radiological Sciences (NIRS). The surface roughness after chemical etching was improved to be 59% of that of the conventional high-sensitivity CR-39 detector (HARZLAS/TD-1). The detectable dynamic range of LET was found to be 3.5–600 keV/μm. The LET and charge resolutions for three ions tested ranged from 5.1% to 1.5% and 0.14 to 0.22 c.u. (charge unit), respectively, in the LET range of 17–230 keV/μm, which represents an improvement over conventional products (HARZLAS/TD-1 and BARYOTRAK). A correction factor for the angular dependence was determined for correcting the LET spectrum in an isotropic radiation field. We have demonstrated the potential of TechnoTrak, with its two key features of high surface quality and high sensitivity to low-LET particles, to improve automatic analysis protocols in radiation dosimetry and various other radiological applications.

  9. Screening of whole genome sequences identified high-impact variants for stallion fertility.

    Science.gov (United States)

    Schrimpf, Rahel; Gottschalk, Maren; Metzger, Julia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

    2016-04-14

    Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant

  10. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    Science.gov (United States)

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. © 2012 John Wiley & Sons Ltd.

  11. A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Myburg Alexander A

    2010-06-01

    Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

  12. Microarray-based ultra-high resolution discovery of genomic deletion mutations

    Science.gov (United States)

    2014-01-01

    Background Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. Results Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. Conclusions Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. PMID:24655320

  13. Purification of high molecular weight genomic DNA from powdery mildew for long-read sequencing

    Science.gov (United States)

    The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which ...

  14. High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond

    DEFF Research Database (Denmark)

    Gong, Xianzhe; Skrivergaard, Stig; Korsgaard, Benjamin

    2017-01-01

    denitrification, and fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (

  15. A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

    NARCIS (Netherlands)

    Nowell, Reuben W.; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher W.; Saastamoinen, Marjo; Saccheri, Ilik J.; Hof, van 't Arjen E.; Wasik, Bethany R.; Connahs, Heidi; Aslam, Muhammad L.; Kumar, Sujai; Challis, Richard J.; Monteiro, Antónia; Brakefield, Paul M.; Blaxter, Mark

    2017-01-01

    The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important

  16. Plastic Zone Analysis of Deep-Buried, Noncircular Tunnel and Application on the High-Speed Railway in the Karst Area

    Directory of Open Access Journals (Sweden)

    Hai Shi

    2017-01-01

    Full Text Available With the conformal mapping function provided by Verruijt, the outland of a noncircular tunnel can be mapped to a circular unit in the complex plane and then spread the analytic function into a Laurent series. The stress unified solution of oval and horseshoe cross section can be determined using Muskhelishvili’s complex variables function method. Subsequently, the solution can be taken into the Griffith strength failure criterion and determine the scale and shape of plastic zone in the tunnel surrounding rock. Aiming at the critical safety thickness between a concealed cave and tunnel in the karst area and determining whether the plastic zone of tunnel surrounding rock is connected with the plastic zone of cave as a judgment standard, the model of critical safety thickness among the concealed caves and tunnels is established. The numerical model is established in comparison with the computing method of rock plate critical safety thickness in actual engineering based on the Doumo tunnel engineering of Shanghai-Kunming (Guizhou segment high-speed railway. The following conclusions can be drawn: the analytical approximation method has less indexes, and the output of this method is approximately close to actual engineering and numerical analysis, in which it is reliable and rational.

  17. Comparison between Duncan and Chang’s EB Model and the Generalized Plasticity Model in the Analysis of a High Earth-Rockfill Dam

    Directory of Open Access Journals (Sweden)

    Weixin Dong

    2013-01-01

    Full Text Available Nonlinear elastic model and elastoplastic model are two main kinds of constitutive models of soil, which are widely used in the numerical analyses of soil structure. In this study, Duncan and Chang's EB model and the generalized plasticity model proposed by Pastor, Zienkiewicz, and Chan was discussed and applied to describe the stress-strain relationship of rockfill materials. The two models were validated using the results of triaxial shear tests under different confining pressures. The comparisons between the fittings of models and test data showed that the modified generalized plasticity model is capable of simulating the mechanical behaviours of rockfill materials. The modified generalized plasticity model was implemented into a finite element code to carry out static analyses of a high earth-rockfill dam in China. Nonlinear elastic analyses were also performed with Duncan and Chang's EB model in the same program framework. The comparisons of FEM results and in situ monitoring data showed that the modified PZ-III model can give a better description of deformation of the earth-rockfill dam than Duncan and Chang’s EB model.

  18. Comparison of high-performance liquid chromatography and supercritical fluid chromatography using evaporative light scattering detection for the determination of plasticizers in medical devices.

    Science.gov (United States)

    Lecoeur, Marie; Decaudin, Bertrand; Guillotin, Yoann; Sautou, Valérie; Vaccher, Claude

    2015-10-23

    Recently, interest in supercritical fluid chromatography (SFC) has increased due to its high throughput and the development of new system improving chromatographic performances. However, most papers dealt with fundamental studies and chiral applications and only few works described validation process of SFC method. Likewise, evaporative light scattering detection (ELSD) has been widely employed in liquid chromatography but only a few recent works presented its quantitative performances hyphenated with SFC apparatus. The present paper discusses about the quantitative performances of SFC-ELSD compared to HPLC-ELSD, for the determination of plasticizers (ATBC, DEHA, DEHT and TOTM) in PVC tubing used as medical devices. After the development of HPLC-ELSD, both methods were evaluated based on the total error approach using accuracy profile. The results show that HPLC-ELSD was more precise than SFC-ELSD but lower limits of quantitation were obtained by SFC. Hence, HPLC was validated in the ± 10% acceptance limits whereas SFC lacks of accuracy to quantify plasticizers. Finally, both methods were used to determine the composition of plasticized-PVC medical devices. Results demonstrated that SFC and HPLC both hyphenated with ELSD provided similar results. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps.

    Science.gov (United States)

    Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip R; Holleley, Clare E; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer A Marshall; Sarre, Stephen D; Zhang, Guojie

    2015-01-01

    The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

  20. Use of Plastic Mulch for Vegetable Production

    OpenAIRE

    Maughan, Tiffany; Drost, Dan

    2016-01-01

    Plastic mulches are used commercially for both vegetables and small fruit crops. Vegetable crops well suited for production with plastic mulch are typically high value row crops. This fact sheet describes the advantages, disadvantages, installation, and planting considerations. It includes sources for plastic and equipment.

  1. Plastic Debris Is a Human Health Issue

    NARCIS (Netherlands)

    Vethaak, A.D.; Leslie, H.A.

    2016-01-01

    The global threat of highly persistent plastic waste accumulating and fragmenting in the world’s oceans, inland waters and terrestrial environments is becoming increasingly evident.1−3 Humans are being exposed to both plastic particles and chemical additives being released from the plastic debris of

  2. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

    Directory of Open Access Journals (Sweden)

    Chao Shiaoman

    2011-01-01

    Full Text Available Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM analysis. Of these, 52 (54% were polymorphic between parents of the Ogle1040 × TAM O-301 (OT mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide

  3. Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome

    Energy Technology Data Exchange (ETDEWEB)

    Chhabra, S.R.; Butland, G.; Elias, D.; Chandonia, J.-M.; Fok, V.; Juba, T.; Gorur, A.; Allen, S.; Leung, C.-M.; Keller, K.; Reveco, S.; Zane, G.; Semkiw, E.; Prathapam, R.; Gold, B.; Singer, M.; Ouellet, M.; Sazakal, E.; Jorgens, D.; Price, M.; Witkowska, E.; Beller, H.; Hazen, T.C.; Biggin, M.; Auer, M.; Wall, J.; Keasling, J.

    2011-07-15

    The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high- throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA “parts” to facilitate chromosomal modification at designated loci. These constructs enable an array of downstream applications including gene replacement and creation of gene fusions with affinity purification or localization tags. We employed this approach to engineer chromosomal modifications in a bacterium that has previously proven difficult to manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of over 700 strains. Furthermore, we demonstrate how these modifications can be used for examining metabolic pathways, protein-protein interactions, and protein localization. The ubiquity of suicide constructs in gene replacement throughout biology suggests that this approach can be applied to engineer a broad range of species for a diverse array of systems biological applications and is amenable to high-throughput implementation.

  4. Imaging brain plasticity after trauma

    Institute of Scientific and Technical Information of China (English)

    Zhifeng Kou; Armin Iraji

    2014-01-01

    The brain is highly plastic after stroke or epilepsy;however, there is a paucity of brain plasticity investigation after traumatic brain injury (TBI). This mini review summarizes the most recent evidence of brain plasticity in human TBI patients from the perspective of advanced magnetic resonance imaging. Similar to other forms of acquired brain injury, TBI patients also demonstrat-ed both structural reorganization as well as functional compensation by the recruitment of other brain regions. However, the large scale brain network alterations after TBI are still unknown, and the ifeld is still short of proper means on how to guide the choice of TBI rehabilitation or treat-ment plan to promote brain plasticity. The authors also point out the new direction of brain plas-ticity investigation.

  5. High Throughput Computing Impact on Meta Genomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Gore, Brooklin

    2011-10-12

    This presentation includes a brief background on High Throughput Computing, correlating gene transcription factors, optical mapping, genotype to phenotype mapping via QTL analysis, and current work on next gen sequencing.

  6. Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production.

    Science.gov (United States)

    Khanna, Namita; Ghosh, Ananta Kumar; Huntemann, Marcel; Deshpande, Shweta; Han, James; Chen, Amy; Kyrpides, Nikos; Mavrommatis, Kostas; Szeto, Ernest; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Nolan, Matt; Woyke, Tanja; Teshima, Hazuki; Chertkov, Olga; Daligault, Hajnalka; Davenport, Karen; Gu, Wei; Munk, Christine; Zhang, Xiaojing; Bruce, David; Detter, Chris; Xu, Yan; Quintana, Beverly; Reitenga, Krista; Kunde, Yulia; Green, Lance; Erkkila, Tracy; Han, Cliff; Brambilla, Evelyne-Marie; Lang, Elke; Klenk, Hans-Peter; Goodwin, Lynne; Chain, Patrick; Das, Debabrata

    2013-12-20

    Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae. The organism was isolated from the leaves of a local plant near the Kharagpur railway station, Kharagpur, West Bengal, India. It has been extensively studied for fermentative hydrogen production because of its high hydrogen yield. For further enhancement of hydrogen production by strain development, complete genome sequence analysis was carried out. Sequence analysis revealed that the genome was linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway of hydrogen production was suggested based on the presence of formate hydrogen lyase complex and other related genes identified in the genome. Thus, in the present study we describe the specific properties of the organism and the generation, annotation and analysis of its genome sequence as well as discuss the putative pathway of hydrogen production by this organism.

  7. The Einstein Genome Gateway using WASP - a high throughput multi-layered life sciences portal for XSEDE.

    Science.gov (United States)

    Golden, Aaron; McLellan, Andrew S; Dubin, Robert A; Jing, Qiang; O Broin, Pilib; Moskowitz, David; Zhang, Zhengdong; Suzuki, Masako; Hargitai, Joseph; Calder, R Brent; Greally, John M

    2012-01-01

    Massively-parallel sequencing (MPS) technologies and their diverse applications in genomics and epigenomics research have yielded enormous new insights into the physiology and pathophysiology of the human genome. The biggest hurdle remains the magnitude and diversity of the datasets generated, compromising our ability to manage, organize, process and ultimately analyse data. The Wiki-based Automated Sequence Processor (WASP), developed at the Albert Einstein College of Medicine (hereafter Einstein), uniquely manages to tightly couple the sequencing platform, the sequencing assay, sample metadata and the automated workflows deployed on a heterogeneous high performance computing cluster infrastructure that yield sequenced, quality-controlled and 'mapped' sequence data, all within the one operating environment accessible by a web-based GUI interface. WASP at Einstein processes 4-6 TB of data per week and since its production cycle commenced it has processed ~ 1 PB of data overall and has revolutionized user interactivity with these new genomic technologies, who remain blissfully unaware of the data storage, management and most importantly processing services they request. The abstraction of such computational complexity for the user in effect makes WASP an ideal middleware solution, and an appropriate basis for the development of a grid-enabled resource - the Einstein Genome Gateway - as part of the Extreme Science and Engineering Discovery Environment (XSEDE) program. In this paper we discuss the existing WASP system, its proposed middleware role, and its planned interaction with XSEDE to form the Einstein Genome Gateway.

  8. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

    Directory of Open Access Journals (Sweden)

    Christie-Oleza Joseph A

    2012-02-01

    Full Text Available Abstract Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera, we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase

  9. High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01.

    Science.gov (United States)

    Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

    2014-06-15

    Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genome sequence of the species Staphylococcus cohnii.

  10. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan

    2009-01-01

    MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...... determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than...

  11. Genomic and epigenomic analysis of high-risk prostate cancer reveals changes in hydroxymethylation and TET1.

    Science.gov (United States)

    Spans, Lien; Van den Broeck, Thomas; Smeets, Elien; Prekovic, Stefan; Thienpont, Bernard; Lambrechts, Diether; Karnes, R Jeffrey; Erho, Nicholas; Alshalalfa, Mohammed; Davicioni, Elai; Helsen, Christine; Gevaert, Thomas; Tosco, Lorenzo; Haustermans, Karin; Lerut, Evelyne; Joniau, Steven; Claessens, Frank

    2016-04-26

    The clinical heterogeneity of prostate cancer (PCa) makes it difficult to identify those patients that could benefit from more aggressive treatments. As a contribution to a better understanding of the genomic changes in the primary tumor that are associated with the development of high-risk disease, we performed exome sequencing and copy number determination of a clinically homogeneous cohort of 47 high-risk PCas. We confirmed recurrent mutations in SPOP, PTEN and TP53 among the 850 point mutations we detected. In seven cases, we discovered genomic aberrations in the TET1 (Ten-Eleven Translocation 1) gene which encodes a DNA hydroxymethylase than can modify methylated cytosines in genomic DNA and thus is linked with gene expression changes. TET1 protein levels were reduced in tumor versus non-tumor prostate tissue in 39 of 40 cases. The clinical relevance of changes in TET1 levels was demonstrated in an independent PCa cohort, in which low TET1 mRNA levels were significantly associated with worse metastases-free survival. We also demonstrate a strong reduction in hydroxymethylated DNA in tumor tissue in 27 of 41 cases. Furthermore, we report the first exploratory (h)MeDIP-Seq analyses of eight high-risk PCa samples. This reveals a large heterogeneity in hydroxymethylation changes in tumor versus non-tumor genomes which can be linked with cell polarity.

  12. Extruding plastic scintillator at Fermilab

    International Nuclear Information System (INIS)

    Pla-Dalmau, Anna; Bross, Alain D.; Rykalin, Viktor V.

    2003-01-01

    An understanding of the costs involved in the production of plastic scintillators and the development of a less expensive material have become necessary with the prospects of building very large plastic scintillation detectors. Several factors contribute to the high cost of plastic scintillating sheets, but the principal reason is the labor-intensive nature of the manufacturing process. In order to significantly lower the costs, the current casting procedures had to be abandoned. Since polystyrene is widely used in the consumer industry, the logical path was to investigate the extrusion of commercial-grade polystyrene pellets with dopants to yield high quality plastic scintillator. This concept was tested and high quality extruded plastic scintillator was produced. The D0 and MINOS experiments are already using extruded scintillator strips in their detectors. An extrusion line has recently been installed at Fermilab in collaboration with NICADD (Northern Illinois Center for Accelerator and Detector Development). This new facility will serve to further develop and improve extruded plastic scintillator. This paper will discuss the characteristics of extruded plastic scintillator and its raw materials, the different manufacturing techniques and the current R andD program at Fermilab

  13. Effects of high hydrostatic pressure on genomic expression profiling of porcine parthenogenetic activated and cloned embryos

    DEFF Research Database (Denmark)

    Lin, Lin; Luo, Yonglun; Sørensen, Peter

    2014-01-01

    derived by PA or HMC. Hierarchical clustering depicted stage-specific genomic expression profiling. At the 4-cell and blastocyst stages, 103 and 163 transcripts were differentially expressed between the HMC and PA embryos, respectively (P

  14. Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting

    DEFF Research Database (Denmark)

    Bjorn-Mortensen, K; Soborg, B; Koch, A

    2016-01-01

    In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome...

  15. Sparse redundancy analysis of high-dimensional genetic and genomic data

    NARCIS (Netherlands)

    Csala, Attila; Voorbraak, Frans P. J. M.; Zwinderman, Aeilko H.; Hof, Michel H.

    2017-01-01

    Motivation: Recent technological developments have enabled the possibility of genetic and genomic integrated data analysis approaches, where multiple omics datasets from various biological levels are combined and used to describe (disease) phenotypic variations. The main goal is to explain and

  16. Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.

    Science.gov (United States)

    Kelly, Benjamin J; Fitch, James R; Hu, Yangqiu; Corsmeier, Donald J; Zhong, Huachun; Wetzel, Amy N; Nordquist, Russell D; Newsom, David L; White, Peter

    2015-01-20

    While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.

  17. A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

    OpenAIRE

    Nowell, RW; Elsworth, B; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher West; Saastamoinen, Marjo Anna Kaarina; Saccheri, Ilik; Van't Hof, AE; Wasik, BR; Connahs, H; Kumar, S; Challis, RJ; Aslam, L; Monteiro, Antonia; Brakefield, Paul M.

    2017-01-01

    Background: The mycalesine butterfly Bicyclus anynana, the 'Squinting bush brown', is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Findings: Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology...

  18. Toxicological Threats of Plastic

    Science.gov (United States)

    Plastics pose both physical (e.g., entanglement, gastrointestinal blockage, reef destruction) and chemical threats (e.g., bioaccumulation of the chemical ingredients of plastic or toxic chemicals sorbed to plastics) to wildlife and the marine ecosystem.

  19. Evolution of genome size and complexity in the rhabdoviridae.

    Directory of Open Access Journals (Sweden)

    Peter J Walker

    2015-02-01

    Full Text Available RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.

  20. Evolution of genome size and complexity in the rhabdoviridae.

    Science.gov (United States)

    Walker, Peter J; Firth, Cadhla; Widen, Steven G; Blasdell, Kim R; Guzman, Hilda; Wood, Thomas G; Paradkar, Prasad N; Holmes, Edward C; Tesh, Robert B; Vasilakis, Nikos

    2015-02-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.

  1. Evolution of Genome Size and Complexity in the Rhabdoviridae

    Science.gov (United States)

    Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos

    2015-01-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. PMID:25679389

  2. Nano-Ceramic Coated Plastics

    Science.gov (United States)

    Cho, Junghyun

    2013-01-01

    Plastic products, due to their durability, safety, and low manufacturing cost, are now rapidly replacing cookware items traditionally made of glass and ceramics. Despite this trend, some still prefer relatively expensive and more fragile ceramic/glassware because plastics can deteriorate over time after exposure to foods, which can generate odors, bad appearance, and/or color change. Nano-ceramic coatings can eliminate these drawbacks while still retaining the advantages of the plastic, since the coating only alters the surface of the plastic. The surface coating adds functionality to the plastics such as self-cleaning and disinfectant capabilities that result from a photocatalytic effect of certain ceramic systems. These ceramic coatings can also provide non-stick surfaces and higher temperature capabilities for the base plastics without resorting to ceramic or glass materials. Titanium dioxide (TiO2) and zinc oxide (ZnO) are the candidates for a nano-ceramic coating to deposit on the plastics or plastic films used in cookware and kitchenware. Both are wide-bandgap semiconductors (3.0 to 3.2 eV for TiO2 and 3.2 to 3.3 eV for ZnO), so they exhibit a photocatalytic property under ultraviolet (UV) light. This will lead to decomposition of organic compounds. Decomposed products can be easily washed off by water, so the use of detergents will be minimal. High-crystalline film with large surface area for the reaction is essential to guarantee good photocatalytic performance of these oxides. Low-temperature processing (nano-ceramic coatings (TiO2, ZnO) on plastic materials (silicone, Teflon, PET, etc.) that can possess both photocatalytic oxide properties and flexible plastic properties. Processing cost is low and it does not require any expensive equipment investment. Processing can be scalable to current manufacturing infrastructure.

  3. COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci

    Directory of Open Access Journals (Sweden)

    Rainer Kaufmann

    2010-10-01

    Full Text Available With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization technique called COMBO-FISH (COMBinatorial Oligo FISH. In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488Ò showed reversible photobleaching (blinking between dark and bright state a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome.

  4. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

    Science.gov (United States)

    Klann, Tyler S; Black, Joshua B; Chellappan, Malathi; Safi, Alexias; Song, Lingyun; Hilton, Isaac B; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles A

    2017-06-01

    Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 KRAB repressor and dCas9 p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.

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

    Science.gov (United States)

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

    2018-06-01

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

  6. COMPUTER MODELING IN DEFORM-3D FOR ANALYSIS OF PLASTIC FLOW IN HIGH-SPEED HOT EXTRUSION OF BIMETALLIC FORMATIVE PARTS OF DIE TOOLING

    Directory of Open Access Journals (Sweden)

    I. V. Kachanov

    2015-01-01

    Full Text Available The modern development of industrial production is closely connected with the use of science-based and high technologies to ensure competitiveness of the manufactured products on the world market. There is also much tension around an energy- and resource saving problem which can be solved while introducing new technological processes and  creation of new materials that provide productivity increase through automation and improvement of tool life. Development and implementation of such technologies are rather often considered as time-consuming processes  which are connected with complex calculations and experimental investigations. Implementation of a simulation modelling for materials processing using modern software products serves an alternative to experimental and theoretical methods of research.The aim of this paper is to compare experimental results while obtaining bimetallic samples of a forming tool through the method of speed hot extrusion and the results obtained with the help of computer simulation using DEFORM-3D package and a finite element method. Comparative analysis of plastic flow of real and model samples has shown that the obtained models provide high-quality and reliable picture of plastic flow during high-speed hot extrusion. Modeling in DEFORM-3D make it possible to eliminate complex calculations and significantly reduce a number of experimental studies while developing new technological processes.

  7. Fiscal 1999 leading research report. High strain-rate super-plasticity (Leading research); 1999 nendo kosoku chososei kenkyu hokokusho. Sendo kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    For solving the global warming problem and constructing the resource recycling society, a demand for highly recyclable light-weight Mg alloys is increasing for energy saving and recycling improvement, in particular, for automobiles and electrical appliances. However, use of Mg materials is limited because its poor workability. This research targets development of the material with a rich recyclability and a rich workability for forming complex shapes, and its working technology. Leading research was made on development of the continuous high-strain rate (more than 10{sup -2}/s) super- plasticity material forming process from raw materials to products of Mg alloys, and establishment of the production technology free from technological barriers. The research result showed that for the recognition of Mg alloy as low- environment load super light-weight industrial material, establishment of the composite resource-saving energy-saving production process including recycling and reusing is necessary at the same time as establishment of the high- strain rate super-plasticity material forming process. (NEDO)

  8. From Modeling of Plasticity in Single-Crystal Superalloys to High-Resolution X-rays Three-Crystal Diffractometer Peaks Simulation

    Science.gov (United States)

    Jacques, Alain

    2016-12-01

    The dislocation-based modeling of the high-temperature creep of two-phased single-crystal superalloys requires input data beyond strain vs time curves. This may be obtained by use of in situ experiments combining high-temperature creep tests with high-resolution synchrotron three-crystal diffractometry. Such tests give access to changes in phase volume fractions and to the average components of the stress tensor in each phase as well as the plastic strain of each phase. Further progress may be obtained by a new method making intensive use of the Fast Fourier Transform, and first modeling the behavior of a representative volume of material (stress fields, plastic strain, dislocation densities…), then simulating directly the corresponding diffraction peaks, taking into account the displacement field within the material, chemical variations, and beam coherence. Initial tests indicate that the simulated peak shapes are close to the experimental ones and are quite sensitive to the details of the microstructure and to dislocation densities at interfaces and within the soft γ phase.

  9. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

    Directory of Open Access Journals (Sweden)

    Zdepski Anna

    2011-05-01

    Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

  10. Final report on neutron irradiation at low temperature to investigate plastic instability and at high temperature to study caviation

    DEFF Research Database (Denmark)

    Singh, B.N; Eldrup, Morten Mostgaard; Golubov, D.J.

    2005-01-01

    Effects of neutron irradiation on defect accumulation and physical and mechanical properties of pure iron and F82H and EUROFER 97 ferritic-martensitic steels have been investigated. Tensile specimens were neutron irradiated to a dose level of 0,23 dpa at333 and 573 K. Electrical resistivity......, based on the production bias model (PBM) were carried out to study the details of evolution of cavitieswith and without helium generation. The phenomena of dislocation decoration and raft formation, which are important for understanding radiation hardening and plastic flow localization, have been...... studied using the Kinetic Monte Carlo (KMC) code during arealistic dynamic irradiation of bcc iron at 300 K. Molecular dynamics (MD) simulations have been carried out to study the stress dependencies of dislocation velocity and drag coefficient for an edge dislocation decorated with small SIA loops...

  11. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

    Science.gov (United States)

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-01-01

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

  12. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity.

    Science.gov (United States)

    Schwessinger, Benjamin; Sperschneider, Jana; Cuddy, William S; Garnica, Diana P; Miller, Marisa E; Taylor, Jennifer M; Dodds, Peter N; Figueroa, Melania; Park, Robert F; Rathjen, John P

    2018-02-20

    A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N 50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is

  13. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were p