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Sample records for extensive genomic plasticity

  1. 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.

  2. 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.

  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. Speciation with gene flow in equids despite extensive chromosomal plasticity

    DEFF Research Database (Denmark)

    Jáónsson, Hákon; Schubert, Mikkel; Seguin-Orlando, Andaine

    2014-01-01

    Significance Thirty years after the first DNA fragment from the extinct quagga zebra was sequenced, we set another milestone in equine genomics by sequencing its entire genome, along with the genomes of the surviving equine species. This extensive dataset allows us to decipher the genetic makeup ...

  5. Speciation with gene flow in equids despite extensive chromosomal plasticity.

    Science.gov (United States)

    Jónsson, Hákon; Schubert, Mikkel; Seguin-Orlando, Andaine; Ginolhac, Aurélien; Petersen, Lillian; Fumagalli, Matteo; Albrechtsen, Anders; Petersen, Bent; Korneliussen, Thorfinn S; Vilstrup, Julia T; Lear, Teri; Myka, Jennifer Leigh; Lundquist, Judith; Miller, Donald C; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Stagegaard, Julia; Strauss, Günter; Bertelsen, Mads Frost; Sicheritz-Ponten, Thomas; Antczak, Douglas F; Bailey, Ernest; Nielsen, Rasmus; Willerslev, Eske; Orlando, Ludovic

    2014-12-30

    Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

  6. Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

    Science.gov (United States)

    Lange, Anna; Beier, Sina; Steimle, Alex; Autenrieth, Ingo B; Huson, Daniel H; Frick, Julia-Stefanie

    2016-04-25

    Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der [California Univ., San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  11. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der (California Univ., San Francisco, CA (United States) Lawrence Berkeley Lab., CA (United States))

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  12. 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

  13. 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

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Use of plastic scintillators for particle density measuring and their influence in the characterization of extensive atmospheric showers

    International Nuclear Information System (INIS)

    Biral, A.R.P.; Chinellato, J.A.; Fauth, A.C.; Kemp, E.; Oliveira, M.A. Leigui de; Manganote, E.J.T.; Nogima, H.; Rigitano, R.C.; Santos, L.G. dos; Silva, E.L.F.; Silva, N. Mengoti; Souza Junior, M.C.; Tamura, E.; Turtelli Junior, A.

    1994-01-01

    The use of plastic scintillators for particle density measuring and their influence in the characterization of extensive atmospheric showers has been studied.Using a experimental system coupled with a plastic scintillator detector with a 'streamer' tubes module, single muon events were selected through tracks rebuilding. The influence of those distributions in the determination of particle density and extensive atmospheric showers fundamental parameters were also studied. 10 refs., 2 figs

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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

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

    Directory of Open Access Journals (Sweden)

    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

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

    KAUST Repository

    Gallego Llorente, M.; Jones, E. R.; Eriksson, Anders; Siska, V.; Arthur, K. W.; Arthur, J. W.; Curtis, M. C.; Stock, J. T.; Coltorti, M.; Pieruccini, P.; Stretton, S.; Brock, F.; Higham, T.; Park, Y.; Hofreiter, M.; Bradley, D. G.; Bhak, J.; Pinhasi, R.; Manica, A.

    2015-01-01

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

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

    KAUST Repository

    Gallego Llorente, M.

    2015-10-09

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

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

    Directory of Open Access Journals (Sweden)

    Henry D Priest

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

  4. A unified model of hydride cracking based on elasto-plastic energy release rate over a finite crack extension

    International Nuclear Information System (INIS)

    Zheng, X.J.; Metzger, D.R.; Sauve, R.G.

    1995-01-01

    A fracture criterion based on energy balance is proposed for elasto-plastic cracking at hydrides in zirconium, assuming a finite length of crack advance. The proposed elasto-plastic energy release rate is applied to the crack initiation at hydrides in smooth and notched surfaces, as well as the subsequent delayed hydride cracking (DHC) considering limited crack-tip plasticity. For a smooth or notched surface of an elastic body, the fracture parameter is related to the stress intensity factor for the initiated crack. For DHC, a unique curve relates the non-dimensionalized elasto-plastic energy release rate with the length of crack extension relative to the plastic zone size. This fracture criterion explains experimental observations concerning DHC in a qualitative manner. Quantitative comparison with experiments is made for fracture toughness and DHC tests on specimens containing certain hydride structures; very good agreement is obtained. ((orig.))

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

    Directory of Open Access Journals (Sweden)

    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.

  6. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Binnewies, Tim Terence; Ussery, David

    2008-01-01

    ://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence......The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced...... genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including...

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Observational Study Unveils the Extensive Presence of Hazardous Elements in Beached Plastics from Lake Geneva

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    Montserrat Filella

    2018-02-01

    Full Text Available Over 3,000 samples of plastic litter have been retrieved from 12 pebble beaches around the shores of Lake Geneva. The plastic stock consisted of identifiable objects of various size and color, including bottles, bottle tops, cotton buds, pens, toys, and straws, an heterogeneous assortment of fragments whose origin was either discernible or unknown, and pieces or blocks of expanded polymer (polystyrene or polyurethane foam. Analysis of 670 samples by portable x-ray fluorescence (XRF spectrometry revealed high concentrations of hazardous elements or compounds among many plastics. These included Cd, Hg, and Pb (with maximum concentrations of 6,760, 810, and 23,500 ppm, respectively as stabilizers in PVC-based materials and/or brightly-colored sulfide or chromate pigments in primary and secondary plastics, and Br (with a maximum concentration of 27,400 ppm as a proxy for brominated flame retardants (BFRs in both plastics and foams. The abundance of hazardous elements in beached plastics that have been restricted or banned reflect the age and residence time of the plastic stock in the lake, coupled with a relatively high length of shoreline to surface area of the system. The migratability of hazardous elements from the polymeric matrix is likely to determine their environmental impacts and is recommended as a future area of research.

  12. 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

  13. The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome.

    Science.gov (United States)

    Cook, R Kimberley; Christensen, Stacey J; Deal, Jennifer A; Coburn, Rachel A; Deal, Megan E; Gresens, Jill M; Kaufman, Thomas C; Cook, Kevin R

    2012-01-01

    Chromosomal deletions are used extensively in Drosophila melanogaster genetics research. Deletion mapping is the primary method used for fine-scale gene localization. Effective and efficient deletion mapping requires both extensive genomic coverage and a high density of molecularly defined breakpoints across the genome. A large-scale resource development project at the Bloomington Drosophila Stock Center has improved the choice of deletions beyond that provided by previous projects. FLP-mediated recombination between FRT-bearing transposon insertions was used to generate deletions, because it is efficient and provides single-nucleotide resolution in planning deletion screens. The 793 deletions generated pushed coverage of the euchromatic genome to 98.4%. Gaps in coverage contain haplolethal and haplosterile genes, but the sizes of these gaps were minimized by flanking these genes as closely as possible with deletions. In improving coverage, a complete inventory of haplolethal and haplosterile genes was generated and extensive information on other haploinsufficient genes was compiled. To aid mapping experiments, a subset of deletions was organized into a Deficiency Kit to provide maximal coverage efficiently. To improve the resolution of deletion mapping, screens were planned to distribute deletion breakpoints evenly across the genome. The median chromosomal interval between breakpoints now contains only nine genes and 377 intervals contain only single genes. Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism. The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers.

  14. 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.

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

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    Fagen Li

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

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

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  17. 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

  18. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

    OpenAIRE

    Opitz, Nina; Marcon, Caroline; Paschold, Anja; Malik, Waqas Ahmed; Lithio, Andrew; Brandt, Ronny; Piepho, Hans-Peter; Nettleton, Dan; Hochholdinger, Frank

    2015-01-01

    Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% o...

  19. 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.

  20. Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes.

    Directory of Open Access Journals (Sweden)

    Joseph Evans

    Full Text Available Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19(th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09 and dw3 (SBI-07 had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.

  1. Improving the Plasticity of LIMS Implementation: LIMS Extension through Microsoft Excel

    Science.gov (United States)

    Culver, Mark

    2017-01-01

    A Laboratory Information Management System (LIMS) is a databasing software with many built-in tools ideal for handling and documenting most laboratory processes in an accurate and consistent manner, making it an indispensable tool for the modern laboratory. However, a lot of LIMS end users will find that in the performance of analyses that have unique considerations such as standard curves, multiple stages incubations, or logical considerations, a base LIMS distribution may not ideally suit their needs. These considerations bring about the need for extension languages, which can extend the functionality of a LIMS. While these languages do provide the implementation team the functionality required to accommodate these special laboratory analyses, they are usually too complex for the end user to modify to compensate for natural changes in laboratory operations. The LIMS utilized by our laboratory offers a unique and easy-to-use choice for an extension language, one that is already heavily relied upon not only in science but also in most academic and business pursuits: Microsoft Excel. The validity of Microsoft Excel as a pseudo programming language and its usability and versatility as a LIMS extension language will be discussed. The NELAC implications and overall drawbacks of this LIMS configuration will also be discussed.

  2. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

    Science.gov (United States)

    Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

    2015-07-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Oxytocin Neurons Exhibit Extensive Functional Plasticity Due To Offspring Age in Mothers and Fathers.

    Science.gov (United States)

    Kelly, Aubrey M; Hiura, Lisa C; Saunders, Alexander G; Ophir, Alexander G

    2017-09-01

    The needs of offspring change as they develop. Thus, parents should concomitantly change their investment based on the age-related needs of the offspring as they mature. Due to the high costs of parental care, it is optimal for parents to exhibit a shift from intense caregiving of young offspring to promoting independence in older offspring. Yet, the neural mechanisms that underlie shifts in parental behavior are poorly understood, and little is known about how the parental brain responds to offspring of different ages. To elucidate mechanisms that relate to shifts in parental behavior as offspring develop, we examined behavioral and neural responses of male and female prairie voles (Microtus ochrogaster), a biparental rodent, to interactions with offspring at different stages of development (ranging from neonatal to weaning age). Importantly, in biparental species, males and females may adjust their behavior differentially as offspring develop. Because the nonapeptides, vasopressin (VP) and oxytocin (OT), are well known for modulating aspects of parental care, we focused on functional activity of distinct VP and OT cell groups within the maternal and paternal brain in response to separation from, reunion (after a brief period of separation) with, or no separation from offspring of different ages. We found several differences in the neural responses of individual VP and OT cell groups that varied based on the age of pups and sex of the parent. Hypothalamic VP neurons exhibit similar functional responses in both mothers and fathers. However, hypothalamic and amygdalar OT neurons exhibit differential functional responses to being separated from pups based on the sex of the parent. Our results also reveal that the developmental stage of offspring significantly impacts neural function within OT, but not VP, cell groups of both mothers and fathers. These findings provide insight into the functional plastic capabilities of the nonapeptide system, specifically in relation

  4. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit.

    Science.gov (United States)

    Opitz, Nina; Marcon, Caroline; Paschold, Anja; Malik, Waqas Ahmed; Lithio, Andrew; Brandt, Ronny; Piepho, Hans-Peter; Nettleton, Dan; Hochholdinger, Frank

    2016-02-01

    Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were 'transcriptional regulation' and 'hormone metabolism', indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  5. Extensive disordering in long-range-ordered Cu3Au induced by severe plastic deformation studied by transmission electron microscopy

    International Nuclear Information System (INIS)

    Rentenberger, C.; Karnthaler, H.P.

    2008-01-01

    Bulk nanocrystalline materials can be made by severe plastic deformation. In L1 2 long-range-ordered alloys, this leads to extensive disordering which influences the highly improved properties of these nanocrystalline alloys. Transmission electron microscopy methods were applied to Cu 3 Au; both diffraction contrast images and diffraction patterns reveal that disordering takes place locally. It is concluded that in addition to disordering by the refinement of the grown-in antiphase boundary domains, the formation of antiphase boundary tubes is a prominent process of disordering. The latter is facilitated by the fact that, unlike dislocations, antiphase boundary tubes can be stored at a very high density without causing long-range stresses. The local disordering indicates that the nanocrystalline structure nucleates inhomogeneously in the highly strained disordered regions

  6. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

    Science.gov (United States)

    Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

    2014-07-04

    Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was

  7. 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

  8. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Energy Technology Data Exchange (ETDEWEB)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  9. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

    Science.gov (United States)

    Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  10. Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

    Directory of Open Access Journals (Sweden)

    Deng Xuemei

    2007-11-01

    Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

  11. A digital repository with an extensible data model for biobanking and genomic analysis management.

    Science.gov (United States)

    Izzo, Massimiliano; Mortola, Francesco; Arnulfo, Gabriele; Fato, Marco M; Varesio, Luigi

    2014-01-01

    Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research

  12. The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

    Directory of Open Access Journals (Sweden)

    Turmel Monique

    2007-07-01

    Full Text Available Abstract Background In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales. Results The 195,081-bp Leptosira chloroplast genome resembles the 150,613-bp Chlorella genome in lacking a large inverted repeat (IR but differs greatly in gene order. Six of the conserved genes present in Chlorella cpDNA are missing from the Leptosira gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in Chlorella but similar to that in the chlorophycean Scenedesmus obliquus, the gene distribution is highly biased over the two DNA strands in Leptosira. Nine genes, compared to only three in Chlorella, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the rpoB gene is fragmented into two ORFs. Short repeats account for 5.1% of the Leptosira genome sequence and are present mainly in intergenic regions. Conclusion Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate

  13. Extensive Genomic Diversity among Bovine-Adapted Staphylococcus aureus: Evidence for a Genomic Rearrangement within CC97.

    Directory of Open Access Journals (Sweden)

    Kathleen E Budd

    Full Text Available Staphylococcus aureus is an important pathogen associated with both human and veterinary disease and is a common cause of bovine mastitis. Genomic heterogeneity exists between S. aureus strains and has been implicated in the adaptation of specific strains to colonise particular mammalian hosts. Knowledge of the factors required for host specificity and virulence is important for understanding the pathogenesis and management of S. aureus mastitis. In this study, a panel of mastitis-associated S. aureus isolates (n = 126 was tested for resistance to antibiotics commonly used to treat mastitis. Over half of the isolates (52% demonstrated resistance to penicillin and ampicillin but all were susceptible to the other antibiotics tested. S. aureus isolates were further examined for their clonal diversity by Multi-Locus Sequence Typing (MLST. In total, 18 different sequence types (STs were identified and eBURST analysis demonstrated that the majority of isolates grouped into clonal complexes CC97, CC151 or sequence type (ST 136. Analysis of the role of recombination events in determining S. aureus population structure determined that ST diversification through nucleotide substitutions were more likely to be due to recombination compared to point mutation, with regions of the genome possibly acting as recombination hotspots. DNA microarray analysis revealed a large number of differences amongst S. aureus STs in their variable genome content, including genes associated with capsule and biofilm formation and adhesion factors. Finally, evidence for a genomic arrangement was observed within isolates from CC97 with the ST71-like subgroup showing evidence of an IS431 insertion element having replaced approximately 30 kb of DNA including the ica operon and histidine biosynthesis genes, resulting in histidine auxotrophy. This genomic rearrangement may be responsible for the diversification of ST71 into an emerging bovine adapted subgroup.

  14. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

    Science.gov (United States)

    Gordon, Sean P; Contreras-Moreira, Bruno; Woods, Daniel P; Des Marais, David L; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E; Amasino, Richard; Caicedo, Ana L; Goodstein, David; Davidson, Patrick; Mur, Luis A J; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P

    2017-12-19

    While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

  15. 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.

  16. 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.

  17. 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.

  18. Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

    KAUST Repository

    Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant A.; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G.; Hasan, Rumina

    2015-01-01

    Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded

  19. Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract

    Directory of Open Access Journals (Sweden)

    Maguin Emmanuelle

    2007-08-01

    Full Text Available Abstract Background While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii and yogurt (Lactobacillus delbrueckii ssp. bulgaricus, is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. Results Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. Conclusion This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive

  20. Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

    KAUST Repository

    Ali, Asho

    2015-02-26

    Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded

  1. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

    KAUST Repository

    Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A.; Nair, Mridul; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O.; Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C.; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R.; Grandjean, Louis; Minh Ha, Dang; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L.; Joloba, Moses; Jones-Ló pez, Edward C.; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J.; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigã o, Joã o; Portugal, Isabel; Rchiad, ‍ Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A.; Sola, Christophe; Oliveira Sousa, Erivelton; Streicher, Elizabeth M.; Helden, Paul Van; Viveiros, Miguel; Warren, Robert M.; McNerney, Ruth; Pain, Arnab; Clark, Taane G.

    2018-01-01

    To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed

  2. Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

    Czech Academy of Sciences Publication Activity Database

    Liu, M.; Stiller, J.; Holušová, Kateřina; Vrána, Jan; Liu, D.; Doležel, Jaroslav; Liu, C.

    2016-01-01

    Roč. 6, NOV 8 (2016), č. článku 36398. ISSN 2045-2322 R&D Projects: GA MŠk(CZ) LO1204; GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * fusarium crown rot * pan-genome * hexaploid wheat * bread wheat * draft genome * rna-seq * maize * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.259, year: 2016

  3. Extensive error in the number of genes inferred from draft genome assemblies.

    Directory of Open Access Journals (Sweden)

    James F Denton

    2014-12-01

    Full Text Available Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

  4. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

    Science.gov (United States)

    Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter; Rüber, Lukas

    2018-01-01

    Abstract The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development. PMID:29684203

  5. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.

    Science.gov (United States)

    Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter; Rüber, Lukas

    2018-04-01

    The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

  6. Presence of extensive Wolbachia symbiont insertions discovered in the genome of its host Glossina morsitans morsitans.

    Directory of Open Access Journals (Sweden)

    Corey Brelsfoard

    2014-04-01

    Full Text Available Tsetse flies (Glossina spp. are the cyclical vectors of Trypanosoma spp., which are unicellular parasites responsible for multiple diseases, including nagana in livestock and sleeping sickness in humans in Africa. Glossina species, including Glossina morsitans morsitans (Gmm, for which the Whole Genome Sequence (WGS is now available, have established symbiotic associations with three endosymbionts: Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia pipientis (Wolbachia. The presence of Wolbachia in both natural and laboratory populations of Glossina species, including the presence of horizontal gene transfer (HGT events in a laboratory colony of Gmm, has already been shown. We herein report on the draft genome sequence of the cytoplasmic Wolbachia endosymbiont (cytWol associated with Gmm. By in silico and molecular and cytogenetic analysis, we discovered and validated the presence of multiple insertions of Wolbachia (chrWol in the host Gmm genome. We identified at least two large insertions of chrWol, 527,507 and 484,123 bp in size, from Gmm WGS data. Southern hybridizations confirmed the presence of Wolbachia insertions in Gmm genome, and FISH revealed multiple insertions located on the two sex chromosomes (X and Y, as well as on the supernumerary B-chromosomes. We compare the chrWol insertions to the cytWol draft genome in an attempt to clarify the evolutionary history of the HGT events. We discuss our findings in light of the evolution of Wolbachia infections in the tsetse fly and their potential impacts on the control of tsetse populations and trypanosomiasis.

  7. How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome

    Directory of Open Access Journals (Sweden)

    José Fabián Reyes Román

    2016-12-01

    Full Text Available The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data. In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG, designed to understand and improve our ontological commitment to the domain and also extend (enrich this schema with the integration of a novel concept: Haplotypes. Our focus is on improving the understanding of the relationship between genotype and phenotype, since new findings show that this question is more complex than was originally thought. Here we present the first steps in our data management approach with haplotypes (variations, frequencies and populations and discuss the database evolution to support this data. Each new version in our conceptual schema (CS introduces changes to the underlying database structure that has essential and practical implications for better understanding and managing the relevant information. A solution based on conceptual models gives a clear definition of the domain with direct implications in the medical field (Precision Medicine, in which Genomic Information Systems (GeIS play a very important role.

  8. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

    DEFF Research Database (Denmark)

    Petersen, Gitte; Cuenca, Argelia; Zervas, Athanasios

    2017-01-01

    The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes...... aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known...... mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus....

  9. Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton).

    Science.gov (United States)

    Guo, Hui; Wang, Xiyin; Gundlach, Heidrun; Mayer, Klaus F X; Peterson, Daniel G; Scheffler, Brian E; Chee, Peng W; Paterson, Andrew H

    2014-08-01

    Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A- and D-genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. Homeologous gene conversion events (HeGCEs) gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At-to-Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt-to-At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the nonspinnable-fibered D-genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A-genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have approximately five times greater abundance of Dt-to-At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural noninvasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants. Copyright © 2014 by the Genetics Society of America.

  10. RECG maintains plastid and mitochondrial genome stability by suppressing extensive recombination between short dispersed repeats.

    Directory of Open Access Journals (Sweden)

    Masaki Odahara

    2015-03-01

    Full Text Available Maintenance of plastid and mitochondrial genome stability is crucial for photosynthesis and respiration, respectively. Recently, we have reported that RECA1 maintains mitochondrial genome stability by suppressing gross rearrangements induced by aberrant recombination between short dispersed repeats in the moss Physcomitrella patens. In this study, we studied a newly identified P. patens homolog of bacterial RecG helicase, RECG, some of which is localized in both plastid and mitochondrial nucleoids. RECG partially complements recG deficiency in Escherichia coli cells. A knockout (KO mutation of RECG caused characteristic phenotypes including growth delay and developmental and mitochondrial defects, which are similar to those of the RECA1 KO mutant. The RECG KO cells showed heterogeneity in these phenotypes. Analyses of RECG KO plants showed that mitochondrial genome was destabilized due to a recombination between 8-79 bp repeats and the pattern of the recombination partly differed from that observed in the RECA1 KO mutants. The mitochondrial DNA (mtDNA instability was greater in severe phenotypic RECG KO cells than that in mild phenotypic ones. This result suggests that mitochondrial genomic instability is responsible for the defective phenotypes of RECG KO plants. Some of the induced recombination caused efficient genomic rearrangements in RECG KO mitochondria. Such loci were sometimes associated with a decrease in the levels of normal mtDNA and significant decrease in the number of transcripts derived from the loci. In addition, the RECG KO mutation caused remarkable plastid abnormalities and induced recombination between short repeats (12-63 bp in the plastid DNA. These results suggest that RECG plays a role in the maintenance of both plastid and mitochondrial genome stability by suppressing aberrant recombination between dispersed short repeats; this role is crucial for plastid and mitochondrial functions.

  11. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae).

    Science.gov (United States)

    Chen, Long; Chen, Peng-Yan; Xue, Xiao-Feng; Hua, Hai-Qing; Li, Yuan-Xi; Zhang, Fan; Wei, Shu-Jun

    2018-05-04

    Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.

  12. Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage

    NARCIS (Netherlands)

    Malinga, L.A.; Abeel, T.; Desjardins, C.A.; Dlamini, T.C.; Cassell, G.; Chapman, S.B.; Birren, B.W.; Earl, A.M.; Van der Walt, M.

    2016-01-01

    We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains belonging to the Euro-American S lineage. The RSA 114 strain showed single-nucleotide polymorphisms predicted to have drug efflux activity.

  13. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

    Directory of Open Access Journals (Sweden)

    Lippold Sebastian

    2011-11-01

    Full Text Available Abstract Background DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region were investigated for larger sample sets. Results In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73% already existed before the beginning of domestication about 5,000 years ago. Conclusions Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the

  14. 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.

  15. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

  16. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.

    Science.gov (United States)

    van den Broek, M; Bolat, I; Nijkamp, J F; Ramos, E; Luttik, M A H; Koopman, F; Geertman, J M; de Ridder, D; Pronk, J T; Daran, J-M

    2015-09-01

    Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. Copyright © 2015, van den Broek et al.

  17. 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.

  18. 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.

  19. 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

  20. Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the lipooligosaccharide.

    Directory of Open Access Journals (Sweden)

    Johanna J Kenyon

    Full Text Available Lipooligosaccharide (LOS is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs. OCL1 (Group A was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates.

  1. New Insights into the genetic diversity of Clostridium botulinum Group III through extensive genome exploration

    Directory of Open Access Journals (Sweden)

    Cédric eWoudstra

    2016-05-01

    Full Text Available Animal botulism is caused by group III Clostridium botulinum strains producing type C and D toxins, or their chimeric forms C/D and D/C. Animal botulism is considered an emerging disease in Europe, notably in poultry production. Before our study, 14 genomes from different countries were available in the public database, but none were from France. In order to investigate the genetic relationship of French strains with different geographical areas and find new potential typing targets, 17 strains of C. botulinum group III were sequenced (16 from France and one from New Caledonia. Fourteen were type C/D strains isolated from chickens, ducks, guinea fowl and turkeys and three were type D/C strains isolated from cattle. The New Caledonian strain was a type D/C strain. Whole genome sequence analysis showed the French strains to be closely related to European strains from C. botulinum group III lineages Ia and Ib. The investigation of CRISPR sequences as genetic targets for differentiating strains in group III proved to be irrelevant for type C/D due to a deficient CRISPR/Cas mechanism, but not for type D/C. Conversely, the extrachromosomal elements of type C/D strains could be used to generate a genetic ID card. The highest level of discrimination was achieved with SNP core phylogeny, which allowed differentiation up to strain level and provide the most relevant information for genetic epidemiology studies and discrimination.

  2. 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.

  3. 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.

  4. 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.

  5. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

    KAUST Repository

    Coll, Francesc

    2018-01-16

    To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

  6. Tobacco smoking leads to extensive genome-wide changes in DNA methylation.

    Science.gov (United States)

    Zeilinger, Sonja; Kühnel, Brigitte; Klopp, Norman; Baurecht, Hansjörg; Kleinschmidt, Anja; Gieger, Christian; Weidinger, Stephan; Lattka, Eva; Adamski, Jerzy; Peters, Annette; Strauch, Konstantin; Waldenberger, Melanie; Illig, Thomas

    2013-01-01

    Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs) comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (-24.40% methylation; p = 2.54E-182), suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers.

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

    Science.gov (United States)

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

    2017-01-01

    Alternative splicing (AS), as one of the most important topics in the post-genomic era, has been extensively studied in numerous organisms. However, little is known about the prevalence and characteristics of AS in Echinococcus species, which can cause significant health problems to humans and domestic animals. Based on high-throughput RNA-sequencing data, we performed a genome-wide survey of AS in two major pathogens of echinococcosis-Echinococcus granulosus and Echinococcus multilocularis. Our study revealed that the prevalence and characteristics of AS in protoscoleces of the two parasites were generally consistent with each other. A total of 6,826 AS events from 3,774 E. granulosus genes and 6,644 AS events from 3,611 E. multilocularis genes were identified in protoscolex transcriptomes, indicating that 33–36% of genes were subject to AS in the two parasites. Strikingly, intron retention instead of exon skipping was the predominant type of AS in Echinococcus species. Moreover, analysis of the Kyoto Encyclopedia of Genes and Genomes pathway indicated that genes that underwent AS events were significantly enriched in multiple pathways mainly related to metabolism (e.g., purine, fatty acid, galactose, and glycerolipid metabolism), signal transduction (e.g., Jak-STAT, VEGF, Notch, and GnRH signaling pathways), and genetic information processing (e.g., RNA transport and mRNA surveillance pathways). The landscape of AS obtained in this study will not only facilitate future investigations on transcriptome complexity and AS regulation during the life cycle of Echinococcus species, but also provide an invaluable resource for future functional and evolutionary studies of AS in platyhelminth parasites. PMID:28588571

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

    Directory of Open Access Journals (Sweden)

    LaDeana W Hillier

    2007-07-01

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

  9. Extensive phenotypic plasticity of a Red Sea coral over a strong latitudinal temperature gradient suggests limited acclimatization potential to warming

    KAUST Repository

    Sawall, Yvonne

    2015-03-10

    Global warming was reported to cause growth reductions in tropical shallow water corals in both, cooler and warmer, regions of the coral species range. This suggests regional adaptation with less heat-tolerant populations in cooler and more thermo-tolerant populations in warmer regions. Here, we investigated seasonal changes in the in situ metabolic performance of the widely distributed hermatypic coral Pocillopora verrucosa along 12° latitudes featuring a steep temperature gradient between the northern (28.5°N, 21-27°C) and southern (16.5°N, 28-33°C) reaches of the Red Sea. Surprisingly, we found little indication for regional adaptation, but strong indications for high phenotypic plasticity: Calcification rates in two seasons (winter, summer) were found to be highest at 28-29°C throughout all populations independent of their geographic location. Mucus release increased with temperature and nutrient supply, both being highest in the south. Genetic characterization of the coral host revealed low inter-regional variation and differences in the Symbiodinium clade composition only at the most northern and most southern region. This suggests variable acclimatization potential to ocean warming of coral populations across the Red Sea: high acclimatization potential in northern populations, but limited ability to cope with ocean warming in southern populations already existing at the upper thermal margin for corals.

  10. Extensive phenotypic plasticity of a Red Sea coral over a strong latitudinal temperature gradient suggests limited acclimatization potential to warming

    KAUST Repository

    Sawall, Yvonne; Al-Sofyani, Abdulmoshin; Hohn, Sö nke; Banguera Hinestroza, Eulalia; Voolstra, Christian R.; Wahl, Martin

    2015-01-01

    Global warming was reported to cause growth reductions in tropical shallow water corals in both, cooler and warmer, regions of the coral species range. This suggests regional adaptation with less heat-tolerant populations in cooler and more thermo-tolerant populations in warmer regions. Here, we investigated seasonal changes in the in situ metabolic performance of the widely distributed hermatypic coral Pocillopora verrucosa along 12° latitudes featuring a steep temperature gradient between the northern (28.5°N, 21-27°C) and southern (16.5°N, 28-33°C) reaches of the Red Sea. Surprisingly, we found little indication for regional adaptation, but strong indications for high phenotypic plasticity: Calcification rates in two seasons (winter, summer) were found to be highest at 28-29°C throughout all populations independent of their geographic location. Mucus release increased with temperature and nutrient supply, both being highest in the south. Genetic characterization of the coral host revealed low inter-regional variation and differences in the Symbiodinium clade composition only at the most northern and most southern region. This suggests variable acclimatization potential to ocean warming of coral populations across the Red Sea: high acclimatization potential in northern populations, but limited ability to cope with ocean warming in southern populations already existing at the upper thermal margin for corals.

  11. Tobacco smoking leads to extensive genome-wide changes in DNA methylation.

    Directory of Open Access Journals (Sweden)

    Sonja Zeilinger

    Full Text Available Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182 as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (-24.40% methylation; p = 2.54E-182, suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers.

  12. Expression plasticity and evolutionary changes extensively shape the sugar-mimic alkaloid adaptation of non-digestive glucosidase in lepidopteran mulberry-specialist insects.

    Science.gov (United States)

    Li, Xiaotong; Shi, Liangen; Dai, Xiangping; Chen, Yajie; Xie, Hongqing; Feng, Min; Chen, Yuyin; Wang, Huabing

    2018-05-12

    During the co-evolutionary arms race between plants and herbivores, insects evolved systematic adaptive plasticity to minimise the chemical defence effects of their host plants. Previous studies mainly focused on the expressional plasticity of enzymes in detoxification and digestion. However, the expressional response and adaptive evolution of other fundamental regulators against host phytochemicals are largely unknown. Glucosidase II (GII), which is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit, is an evolutionarily conserved enzyme that regulates glycoprotein folding. In this study, we found that GIIα expression of the mulberry-specialist insect was significantly induced by mulberry leaf extract, 1-Deoxynojirimycin (1-DNJ), whereas GIIβ transcripts were not significantly changed. Moreover, positive selection was detected in GIIα when the mulberry-specialist insects diverged from the lepidopteran order; whereas GIIβ was mainly subjected to purifying selection, thus indicating an asymmetrically selective pressure of GII subunits. In addition, positively selected sites were enriched in the GIIα of mulberry-specialist insects, and located around the 1-DNJ binding sites and in the C-terminal region, which could result in conformational changes that affect catalytic activity and substrate-binding efficiency. These results show that expression plasticity and evolutionary changes extensively shape sugar-mimic alkaloids adaptation of non-digestive glucosidase in lepidopteran mulberry-specialist insects. Our study provides novel insights into a deep understanding of the sequestration and adaptation of phytophagous specialists to host defensive compounds. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  13. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  14. 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...

  15. 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.

  16. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss.

    Science.gov (United States)

    Braukmann, Thomas; Kuzmina, Maria; Stefanovic, Sasa

    2013-02-01

    The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a

  17. Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy▿ †

    Science.gov (United States)

    White, James R.; Escobar-Paramo, Patricia; Mongodin, Emmanuel F.; Nelson, Karen E.; DiRuggiero, Jocelyne

    2008-01-01

    The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties. PMID:18723649

  18. Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.

    Science.gov (United States)

    White, James R; Escobar-Paramo, Patricia; Mongodin, Emmanuel F; Nelson, Karen E; DiRuggiero, Jocelyne

    2008-10-01

    The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.

  19. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

    KAUST Repository

    Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant A.; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G.; Hasan, Rumina

    2015-01-01

    Objectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and

  20. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

    KAUST Repository

    Hasan, Zahra

    2015-03-01

    Objectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and

  1. 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.

  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. 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...

  4. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

    KAUST Repository

    Voolstra, Christian R.

    2017-12-08

    Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates corals into a robust and complex clade dating back to at least 245 mya. However, the genomic consequences and clade-specific evolution remain unexplored. In this study we have produced the genome of a robust coral, Stylophora pistillata, and compared it to the available genome of a complex coral, Acropora digitifera. We conducted a fine-scale gene-based analysis focusing on ortholog groups. Among the core set of conserved proteins, we found an emphasis on processes related to the cnidarian-dinoflagellate symbiosis. Genes associated with the algal symbiosis were also independently expanded in both species, but both corals diverged on the identity of ortholog groups expanded, and we found uneven expansions in genes associated with innate immunity and stress response. Our analyses demonstrate that coral genomes can be surprisingly disparate. Future analyses incorporating more genomic data should be able to determine whether the patterns elucidated here are not only characteristic of the differences between S. pistillata and A. digitifera but also representative of corals from the robust and complex clade at large.

  5. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

    KAUST Repository

    Voolstra, Christian R.; Li, Yong; Liew, Yi Jin; Baumgarten, Sebastian; Zoccola, Didier; Flot, Jean-Franç ois; Tambutté , Sylvie; Allemand, Denis; Aranda, Manuel

    2017-01-01

    Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates corals into a robust and complex clade dating back to at least 245 mya. However, the genomic consequences and clade-specific evolution remain unexplored. In this study we have produced the genome of a robust coral, Stylophora pistillata, and compared it to the available genome of a complex coral, Acropora digitifera. We conducted a fine-scale gene-based analysis focusing on ortholog groups. Among the core set of conserved proteins, we found an emphasis on processes related to the cnidarian-dinoflagellate symbiosis. Genes associated with the algal symbiosis were also independently expanded in both species, but both corals diverged on the identity of ortholog groups expanded, and we found uneven expansions in genes associated with innate immunity and stress response. Our analyses demonstrate that coral genomes can be surprisingly disparate. Future analyses incorporating more genomic data should be able to determine whether the patterns elucidated here are not only characteristic of the differences between S. pistillata and A. digitifera but also representative of corals from the robust and complex clade at large.

  6. 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 ...

  7. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

    Science.gov (United States)

    Robert Riley; Asaf A. Salamov; Daren W. Brown; Laszlo G. Nagy; Dimitrios Floudas; Benjamin W. Held; Anthony Levasseur; Vincent Lombard; Emmanuelle Morin; Robert Otillar; Erika A. Lindquist; Hui Sun; Kurt M. LaButti; Jeremy Schmutz; Dina Jabbour; Hong Luo; Scott E. Baker; Antonio G. Pisabarro; Jonathan D. Walton; Robert A. Blanchette; Bernard Henrissat; Francis Martin; Daniel Cullen; David S. Hibbett; Igor V. Grigoriev

    2014-01-01

    Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic...

  8. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Brown, Daren W.; Nagy, Laszlo G.; Floudas, Dimitris; Held, Benjamin; Levasseur, Anthony; Lombard, Vincent; Morin, Emmanuelle; Otillar, Robert; Lindquist, Erika; Sun, Hui; LaButti, Kurt; Schmutz, Jeremy; Jabbour, Dina; Luo, Hong; Baker, Scott E.; Pisabarro, Antonio; Walton, Jonathan D.; Blanchette, Robert; Henrissat, Bernard; Martin, Francis; Cullen, Dan; Hibbett, David; Grigoriev, Igor V.

    2014-03-14

    Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

  9. Complete mitochondrial genome of Skylark, Alauda arvensis (Aves: Passeriformes): the first representative of the family Alaudidae with two extensive heteroplasmic control regions.

    Science.gov (United States)

    Qian, Chaoju; Wang, Yuanxiu; Guo, Zhichun; Yang, Jianke; Kan, Xianzhao

    2013-06-01

    The circular mitochondrial genome of Alauda arvensis is 17,018 bp in length, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and 2 extensive heteroplasmic control regions. All of the genes encoded on the H-strand, with the exceptions of one PCG (nad6) and eight tRNA genes (tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser(UCN)), tRNA(Pro), and tRNA(Glu)), as found in other birds' mitochondrial genomes. All of these PCGs are initiated with ATG, while stopped by six types of stop codons. All tRNA genes have the potential to fold into typical clover-leaf structure. Two extensive heteroplasmic control regions were found, and more interestingly, a minisatellite of 37 nucleotides (5'-TCAATCCCATTGATTTCATTATATTAGTATAAAGAAA-3') with 6 tandem repeats was detected at the end of CR2.

  10. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

    Directory of Open Access Journals (Sweden)

    Xueli Zhang

    Full Text Available Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP, sequence-specific amplification polymorphism (SSAP and methylation-sensitive amplified polymorphism (MSAP were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8% and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

  11. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

    Science.gov (United States)

    Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

    2013-01-01

    Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

  12. 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....

  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. 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.

  15. An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

    Directory of Open Access Journals (Sweden)

    Gregersen Peter K

    2009-07-01

    Full Text Available Abstract Background Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia. Results In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups. Conclusion These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.

  16. Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences.

    Science.gov (United States)

    Getlekha, Nuntaporn; Cioffi, Marcelo de Bello; Maneechot, Nuntiya; Bertollo, Luiz Antônio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod; Molina, Wagner Franco

    2018-02-01

    Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA) 15 , (GA) 15 , (CAA) 10 , Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.

  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. Handbook of Plastic Welding

    DEFF Research Database (Denmark)

    Islam, Aminul

    The purpose of this document is to summarize the information about the laser welding of plastic. Laser welding is a matured process nevertheless laser welding of micro dimensional plastic parts is still a big challenge. This report collects the latest information about the laser welding of plastic...... materials and provides an extensive knowhow on the industrial plastic welding process. The objectives of the report include: - Provide the general knowhow of laser welding for the beginners - Summarize the state-of-the-art information on the laser welding of plastics - Find the technological limits in terms...... of design, materials and process - Find the best technology, process and machines adaptive to Sonion’s components - Provide the skills to Sonion’s Design Engineers for successful design of the of the plastic components suitable for the laser welding The ultimate goal of this report is to serve...

  19. 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.

  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. Genome Analysis of the First Extensively Drug-Resistant (XDR Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance.

    Directory of Open Access Journals (Sweden)

    Chee Sian Kuan

    Full Text Available The outbreak of extensively drug-resistant tuberculosis (XDR-TB has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia.

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

    Directory of Open Access Journals (Sweden)

    Keira A Cohen

    2015-01-01

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

  3. Use of reiterative primer extension methodology to map UV-induced photoproducts at the nucleotide level in the laci gene from genomic DNA

    International Nuclear Information System (INIS)

    Chandrasekhar, D.; Houten, B. Van

    1994-01-01

    A newly developed reiterative primer extension assay has been employed to examine photoproduct formation and repair at the nucleotide level. Analysis of UV-induced DNA photoproduct hotspots in the first 184 base pairs of the laci genes of genomic E. coli DNA has revealed that photoproducts are formed linearly with dose and display a sequence-dependent increase. Generally, pyrimdine dimers were twice as frequent as all other UV-induced photoproducts. However, specific sites showed differing distributions. A post-irradiation recovery period revealed differences in the repair efficiency at individual nucleotides. Repair of photoproducts on the transcribed strand was generally twice as efficient as repair of photoproducts on the nontranscribed strand, indicating that strand-specific DNA repair occurs in the constitutively transcribed laci gene of E. coli. The UV-induced DNA photoproduct distribution following repair was well correlated with an established UV-induced mutation spectrum for wild-type E. coli cells. This analysis revealed that photoproduct hotspots on the efficiently repaired transcribed strand did not correlate with mutagenic hotspots. These data strongly support the hypothesis that mutations arise at inefficiently repaired sites on the nontranscribed strand

  4. 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

  5. Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic

    DEFF Research Database (Denmark)

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S. K.

    2014-01-01

    In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree...

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

    KAUST Repository

    Kanji, Akbar

    2015-01-21

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

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

    KAUST Repository

    Kanji, Akbar

    2015-03-01

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

  8. Marine microbe with potential to adhere and degrade plastic structures

    Directory of Open Access Journals (Sweden)

    Alka Kumari

    2017-10-01

    Full Text Available Extensive usages of plastics have led to their accumulation as a contaminant in natural environment worldwide. Plastic is an inert and non-biodegradable material, due to its complex structure and hydrophobic backbone [1]. Conventional methods for reduction of plastic waste such as burning, land-filling release unwanted toxic chemicals to the environment and harming living organism of land as well as the ocean. There is growing interest in development of strategies for the degradation of plastic wastes to clean the environment [2]. Marine bacteria have evolved with the capability to adapt and grow in the diverse environmental conditions [3]. We studied the ability of marine bacteria for destabilization and utilization of different plastic films (LDPE, HDPE, PVC and PET as a sole source of carbon. An active bacterial strain AIIW2 was selected based on the triphenyl tetrazolium chloride reduction assay, and it was identified as Bacillus species based on 16S rRNA gene sequence. The viability of the strain over the plastic surface was studied and confirmed by bacLight assay with fluorescent probes. Scanning Electron Microscope and Atomic Force Microscope images suggested that bacterial interaction over the plastic surface is causing deterioration and roughness with increasing bacterial incubation time. In Fourier transform infrared spectra of treated plastic film evidenced stretching of the (-CH alkane rock chain and (-CO carbonyl region, suggested the oxidative activities of the bacteria. The results revealed that ability of bacterial strain for instigating their colonization over plastic films and deteriorating the polymeric structure in the absence of other carbon sources [4]. Moreover, production of extracellular enzymes such as esterase, laccase, and dehalogenase which are reported to support utilization of plastics was confirmed by plate assays. In concise, our results suggested that the marine bacterial strain AIIW2 have the ability to utilize

  9. Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages.

    Science.gov (United States)

    Marandino, Ana; Tomás, Gonzalo; Panzera, Yanina; Greif, Gonzalo; Parodi-Talice, Adriana; Hernández, Martín; Techera, Claudia; Hernández, Diego; Pérez, Ruben

    2017-10-01

    Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Genome-wide significant associations in schizophrenia to ITIH3/4, CACNA1C and SDCCAG8, and extensive replication of associations reported by the Schizophrenia PGC

    DEFF Research Database (Denmark)

    Hamshere, M L; Walters, J T R; Smith, R

    2013-01-01

    The Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC) highlighted 81 single-nucleotide polymorphisms (SNPs) with moderate evidence for association to schizophrenia. After follow-up in independent samples, seven loci attained genome-wide significance (GWS), but multi-locus t...... interval (CI) 78-100%) of the original set of 78 SNPs represent true associations. We also provide strong evidence for overlap in genetic risk between schizophrenia and bipolar disorder.Molecular Psychiatry advance online publication, 22 May 2012; doi:10.1038/mp.2012.67....

  11. 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.)

  12. Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

    Science.gov (United States)

    Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

    2016-06-01

    In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

  13. 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.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Papa Maria

    2011-01-01

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

  16. 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.

    Science.gov (United States)

    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

  17. 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...

  18. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Sakakibara, Yasumbumi

    2011-10-13

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. 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...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    and correlate with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the roles of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligand-regulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily......The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs...

  1. 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

  2. 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

  3. Plastic condoms.

    Science.gov (United States)

    1968-01-01

    Only simple equipment, simple technology and low initial capital investment are needed in their manufacture. The condoms can be made by people who were previously unskilled or only semi-skilled workers. Plastic condoms differ from those made of latex rubber in that the nature of the plastic film allows unlimited shelf-life. Also, the plastic has a higher degree of lubricity than latex rubber; if there is a demand for extra lubrication in a particular market, this can be provided. Because the plastic is inert, these condoms need not be packaged in hermetically sealed containers. All these attributes make it possible to put these condoms on the distributors' shelves in developing countries competitively with rubber condoms. The shape of the plastic condom is based on that of the lamb caecum, which has long been used as luxury-type condom. The plastic condom is made from plastic film (ethylene ethyl acrilate) of 0.001 inch (0.0254 mm.) thickness. In addition, a rubber ring is provided and sealed into the base of the condom for retention during coitus. The advantage of the plastic condom design and the equipment on which it is made is that production can be carried out either in labour-intensive economy or with varying degrees of mechanization and automation. The uniform, finished condom if made using previously untrained workers. Training of workers can be done in a matter of hours on the two machines which are needed to produce and test the condoms. The plastic film is provided on a double wound roll, and condom blanks are prepared by means of a heat-sealing die on the stamping machine. The rubber rings are united to the condom blanks on an assembly machine, which consists of a mandrel and heat-sealing equipment to seal the rubber ring to the base of the condom. Built into the assembly machine is a simple air-testing apparatus that can detect the smallest pinhole flaw in a condom. The manufacturing process is completed by unravelling the condom from the assembly

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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

  11. 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.

  12. 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) ...

  13. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    KAUST Repository

    Barbrook, Adrian C.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as \\'minicircles\\'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any \\'empty\\' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  14. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    KAUST Repository

    Barbrook, Adrian C.; Voolstra, Christian R.; Howe, Christopher J.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as 'minicircles'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any 'empty' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  15. Synaptic plasticity in drug reward circuitry.

    Science.gov (United States)

    Winder, Danny G; Egli, Regula E; Schramm, Nicole L; Matthews, Robert T

    2002-11-01

    Drug addiction is a major public health issue worldwide. The persistence of drug craving coupled with the known recruitment of learning and memory centers in the brain has led investigators to hypothesize that the alterations in glutamatergic synaptic efficacy brought on by synaptic plasticity may play key roles in the addiction process. Here we review the present literature, examining the properties of synaptic plasticity within drug reward circuitry, and the effects that drugs of abuse have on these forms of plasticity. Interestingly, multiple forms of synaptic plasticity can be induced at glutamatergic synapses within the dorsal striatum, its ventral extension the nucleus accumbens, and the ventral tegmental area, and at least some of these forms of plasticity are regulated by behaviorally meaningful administration of cocaine and/or amphetamine. Thus, the present data suggest that regulation of synaptic plasticity in reward circuits is a tractable candidate mechanism underlying aspects of addiction.

  16. 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

  17. Towards the effective plastic waste management in Bangladesh: a review.

    Science.gov (United States)

    Mourshed, Monjur; Masud, Mahadi Hasan; Rashid, Fazlur; Joardder, Mohammad Uzzal Hossain

    2017-12-01

    The plastic-derived product, nowadays, becomes an indispensable commodity for different purposes. A huge amount of used plastic causes environmental hazards that turn in danger for marine life, reduces the fertility of soil, and contamination of ground water. Management of this enormous plastic waste is challenging in particular for developing countries like Bangladesh. Lack of facilities, infrastructure development, and insufficient budget for waste management are some of the prime causes of improper plastic management in Bangladesh. In this study, the route of plastic waste production and current plastic waste management system in Bangladesh have been reviewed extensively. It emerges that no technical and improved methods are adapted in the plastic management system. A set of the sustainable plastic management system has been proposed along with the challenges that would emerge during the implementation these strategies. Successful execution of the proposed systems would enhance the quality of plastic waste management in Bangladesh and offers enormous energy from waste.

  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. Finite strain logarithmic hyperelasto-plasticity with softening: a strongly non-local implicit gradient framework

    NARCIS (Netherlands)

    Geers, M.G.D.

    2004-01-01

    This paper addresses the extension of a Eulerian logarithmic finite strain hyperelasto-plasticity model in order to incorporate an isotropic plastic damage variable that leads to softening and failure of the plastic material. It is shown that a logarithmic elasto-plastic model with a strongly

  20. Recycling of Plastic

    DEFF Research Database (Denmark)

    Christensen, Thomas Højlund; Fruergaard, Thilde

    2011-01-01

    Plastic is produced from fossil oil. Plastic is used for many different products. Some plastic products like, for example, wrapping foil, bags and disposable containers for food and beverage have very short lifetimes and thus constitute a major fraction of most waste. Other plastic products like...

  1. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  2. 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

  3. Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change.

    Science.gov (United States)

    Supple, Megan Ann; Bragg, Jason G; Broadhurst, Linda M; Nicotra, Adrienne B; Byrne, Margaret; Andrew, Rose L; Widdup, Abigail; Aitken, Nicola C; Borevitz, Justin O

    2018-04-24

    As species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions. Eucalyptus melliodora is a foundation species of a critically endangered community in Australia that is a target for restoration. We examined genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining high levels of gene flow extending for 500 km and correlations with climate and soil variables. Growth experiments revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Model predictions suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model to E. melliodora restoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration. © 2018, Supple et al.

  4. Wood-plastic combination

    International Nuclear Information System (INIS)

    Schaudy, R.

    1978-02-01

    A review on wood-plastic combinations is given including the production (wood and plastic component, radiation hardening, curing), the obtained properties, present applications and prospects for the future of these materials. (author)

  5. DESIGNERS’ KNOWLEDGE IN PLASTICS

    DEFF Research Database (Denmark)

    Eriksen, Kaare

    2013-01-01

    The Industrial designers’ knowledge in plastics materials and manufacturing principles of polymer products is very important for the innovative strength of the industry, according to a group of Danish plastics manufacturers, design students and practicing industrial designers. These three groups ...

  6. Methodology for plastic fracture - a progress report

    International Nuclear Information System (INIS)

    Wilkinson, J.P.D.; Smith, R.E.E.

    1977-01-01

    This paper describes the progress of a study to develop a methodology for plastic fracture. Such a fracture mechanics methodology, having application in the plastic region, is required to assess the margin of safety inherent in nuclear reactor pressure vessels. The initiation and growth of flaws in pressure vessels under overload conditions is distinguished by a number of unique features, such as large scale yielding, three-dimensional structural and flaw configurations, and failure instabilities that may be controlled by either toughness or plastic flow. In order to develop a broadly applicable methodology of plastic fracture, these features require the following analytical and experimental studies: development of criteria for crack initiation and growth under large scale yielding; the use of the finite element method to describe elastic-plastic behaviour of both the structure and the crack tip region; and extensive experimental studies on laboratory scale and large scale specimens, which attempt to reproduce the pertinent plastic flow and crack growth phenomena. This discussion centers on progress to date on the selection, through analysis and laboratory experiments, of viable criteria for crack initiation and growth during plastic fracture. (Auth.)

  7. Plastic value chains

    DEFF Research Database (Denmark)

    Baxter, John; Wahlstrom, Margareta; Zu Castell-Rüdenhausen, Malin

    2014-01-01

    Optimizing plastic value chains is regarded as an important measure in order to increase recycling of plastics in an efficient way. This can also lead to improved awareness of the hazardous substances contained in plastic waste, and how to avoid that these substances are recycled. As an example......, plastics from WEEE is chosen as a Nordic case study. The project aims to propose a number of improvements for this value chain together with representatives from Nordic stakeholders. Based on the experiences made, a guide for other plastic value chains shall be developed....

  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. Challenges in plastics recycling

    DEFF Research Database (Denmark)

    Pivnenko, Kostyantyn; Jakobsen, L. G.; Eriksen, Marie Kampmann

    2015-01-01

    Recycling of waste plastics still remains a challenging area in the waste management sector. The current and potential goals proposed on EU or regional levels are difficult to achieve, and even to partially fullfil them the improvements in collection and sorting should be considerable. A study...... was undertaken to investigate the factors affecting quality in plastics recycling. The preliminary results showed factors primarily influencing quality of plastics recycling to be polymer cross contamination, presence of additives, non-polymer impurities, and polymer degradation. Deprivation of plastics quality......, with respect to recycling, has been shown to happen throughout the plastics value chain, but steps where improvements may happen have been preliminary identified. Example of Cr in plastic samples analysed showed potential spreading and accumulation of chemicals ending up in the waste plastics. In order...

  11. Using Nematostella vectensis to study the interactions between genome, epigenome and bacteria in a changing environment

    Directory of Open Access Journals (Sweden)

    Sebastian Fraune

    2016-08-01

    Full Text Available The phenotype of an animal cannot be explained entirely by its genes. It is now clear that factors other than the genome contribute to the ecology and evolution of animals. Two fundamentally important factors are the associated microbiota and epigenetic regulations. Unlike the genes and regulatory regions of the genome, epigenetics and microbial composition can be rapidly modified, and may thus represent mechanisms for rapid acclimation to a changing environment. At present, the individual functions of epigenetics, microbiomes, and genomic mutations are largely studied in isolation, particularly for species in marine ecosystems. This single variable approach leaves significant questions open for how these mechanisms intersect in the acclimation and adaptation of organisms in different environments. Here, we propose that the starlet sea anemone, Nematostella vectensis, is a model of choice to investigate the complex interplay between adaptation as well as physiological and molecular plasticity in coastal ecosystems. N. vectensis’ geographic range spans four distinct coastlines, including a wide thermocline along the Atlantic coast of North America. N. vectensis is a particularly powerful invertebrate model for studying genome-environment interactions due to (1 the availability of a well-annotated genome, including preexisting data on genome methylation, histone modifications and miRNAs, (2 an extensive molecular toolkit including well-developed protocols for gene suppression and transgenesis, and (3 the simplicity of culture and experimentation in the laboratory. Taken together, N. vectensis has the tractability to connect the functional relationships between a host animal, microbes, and genome modifications to determine mechanisms underlying phenotypic plasticity and local adaptation.

  12. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    2006-12-18

    Dec 18, 2006 ... Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these ...

  13. Fungal genomics beyond Saccharomyces cerevisiae?

    DEFF Research Database (Denmark)

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...

  14. Plasticity - a limiting case of creep

    International Nuclear Information System (INIS)

    Cords, H.; Kleist, G.; Zimmermann, R.

    1986-11-01

    The present work is an attempt to develop further the so-called unified theory for viscoplastic constitutive equations as used for metals or metal alloys. Typically, in similar approaches creep strains and plastic strains are derived from one common stress-strain relationship for inelastic strain rates employing an internal stress function as a back stress. Some novel concepts concerning the definition of the internal stress, plastic yielding and material hardening have been introduced, formulated mathematically and tested for correspondence with a standard type of materials behaviour. As a result of the investigations a system of simultaneous differential equations is defined which has been used to elaborate a common view on a number of different material effects observed in creep and plasticity i.e. normal and inverted primary creep, recoverable creep, incubation time and anelasticity in stress reduction, negative stress relaxation, plastic yielding, perfect plasticity, negative strain rate sensitivity, serrated flow, strain hardening in monotonic and cyclic loading. The theoretical approach is mainly based on a lateral contraction movement not following rigidly the longitudinal extension of the material specimen by a prescribed constant value of Poisson's ratio as usual, but following the axial extension in a process of drag which allows for retardation and which simultaneously impedes the longitudinal straining. (orig.) [de

  15. Higher harmonic imaging of tensile plastic deformation in loading and reloading processes by local resonance method

    International Nuclear Information System (INIS)

    Kawashima, Koichiro; Yasui, Hajime

    2015-01-01

    We have imaged plastically deformed region in a 5052 aluminum plate under tensile loading, unloading and reloading processes by using an immersion local resonance method. By transmitting large-amplitude burst wave of which frequency is a through-thickness resonant frequency of the plate, dislocation loops in plastic zone are forced to vibrate. The higher harmonic amplitude excited by the dislocation movement is mapped for the transducer position. The extension of plastic zone under monotonically increased loading, decrease in harmonic amplitude under unloading process and marked extension of plastic zone in reloading up to 0.4% plastic strain are clearly imaged. (author)

  16. Our plastic age.

    Science.gov (United States)

    Thompson, Richard C; Swan, Shanna H; Moore, Charles J; vom Saal, Frederick S

    2009-07-27

    Within the last few decades, plastics have revolutionized our daily lives. Globally we use in excess of 260 million tonnes of plastic per annum, accounting for approximately 8 per cent of world oil production. In this Theme Issue of Philosophical Transactions of the Royal Society, we describe current and future trends in usage, together with the many benefits that plastics bring to society. At the same time, we examine the environmental consequences resulting from the accumulation of waste plastic, the effects of plastic debris on wildlife and concerns for human health that arise from the production, usage and disposal of plastics. Finally, we consider some possible solutions to these problems together with the research and policy priorities necessary for their implementation.

  17. Our plastic age

    Science.gov (United States)

    Thompson, Richard C.; Swan, Shanna H.; Moore, Charles J.; vom Saal, Frederick S.

    2009-01-01

    Within the last few decades, plastics have revolutionized our daily lives. Globally we use in excess of 260 million tonnes of plastic per annum, accounting for approximately 8 per cent of world oil production. In this Theme Issue of Philosophical Transactions of the Royal Society, we describe current and future trends in usage, together with the many benefits that plastics bring to society. At the same time, we examine the environmental consequences resulting from the accumulation of waste plastic, the effects of plastic debris on wildlife and concerns for human health that arise from the production, usage and disposal of plastics. Finally, we consider some possible solutions to these problems together with the research and policy priorities necessary for their implementation. PMID:19528049

  18. Plastic Pollution from Ships

    OpenAIRE

    Čulin, Jelena; Bielić, Toni

    2016-01-01

    The environmental impact of shipping on marine environment includes discharge of garbage. Plastic litter is of particular concern due to abundance, resistance to degradation and detrimental effect on marine biota. According to recently published studies, a further research is required to assess human health risk. Monitoring data indicate that despite banning plastic disposal at sea, shipping is still a source of plastic pollution. Some of the measures to combat the problem are discussed.

  19. ENVIRONMENTAL ISSUE-PLASTIC

    OpenAIRE

    Sunita Shakle

    2017-01-01

    Polythene is the most common plastic, the annual global production is approximately 60 million tones, and its primary use is in packing. Plastic bags pollute soil and waters and kill thousands of marine generalize plastic bags are not biodegradable they clog water ways, spoil the land scape and end up in landfills. Where they may take 1000 year or more to break down into ever smaller particals that continue to pollution the soil and water.

  20. Our plastic age

    OpenAIRE

    Thompson, Richard C.; Swan, Shanna H.; Moore, Charles J.; vom Saal, Frederick S.

    2009-01-01

    Within the last few decades, plastics have revolutionized our daily lives. Globally we use in excess of 260 million tonnes of plastic per annum, accounting for approximately 8 per cent of world oil production. In this Theme Issue of Philosophical Transactions of the Royal Society, we describe current and future trends in usage, together with the many benefits that plastics bring to society. At the same time, we examine the environmental consequences resulting from the accumulation of waste pl...

  1. Plasticity: modeling & computation

    National Research Council Canada - National Science Library

    Borja, Ronaldo Israel

    2013-01-01

    .... "Plasticity Modeling & Computation" is a textbook written specifically for students who want to learn the theoretical, mathematical, and computational aspects of inelastic deformation in solids...

  2. Synaptic Plasticity and Nociception

    Institute of Scientific and Technical Information of China (English)

    ChenJianguo

    2004-01-01

    Synaptic plasticity is one of the fields that progresses rapidly and has a lot of success in neuroscience. The two major types of synaptie plasticity: long-term potentiation ( LTP and long-term depression (LTD are thought to be the cellular mochanisms of learning and memory. Recently, accumulating evidence suggests that, besides serving as a cellular model for learning and memory, the synaptic plasticity involves in other physiological or pathophysiological processes, such as the perception of pain and the regulation of cardiovascular system. This minireview will focus on the relationship between synaptic plasticity and nociception.

  3. Plastics and health risks.

    Science.gov (United States)

    Halden, Rolf U

    2010-01-01

    By 2010, the worldwide annual production of plastics will surpass 300 million tons. Plastics are indispensable materials in modern society, and many products manufactured from plastics are a boon to public health (e.g., disposable syringes, intravenous bags). However, plastics also pose health risks. Of principal concern are endocrine-disrupting properties, as triggered for example by bisphenol A and di-(2-ethylhexyl) phthalate (DEHP). Opinions on the safety of plastics vary widely, and despite more than five decades of research, scientific consensus on product safety is still elusive. This literature review summarizes information from more than 120 peer-reviewed publications on health effects of plastics and plasticizers in lab animals and humans. It examines problematic exposures of susceptible populations and also briefly summarizes adverse environmental impacts from plastic pollution. Ongoing efforts to steer human society toward resource conservation and sustainable consumption are discussed, including the concept of the 5 Rs--i.e., reduce, reuse, recycle, rethink, restrain--for minimizing pre- and postnatal exposures to potentially harmful components of plastics.

  4. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  5. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  6. Sociologists in Extension

    Science.gov (United States)

    Christenson, James A.; And Others

    1977-01-01

    The article describes the work activities of the extension sociologist, the relative advantage and disadvantage of extension roles in relation to teaching/research roles, and the relevance of sociological training and research for extension work. (NQ)

  7. Epigenetic Basis of Neuronal and Synaptic Plasticity.

    Science.gov (United States)

    Karpova, Nina N; Sales, Amanda J; Joca, Samia R

    2017-01-01

    Neuronal network and plasticity change as a function of experience. Altered neural connectivity leads to distinct transcriptional programs of neuronal plasticity-related genes. The environmental challenges throughout life may promote long-lasting reprogramming of gene expression and the development of brain disorders. The modifications in neuronal epigenome mediate gene-environmental interactions and are required for activity-dependent regulation of neuronal differentiation, maturation and plasticity. Here, we highlight the latest advances in understanding the role of the main players of epigenetic machinery (DNA methylation and demethylation, histone modifications, chromatin-remodeling enzymes, transposons, and non-coding RNAs) in activity-dependent and long- term neural and synaptic plasticity. The review focuses on both the transcriptional and post-transcriptional regulation of gene expression levels, including the processes of promoter activation, alternative splicing, regulation of stability of gene transcripts by natural antisense RNAs, and alternative polyadenylation. Further, we discuss the epigenetic aspects of impaired neuronal plasticity and the pathogenesis of neurodevelopmental (Rett syndrome, Fragile X Syndrome, genomic imprinting disorders, schizophrenia, and others), stressrelated (mood disorders) and neurodegenerative Alzheimer's, Parkinson's and Huntington's disorders. The review also highlights the pharmacological compounds that modulate epigenetic programming of gene expression, the potential treatment strategies of discussed brain disorders, and the questions that should be addressed during the development of effective and safe approaches for the treatment of brain disorders.

  8. Global change and the evolution of phenotypic plasticity in plants.

    Science.gov (United States)

    Matesanz, Silvia; Gianoli, Ernesto; Valladares, Fernando

    2010-09-01

    Global change drivers create new environmental scenarios and selective pressures, affecting plant species in various interacting ways. Plants respond with changes in phenology, physiology, and reproduction, with consequences for biotic interactions and community composition. We review information on phenotypic plasticity, a primary means by which plants cope with global change scenarios, recommending promising approaches for investigating the evolution of plasticity and describing constraints to its evolution. We discuss the important but largely ignored role of phenotypic plasticity in range shifts and review the extensive literature on invasive species as models of evolutionary change in novel environments. Plasticity can play a role both in the short-term response of plant populations to global change as well as in their long-term fate through the maintenance of genetic variation. In new environmental conditions, plasticity of certain functional traits may be beneficial (i.e., the plastic response is accompanied by a fitness advantage) and thus selected for. Plasticity can also be relevant in the establishment and persistence of plants in novel environments that are crucial for populations at the colonizing edge in range shifts induced by climate change. Experimental studies show taxonomically widespread plastic responses to global change drivers in many functional traits, though there is a lack of empirical support for many theoretical models on the evolution of phenotypic plasticity. Future studies should assess the adaptive value and evolutionary potential of plasticity under complex, realistic global change scenarios. Promising tools include resurrection protocols and artificial selection experiments. © 2010 New York Academy of Sciences.

  9. Design principles of electrical synaptic plasticity.

    Science.gov (United States)

    O'Brien, John

    2017-09-08

    Essentially all animals with nervous systems utilize electrical synapses as a core element of communication. Electrical synapses, formed by gap junctions between neurons, provide rapid, bidirectional communication that accomplishes tasks distinct from and complementary to chemical synapses. These include coordination of neuron activity, suppression of voltage noise, establishment of electrical pathways that define circuits, and modulation of high order network behavior. In keeping with the omnipresent demand to alter neural network function in order to respond to environmental cues and perform tasks, electrical synapses exhibit extensive plasticity. In some networks, this plasticity can have dramatic effects that completely remodel circuits or remove the influence of certain cell types from networks. Electrical synaptic plasticity occurs on three distinct time scales, ranging from milliseconds to days, with different mechanisms accounting for each. This essay highlights principles that dictate the properties of electrical coupling within networks and the plasticity of the electrical synapses, drawing examples extensively from retinal networks. Copyright © 2017 The Author. Published by Elsevier B.V. All rights reserved.

  10. Smart apps for the smart plastic surgeon

    Directory of Open Access Journals (Sweden)

    Aniketh Venkataram

    2015-01-01

    Full Text Available Smartphones have the ability to benefit plastic surgeons in all aspects of patient care and education. With the sheer number of applications available and more being created everyday, it is easy to miss out on apps which could be of great relevance. Moreover, the range of android applications available has not been extensively discussed in the literature. To this end, we have compiled an exhaustive list of android smartphone applications, which we feel can help our day to day functioning. The apps have been extensively reviewed and neatly described along with all their potential uses. In addition, we have made an effort to highlight ′non-medical′ or efficiency apps which can improve departmental functioning. These apps have not been described in prior articles, and their functionality might not be known to all. We believe that the technology savvy plastic surgeon can make maximum use of these apps to his benefit.

  11. Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

    Directory of Open Access Journals (Sweden)

    Gounder Kamini

    2011-11-01

    Full Text Available Abstract Background Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different Thermus thermophilus strains have been completed. This paper represents the completed genome from a second Thermus species - T. scotoductus. Results The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T. scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative

  12. Recent advancements and prospects of plastic surgery

    Directory of Open Access Journals (Sweden)

    Xin XING

    2011-09-01

    Full Text Available Objective To summarize the recent advancements and developmental prospects of plastic surgery worldwide,and to describe the future directions,aims,and highlights of Chinese military plastic surgery.Methods Relevant articles published in the last five years were retrieved through a search in PubMed,Medline,and CMCC.A statistical survey was conducted to summarize the achievements obtained by the Chinese military plastic surgery unit in the last five years.Results Considerable progress has been achieved in both clinical treatment and basic research of plastic surgery in the past five years.Its important role in the early treatment of combat injury and trauma has been recognized and emphasized.Chinese military plastic surgery has achieved considerable accomplishments in the last five years,especially in chronic wound repair;mechanism,prevention,and treatment of explosive soft tissue injuries and seawater immersion wounds;and new remedies of maxillofacial traumatic deformity,composite facial tissue allograft,and so on.Conclusions The repair and reconstruction of tissue defect and deformity caused by war injury and trauma will be the future major research direction of military plastic surgery.Research work should focus on tissue engineering,composite tissue allograft,stem cell therapy,mechanism of abnormal scar formation,among others,to solve the clinical problems of destructive facial injuries,extensive thora-abdominal wall defects,chronic ulcer,abnormal scars,and so on.Furthermore,plastic surgeons should fully utilize their special skills and take active part in the early treatment of war injury and trauma.

  13. Environmental sustainability: plastic's evolving role in the automotive life cycle

    International Nuclear Information System (INIS)

    Jekel, L.; Tam, E.K.L.

    2002-01-01

    One method of assessing the sustainability of manufactured products involves performing a life cycle analysis for a product and comparing it to alternative ones, or else examining if individual stages of the product can be modified. LCA applications are being used more extensively, especially in the automotive and related industries. Automotive plastics in particular are being scrutinized with much greater care. Plastic components have replaced metal ones in vehicle manufacturing to improve vehicle fuel efficiency and aesthetics. However, at the end of a vehicle's life, recycling rates for plastic are negligible when compared to those of steel. In order to gain the full environmental benefits of using plastic as a vehicle material, plastics must be recycled at the end of a vehicle's life, especially given their increasing use. While a variety of processes have been developed for the recycling of automotive plastics, the challenges of sorting, processing, and finally recycling a heterogeneous mixture of used plastics have yet to be effectively solved. A preliminary life cycle assessment of a plastic automotive fascia demonstrates the usefulness of this eco-balance technique in evaluating potential improvements to manufacturing and end-of-life processes. Improving the manufacturing process may reduce environmental burdens to a larger extent than just recycling the plastic. (author)

  14. Stem cell plasticity.

    Science.gov (United States)

    Lakshmipathy, Uma; Verfaillie, Catherine

    2005-01-01

    The central dogma in stem cell biology has been that cells isolated from a particular tissue can renew and differentiate into lineages of the tissue it resides in. Several studies have challenged this idea by demonstrating that tissue specific cell have considerable plasticity and can cross-lineage restriction boundary and give rise to cell types of other lineages. However, the lack of a clear definition for plasticity has led to confusion with several reports failing to demonstrate that a single cell can indeed differentiate into multiple lineages at significant levels. Further, differences between results obtained in different labs has cast doubt on some results and several studies still await independent confirmation. In this review, we critically evaluate studies that report stem cell plasticity using three rigid criteria to define stem cell plasticity; differentiation of a single cell into multiple cell lineages, functionality of differentiated cells in vitro and in vivo, robust and persistent engraft of transplanted cells.

  15. Plastics and environment

    International Nuclear Information System (INIS)

    Avenas, P.

    1996-01-01

    Synthetic organic polymers, such as plastics, PVC, polyamides etc are considered less ecological than natural materials such as wood. Other artificial materials such as metals, glass or biodegradable plastics have also a better image than petroleum products. This short paper demonstrates that the manufacturing or the transport of every material uses energy and that the complete energy balance sheet of a plastic bottle, for instance, is more favourable than the one of a glass bottle. Plastic materials are also easily valorized and recycled and part of the energy spent during manufacturing can be recovered during incineration for district heating. During the life-cycle of such a synthetic material, the same petroleum quantity can be used twice which leads to less negative effects on the environment. Finally, the paper focusses on the problem of biodegradable materials which are not degradable when buried under several meters of wastes and which are a nuisance to recycling. (J.S.)

  16. Plastics: Friend or foe?

    Directory of Open Access Journals (Sweden)

    O P Gupta

    2018-01-01

    Full Text Available Plastics has been playing a very significant role in our life. Being light weight, inexpensive and heving good insulating properties it is being used in all aspects of life, from clothes to contact lenses and from mobile phones to automobiles as well as in medical equipments, However it is not biodegradable, and while degrading to fragments it gets converted in to microplastics and nanoplastics The plastic waste is being recognized as an environmental hazard, since these micr- and nanoplastics find way from landfills to water and foods, It is said that we are not only using, but we are eating, drinking and even braething the plastics. These microplastics in body release certain hazardous chemicals and found to be disrupting functions of certain endocrine organs. Whether the rising prevalence of Diabetes, thyroid disorders or infirtility etc., are realated to the plastics?

  17. Recycling of plastics

    Energy Technology Data Exchange (ETDEWEB)

    Kaminsky, W; Menzel, J; Sinn, H

    1976-01-01

    Considering the shortage of raw materials and environmental pollution, the recycling of plastic waste is a very important topic. Pilot plants for research in Funabashi Japan, Franklin (Ohio) U.S.A., and the R 80-process of Krauss Maffei, W. Germany, have demonstrated the possibility of reclaiming plastics from refuse. Old tires and waste from the plastic producing and manufacturing industries are readily available. The pyrolysis of plastic yields gaseous and liquid products, and the exploitation of this cracking reaction has been demonstrated by pilot plants in Japan and Great Britain. Further laboratory scale experiments are taking place in W. Germany. In continuous fluidized beds and in molten salts, polyethylene, polypropylene, polyvinylchloride, polystyrene and rubber are pyrolysed and better than 98 percent conversion is obtained. Up to 40 percent of the feed can be obtained as aromatic compounds, and a pilot plant is under construction. As a first step PVC-containing material can be almost quantitatively dehydrochlorinated.

  18. A Plastic Menagerie

    Science.gov (United States)

    Hadley, Mary Jane

    2010-01-01

    Bobble heads had become quite popular, depicting all sorts of sports figures, animals, and even presidents. In this article, the author describes how her fourth graders made bobble head sculptures out of empty plastic drink bottles. (Contains 1 online resource.)

  19. Art and Plastic Surgery.

    Science.gov (United States)

    Fernandes, Julio Wilson; Metka, Susanne

    2016-04-01

    The roots of science and art of plastic surgery are very antique. Anatomy, drawing, painting, and sculpting have been very important to the surgery and medicine development over the centuries. Artistic skills besides shape, volume, and lines perception can be a practical aid to the plastic surgeons' daily work. An overview about the interactions between art and plastic surgery is presented, with a few applications to rhinoplasty, cleft lip, and other reconstructive plastic surgeries. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

  20. DEVELOPMENT OF PLASTIC SURGERY.

    Science.gov (United States)

    Pećanac, Marija Đ

    2015-01-01

    Plastic surgery is a medical specialty dealing with corrections of defects, improvements in appearance and restoration of lost function. Ancient times. The first recorded account of reconstructive plastic surgery was found in ancient Indian Sanskrit texts, which described reconstructive surgeries of the nose and ears. In ancient Greece and Rome, many medicine men performed simple plastic cosmetic surgeries to repair damaged parts of the body caused by war mutilation, punishment or humiliation. In the Middle Ages, the development of all medical braches, including plastic surgery was hindered. New age. The interest in surgical reconstruction of mutilated body parts was renewed in the XVIII century by a great number of enthusiastic and charismatic surgeons, who mastered surgical disciplines and became true artists that created new forms. Modern era. In the XX century, plastic surgery developed as a modern branch in medicine including many types of reconstructive surgery, hand, head and neck surgery, microsurgery and replantation, treatment of burns and their sequelae, and esthetic surgery. Contemporary and future plastic surgery will continue to evolve and improve with regenerative medicine and tissue engineering resulting in a lot of benefits to be gained by patients in reconstruction after body trauma, oncology amputation, and for congenital disfigurement and dysfunction.

  1. 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)

  2. Bacterial production of the biodegradable plastics polyhydroxyalkanoates.

    Science.gov (United States)

    Urtuvia, Viviana; Villegas, Pamela; González, Myriam; Seeger, Michael

    2014-09-01

    Petroleum-based plastics constitute a major environmental problem due to their low biodegradability and accumulation in various environments. Therefore, searching for novel biodegradable plastics is of increasing interest. Microbial polyesters known as polyhydroxyalkanoates (PHAs) are biodegradable plastics. Life cycle assessment indicates that PHB is more beneficial than petroleum-based plastics. In this report, bacterial production of PHAs and their industrial applications are reviewed and the synthesis of PHAs in Burkholderia xenovorans LB400 is described. PHAs are synthesized by a large number of microorganisms during unbalanced nutritional conditions. These polymers are accumulated as carbon and energy reserve in discrete granules in the bacterial cytoplasm. 3-hydroxybutyrate and 3-hydroxyvalerate are two main PHA units among 150 monomers that have been reported. B. xenovorans LB400 is a model bacterium for the degradation of polychlorobiphenyls and a wide range of aromatic compounds. A bioinformatic analysis of LB400 genome indicated the presence of pha genes encoding enzymes of pathways for PHA synthesis. This study showed that B. xenovorans LB400 synthesize PHAs under nutrient limitation. Staining with Sudan Black B indicated the production of PHAs by B. xenovorans LB400 colonies. The PHAs produced were characterized by GC-MS. Diverse substrates for the production of PHAs in strain LB400 were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Recombination rate plasticity: revealing mechanisms by design

    Science.gov (United States)

    Sefick, Stephen; Rushton, Chase

    2017-01-01

    For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

  4. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  5. Fully plastic solutions of semi-elliptical surface cracks

    International Nuclear Information System (INIS)

    Yagawa, Genki; Yoshimura, Shinobu; Kitajima, Yasumi; Ueda, Hiroyoshi.

    1990-01-01

    Nonlinear finite element analyses of semi-elliptical surface cracks are performed under the fully plastic condition. The power-law hardening materials and the deformation theory of plasticity are assumed. Either the penalty function method or the Uzawa's algorithm is utilized to treat the incompressibility of plastic strains. The local and global J-integral values are obtained using a virtual crack extension technique for plates and cylinders with semi-elliptical surface cracks subjected to uniform tensions. The fully plastic solutions for surface cracked plates are given in the form of polynominals with geometric parameters a/t, a/c and the strain hardening exponent (n). In addition, the effects of curvature on fully plastic solutions are discussed through the comparison between the results of plates and cylinders. (author)

  6. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  7. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. Improved airline-type supplied-air plastic suit

    International Nuclear Information System (INIS)

    Jolley, L. Jr.; Zippler, D.B.; Cofer, C.H.; Harper, J.A.

    1978-06-01

    Two piece supplied-air plastic suits are used extensively at the Savannah River Plant for personnel protection against inhalation of airborne plutonium and tritium. Worker comfort and noise level problems gave impetus to development of an improved suit and aid distribution system. The resulting plastic suit and development work are discussed. The plastic suit unit cost is less than $20, the hearing zone noise level is less than 75 dBA, protection factors exceed 10,000, and user comfort is approved. This suit is expected to meet performance requirements for unrestricted use

  9. The loci controlling plasticity in flax

    Directory of Open Access Journals (Sweden)

    Bickel CL

    2012-02-01

    Full Text Available Cory L Bickel, Marshall Lukacs, Christopher A CullisCase Western Reserve University, Cleveland OH, USAAbstract: Flax undergoes heritable genomic changes in response to nutrient stress, including changes in total DNA content, rDNA copy number variation, and the appearance of Linum Insertion Sequence 1 (LIS-1. The nature of the genomic changes suggests a very different mechanism, which is not yet understood, from that of other DNA changes in response to stress, such as the activation of transposable elements. To identify the genes that control genomic changes in response to stress in flax, reciprocal crosses were made between a responsive flax line, Stormont cirrus, and an unresponsive line, Bethune. The ability of the F2 generation (from selfed F1 plants to respond to nutrient stress was assayed using the insertion of LIS-1 as the criteria for responsiveness. Twenty-nine out of 89 F2s responded at 5 weeks, suggesting that 3-4 dominant loci were all necessary for early LIS-1 insertion. Seventy out of 76 responded at 10 weeks, indicating two dominant loci independently capable of initiating LIS-1 insertion under prolonged nutrient stress. F1 plants and their progeny with either P1 or Bethune as the maternal parent were capable of responding with LIS-1 insertion, indicating that LIS-1 insertion is under nuclear genetic control and does not involve maternal factors. Thus, a small number of loci within the genome of Stormont cirrus appear to control the ability to respond to nutrient stress with LIS-1 insertion. A genetic map of the flax genome is currently under construction, and will be used to identify these loci within the genome.Keywords: nutrient stress, genomic plasticity, flax, Linum usitatissimum, LIS-1 

  10. 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

  11. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter

    Quantitative genetic models recognize the potential for genotype by environment interaction, whereby different genotypes have different plastic responses to changes in macro-environmental conditions. Recently, it has been recognized that micro-environmental plasticity (‘residual’ variance) may also...... be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time and startle response. Estimates of broad sense heritabilities for both traits are substantial (from 0.51 to 0.......77), of the same order as the heritability at the level of the trait mean for startle response and even larger for chill coma recovery. Genome wide association analyses identified molecular variants (from 15 to 31 depending on the sex and the trait) associated with micro-environmental plasticity. These findings...

  12. The plasticity of clays

    Science.gov (United States)

    Group, F.F.

    1905-01-01

    (1) Sand injures plasticity little at first because the grains are suspended in a plastic mass. It is only when grains are abundant enough to come in contact with their neighbors, that the effect becomes serious, and then both strength and amount of possible flow are injured. (2) Certain rare organic colloids increase the plasticity by rendering the water viscous. (3) Fineness also tends to increase plasticity. (4) Plane surfaces (plates) increase the amount of possible flow. They also give a chance for lubrication by thinner films, thus increasing the friction of film, and the strength of the whole mass. The action of plates is thus twofold ; but fineness may be carried to such an extent as to break up plate-like grains into angular fragments. The beneficial effects of plates are also decreased by the fact that each is so closely surrounded by others in the mass. (5) Molecular attraction is twofold in increasing plasticity. As the attraction increases, the coherence and strength of the mass increase, and the amount of possible deformation before crumbling also increases. Fineness increases this action by requiring more water. Colloids and crystalloids in solution may also increase the attraction. It is thus seen to be more active than any other single factor.

  13. 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.

  14. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

    2015-01-01

    DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage...... and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

  15. Life cycle assessment of post-consumer plastics production from waste electrical and electronic equipment (WEEE) treatment residues in a Central European plastics recycling plant

    International Nuclear Information System (INIS)

    Wäger, Patrick A.; Hischier, Roland

    2015-01-01

    Plastics play an increasingly important role in reaching the recovery and recycling rates defined in the European WEEE Directive. In a recent study we have determined the life cycle environmental impacts of post-consumer plastics production from mixed, plastics-rich WEEE treatment residues in the Central European plant of a market-leading plastics recycler, both from the perspective of the customers delivering the residues and the customers buying the obtained post-consumer recycled plastics. The results of our life cycle assessments, which were extensively tested with sensitivity analyses, show that from both perspectives plastics recycling is clearly superior to the alternatives considered in this study (i.e. municipal solid waste incineration (MSWI) and virgin plastics production). For the three ReCiPe endpoint damage categories, incineration in an MSWI plant results in an impact exceeding that of the examined plastics recycling facility each by about a factor of 4, and the production of virgin plastics has an impact exceeding that of the post-consumer recycled (PCR) plastics production each by a factor of 6–10. On a midpoint indicator level the picture is more differentiated, showing that the environmental impacts of the recycling options are lower by 50% and more for almost all impact factors. While this provides the necessary evidence for the environmental benefits of plastics recycling compared to existing alternatives, it can, however, not be taken as conclusive evidence. To be conclusive, future research will have to address the fate of hazardous substances in the outputs of such recycling systems in more detail. - Highlights: • LCA of plastics production from plastics-rich WEEE treatment residues • Multiple stakeholder perspectives addressed via different research questions • Plastics production from WEEE treatment residues clearly superior to alternatives • Robust results as demonstrated by extensive sensitivity analyses

  16. Life cycle assessment of post-consumer plastics production from waste electrical and electronic equipment (WEEE) treatment residues in a Central European plastics recycling plant

    Energy Technology Data Exchange (ETDEWEB)

    Wäger, Patrick A., E-mail: patrick.waeger@empa.ch; Hischier, Roland

    2015-10-01

    Plastics play an increasingly important role in reaching the recovery and recycling rates defined in the European WEEE Directive. In a recent study we have determined the life cycle environmental impacts of post-consumer plastics production from mixed, plastics-rich WEEE treatment residues in the Central European plant of a market-leading plastics recycler, both from the perspective of the customers delivering the residues and the customers buying the obtained post-consumer recycled plastics. The results of our life cycle assessments, which were extensively tested with sensitivity analyses, show that from both perspectives plastics recycling is clearly superior to the alternatives considered in this study (i.e. municipal solid waste incineration (MSWI) and virgin plastics production). For the three ReCiPe endpoint damage categories, incineration in an MSWI plant results in an impact exceeding that of the examined plastics recycling facility each by about a factor of 4, and the production of virgin plastics has an impact exceeding that of the post-consumer recycled (PCR) plastics production each by a factor of 6–10. On a midpoint indicator level the picture is more differentiated, showing that the environmental impacts of the recycling options are lower by 50% and more for almost all impact factors. While this provides the necessary evidence for the environmental benefits of plastics recycling compared to existing alternatives, it can, however, not be taken as conclusive evidence. To be conclusive, future research will have to address the fate of hazardous substances in the outputs of such recycling systems in more detail. - Highlights: • LCA of plastics production from plastics-rich WEEE treatment residues • Multiple stakeholder perspectives addressed via different research questions • Plastics production from WEEE treatment residues clearly superior to alternatives • Robust results as demonstrated by extensive sensitivity analyses.

  17. Investigation into Plastic Cards

    Directory of Open Access Journals (Sweden)

    Neringa Stašelytė

    2015-03-01

    Full Text Available The article examines the strength of laminating plastic cards at different lamination temperatures. For investigation purposes, two types of plastic substrate and films have been used. Laminate strength has been tested (CMYK to establish the impact of colours on the strength of laminate. The paper compares inks supplied by two different producers. The colour characteristics of CIE L*a*b* space before and after the lamination process have been found. According to lamination strength and characteristics of the colours, the most suitable inks, temperature and films have been chosen.

  18. Joining by plastic deformation

    DEFF Research Database (Denmark)

    Mori, Ken-ichiro; Bay, Niels; Fratini, Livan

    2013-01-01

    As the scale and complexity of products such as aircraft and cars increase, demand for new functional processes to join mechanical parts grows. The use of plastic deformation for joining parts potentially offers improved accuracy, reliability and environmental safety as well as creating opportuni......As the scale and complexity of products such as aircraft and cars increase, demand for new functional processes to join mechanical parts grows. The use of plastic deformation for joining parts potentially offers improved accuracy, reliability and environmental safety as well as creating...

  19. Elastic plastic fracture mechanics

    International Nuclear Information System (INIS)

    Simpson, L.A.

    1978-07-01

    The application of linear elastic fracture mechanics (LEFM) to crack stability in brittle structures is now well understood and widely applied. However, in many structural materials, crack propagation is accompanied by considerable crack-tip plasticity which invalidates the use of LEFM. Thus, present day research in fracture mechanics is aimed at developing parameters for predicting crack propagation under elastic-plastic conditions. These include critical crack-opening-displacement methods, the J integral and R-curve techniques. This report provides an introduction to these concepts and gives some examples of their applications. (author)

  20. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  1. Software for computing and annotating genomic ranges.

    Science.gov (United States)

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  2. 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.

  3. Plasticity resembling spike-timing dependent synaptic plasticity: the evidence in human cortex

    Directory of Open Access Journals (Sweden)

    Florian Müller-Dahlhaus

    2010-07-01

    Full Text Available Spike-timing dependent plasticity (STDP has been studied extensively in a variety of animal models during the past decade but whether it can be studied at the systems level of the human cortex has been a matter of debate. Only recently newly developed non-invasive brain stimulation techniques such as transcranial magnetic stimulation (TMS have made it possible to induce and assess timing dependent plasticity in conscious human subjects. This review will present a critical synopsis of these experiments, which suggest that several of the principal characteristics and molecular mechanisms of TMS-induced plasticity correspond to those of STDP as studied at a cellular level. TMS combined with a second phasic stimulation modality can induce bidirectional long-lasting changes in the excitability of the stimulated cortex, whose polarity depends on the order of the associated stimulus-evoked events within a critical time window of tens of milliseconds. Pharmacological evidence suggests an NMDA receptor mediated form of synaptic plasticity. Studies in human motor cortex demonstrated that motor learning significantly modulates TMS-induced timing dependent plasticity, and, conversely, may be modulated bidirectionally by prior TMS-induced plasticity, providing circumstantial evidence that long-term potentiation-like mechanisms may be involved in motor learning. In summary, convergent evidence is being accumulated for the contention that it is now possible to induce STDP-like changes in the intact human central nervous system by means of TMS to study and interfere with synaptic plasticity in neural circuits in the context of behaviour such as learning and memory.

  4. 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

  5. Plastic Surgery: Tackling Misconceptions

    African Journals Online (AJOL)

    will succeed. First impressions tend to last, and if young people's first impression of plastic surgeons is that they spend much of their time doing cosmetic surgery then this is a first impression that might be long ... Res 2014;4 Suppl S3:169‑70. Access this article online. Quick Response Code: Website: www.amhsr.org. DOI:.

  6. Biobased Plastics 2012

    NARCIS (Netherlands)

    Bolck, C.H.; Ravenstijn, J.; Molenveld, K.; Harmsen, P.F.H.

    2011-01-01

    Dit boek geeft inzicht in de huidige op de markt verkrijgbare biobased plastics en de te verwachten ontwikkelingen. Er wordt gekeken naar zowel thermoplastische als thermohardende materialen. Het boek biedt inzicht in de productie, verwerking en eigenschappen van de verschillende types. Daarnaast

  7. 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...

  8. Reliability of Plastic Slabs

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    1989-01-01

    In the paper it is shown how upper and lower bounds for the reliability of plastic slabs can be determined. For the fundamental case it is shown that optimal bounds of a deterministic and a stochastic analysis are obtained on the basis of the same failure mechanisms and the same stress fields....

  9. Individual differences in behavioural plasticities.

    Science.gov (United States)

    Stamps, Judy A

    2016-05-01

    Interest in individual differences in animal behavioural plasticities has surged in recent years, but research in this area has been hampered by semantic confusion as different investigators use the same terms (e.g. plasticity, flexibility, responsiveness) to refer to different phenomena. The first goal of this review is to suggest a framework for categorizing the many different types of behavioural plasticities, describe examples of each, and indicate why using reversibility as a criterion for categorizing behavioural plasticities is problematic. This framework is then used to address a number of timely questions about individual differences in behavioural plasticities. One set of questions concerns the experimental designs that can be used to study individual differences in various types of behavioural plasticities. Although within-individual designs are the default option for empirical studies of many types of behavioural plasticities, in some situations (e.g. when experience at an early age affects the behaviour expressed at subsequent ages), 'replicate individual' designs can provide useful insights into individual differences in behavioural plasticities. To date, researchers using within-individual and replicate individual designs have documented individual differences in all of the major categories of behavioural plasticities described herein. Another important question is whether and how different types of behavioural plasticities are related to one another. Currently there is empirical evidence that many behavioural plasticities [e.g. contextual plasticity, learning rates, IIV (intra-individual variability), endogenous plasticities, ontogenetic plasticities) can themselves vary as a function of experiences earlier in life, that is, many types of behavioural plasticity are themselves developmentally plastic. These findings support the assumption that differences among individuals in prior experiences may contribute to individual differences in behavioural

  10. Søvind Marl - Behaviour of a plastic fissured Eocene clay

    DEFF Research Database (Denmark)

    Grønbech, Gitte Lyng

    The thesis regards the characterisation and determination of properties of Søvind Marl, a Danish highly fissured and plastic clay. Highly fissured, plastic clays are present at great depths several places in Denmark, where extensive development activity is currently ongoing. Nonetheless...... will determine the correlation factors from field tests to undrained shear strength. Finally, the thesis is concluded with recommendations for further work within the field of plastic clays....

  11. Journal of Agricultural Extension

    African Journals Online (AJOL)

    Scope of journal The Journal of Agricultural Extension" is devoted to the advancement of knowledge of agricultural extension services and practice through the publication of original and empirically based research, ... Vol 22, No 1 (2018) ... Symbol recognition and interpretation of HIV/AIDS pictorial messages among rural ...

  12. Priorities for Extension.

    Science.gov (United States)

    Hayward, J. A.

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

  13. Plasticity characteristic obtained by indentation

    International Nuclear Information System (INIS)

    Mil'man, Yu.V.; Chugunova, S.I.; Goncharova, I.V.

    2011-01-01

    Methods for determination plasticity characteristic δH in the measurement of hardness and nanohardness are considered. Parameter δH characterizes the plasticity of a material by the part of plastic deformation in the total elastic-plastic deformation. The value of δH is defined for metals with different types of crystal lattice, covalent and partially covalent crystals, intermetallics, metallic glasses and quasicrystals. It is discussed the dependence of the plasticity characteristic δH on structural factors and temperature. Parameter δH allows to analyze and compare the plasticity of materials which are brittle at standard mechanical tests. The combination of hardness H, as the strength characteristic, and the plasticity characteristic δH makes possible the better characterization of mechanical behavior of materials than only the hardness H. The examples of plasticity characteristic δH application are represented.

  14. Nuclear plant life extension

    International Nuclear Information System (INIS)

    Negin, C.A.

    1989-01-01

    The nuclear power industry's addressing of life extension is a natural trend in the maturation of this technology after 20 years of commercial operation. With increasing emphasis on how plants are operated, and less on how to build them, attention is turning on to maximizing the use of these substantial investments. The first studies of life extension were conducted in the period from 1978 and 1982. These were motivated by the initiation, by the Nuclear Regulatory Commission (NRC), of studies to support decommissioning rulemaking. The basic conclusions of those early studies that life extension is feasible and worth pursuing have not been changed by the much more extensive investigations that have since been conducted. From an engineering perspective, life extension for nuclear plants is fundamentally the same as for fossil plants

  15. Plastic pollutants in water environment

    OpenAIRE

    Mrowiec Bożena

    2017-01-01

    Nowadays, wide applications of plastics result in plastic waste being present in the water environment in a wide variety of sizes. Plastic wastes are in water mainly as microplastics (the size range of 1 nm to < 5 mm). Microplastics have been recognized as an emerging threat, as well as ecotoxicological and ecological risk for water ecosystems. In this review are presented some of the physicochemical properties of plastic materials that determine their toxic effect on the aquatic environment....

  16. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  17. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  18. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  19. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  20. Evaluation of biodegradable plastics for rubber seedling applications

    Science.gov (United States)

    Mansor, Mohd Khairulniza; Dayang Habibah A. I., H.; Kamal, Mazlina Mustafa

    2015-08-01

    The main negative consequence of conventional plastics in agriculture is related to handling the wastes plasticand the associated environmental impact. Hence, a study of different types of potentially biodegradable plastics used for nursery applications have been evaluated on its mechanical,water absorption propertiesand Fourier transform infra-red (FTIR) spectroscopy. Supplied samples from different companies were designated as SF, CF and CO. Most of the polybags exhibited mechanical properties quite similar to the conventional plastics (polybag LDPE). CO polybag which is based on PVA however had extensively higher tensile strength and water absorption properties. FTIR study revealed a characteristics absorbance of conventional plastic, SF, CF and CO biodegradable polybag are associated with polyethylene, poly(butylene adipate-co-terephthalate) (PBAT), polyethylene and polyvinyl alcohol (PVA) structures respectively.

  1. Introduction to Computational Plasticity

    International Nuclear Information System (INIS)

    Hartley, P

    2006-01-01

    The focus of the book on computational plasticity embodies techniques of relevance not only to academic researchers, but also of interest to industrialists engaged in the production of components using bulk or sheet forming processes. Of particular interest is the guidance on how to create modules for use with the commercial system Abaqus for specific types of material behaviour. The book is in two parts, the first of which contains six chapters, starting with microplasticity, but predominantly on continuum plasticity. The first chapter on microplasticty gives a brief description of the grain structure of metals and the existence of slip systems within the grains. This provides an introduction to the concept of incompressibility during plastic deformation, the nature of plastic yield and the importance of the critically resolved shear stress on the slip planes (Schmid's law). Some knowledge of the notation commonly used to describe slip systems is assumed, which will be familiar to students of metallurgy, but anyone with a more general engineering background may need to undertake additional reading to understand the various descriptions. Chapter two introduces one of several yield criteria, that normally attributed to von Mises (though historians of mechanics might argue over who was first to develop the theory of yielding associated with strain energy density), and its two or three-dimensional representation as a yield surface. The expansion of the yield surface during plastic deformation, its translation due to kinematic hardening and the Bauschinger effect in reversed loading are described with a direct link to the material stress-strain curve. The assumption, that the increment of strain is normal to the yield surface, the normality principle, is introduced. Uniaxial loading of an elastic-plastic material is used as an example in which to develop expressions to describe increments in stress and strain. The full presentation of numerous expressions, tensors and

  2. Dettol: Managing Brand Extensions

    OpenAIRE

    Anand Kumar Jaiswal; Arpita Srivastav; Dhwani Kothari

    2009-01-01

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

  3. 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.

  4. Biodegradation of plastics: current scenario and future prospects for environmental safety.

    Science.gov (United States)

    Ahmed, Temoor; Shahid, Muhammad; Azeem, Farrukh; Rasul, Ijaz; Shah, Asad Ali; Noman, Muhammad; Hameed, Amir; Manzoor, Natasha; Manzoor, Irfan; Muhammad, Sher

    2018-03-01

    Plastic is a general term used for a wide range of high molecular weight organic polymers obtained mostly from the various hydrocarbon and petroleum derivatives. There is an ever-increasing trend towards the production and consumption of plastics due to their extensive industrial and domestic applications. However, a wide spectrum of these polymers is non-biodegradable with few exceptions. The extensive use of plastics, lack of waste management, and casual community behavior towards their proper disposal pose a significant threat to the environment. This has raised growing concerns among various stakeholders to devise policies and innovative strategies for plastic waste management, use of biodegradable polymers especially in packaging, and educating people for their proper disposal. Current polymer degradation strategies rely on chemical, thermal, photo, and biological procedures. In the presence of proper waste management strategies coupled with industrially controlled biodegradation facilities, the use of biodegradable plastics for some applications such as packaging or health industry is a promising and attractive option for economic, environmental, and health benefits. This review highlights the classification of plastics with special emphasis on biodegradable plastics and their rational use, the identified mechanisms of plastic biodegradation, the microorganisms involved in biodegradation, and the current insights into the research on biodegradable plastics. The review has also identified the research gaps in plastic biodegradation followed by future research directions.

  5. Plasticity modeling & computation

    CERN Document Server

    Borja, Ronaldo I

    2013-01-01

    There have been many excellent books written on the subject of plastic deformation in solids, but rarely can one find a textbook on this subject. “Plasticity Modeling & Computation” is a textbook written specifically for students who want to learn the theoretical, mathematical, and computational aspects of inelastic deformation in solids. It adopts a simple narrative style that is not mathematically overbearing, and has been written to emulate a professor giving a lecture on this subject inside a classroom. Each section is written to provide a balance between the relevant equations and the explanations behind them. Where relevant, sections end with one or more exercises designed to reinforce the understanding of the “lecture.” Color figures enhance the presentation and make the book very pleasant to read. For professors planning to use this textbook for their classes, the contents are sufficient for Parts A and B that can be taught in sequence over a period of two semesters or quarters.

  6. Sub-nanosecond plastic scintillators

    International Nuclear Information System (INIS)

    Lyons, P.B.; Caldwell, S.E.; Hocker, L.P.; Crandall, D.G.; Zagarino, P.A.; Cheng, J.; Tirsell, G.; Hurlbut, C.R.

    1977-01-01

    Quenched plastic scintillators have been developed that yield much faster short decay components and greatly reduced long decay components compared to conventional plastic scintillators. The plastics are produced through the addition of selected quench agents to NE111 plastic scintillator that result in reduced total light output. Eight different agents have been studied. Benzophenone and piperidine are two of the most effective quench agents. Data are presented both for short and long decay components. The plastics are expected to make significant contributions in areas of plasma diagnostics

  7. Sub-nanosecond plastic scintillators

    International Nuclear Information System (INIS)

    Lyons, P.B.; Caldwell, S.E.; Hocker, L.P.; Crandall, D.G.; Zagarino, P.A.; Cheng, J.; Tirsell, G.; Hurlbut, C.R.

    1976-01-01

    Quenched plastic scintillators have been developed that yield much faster short decay components and greatly reduced long decay components compared to conventional plastic scintillators. The plastics are produced through the addition of selected quench agents to NE111 plastic scintillator that result in reduced total light output. Eight different agents have been studied. Benzophenone and piperidine are two of the most effective quench agents. Data are presented both for short and long decay components. The plastics are expected to make significant contributions in areas of plasma diagnostics

  8. Compensatory plasticity: time matters

    Directory of Open Access Journals (Sweden)

    Latifa eLazzouni

    2014-06-01

    Full Text Available Plasticity in the human and animal brain is the rule, the base for development, and the way to deal effectively with the environment for making the most efficient use of all the senses. When the brain is deprived of one sensory modality, plasticity becomes compensatory: the exception that invalidates the general loss hypothesis giving the opportunity of effective change. Sensory deprivation comes with massive alterations in brain structure and function, behavioural outcomes, and neural interactions. Blind individuals do as good as the sighted and even more, show superior abilities in auditory, tactile and olfactory processing. This behavioural enhancement is accompanied with changes in occipital cortex function, where visual areas at different levels become responsive to non-visual information. The intact senses are in general used more efficiently in the blind but are also used more exclusively. New findings are disentangling these two aspects of compensatory plasticity. What is due to visual deprivation and what is dependent on the extended use of spared modalities? The latter seems to contribute highly to compensatory changes in the congenitally blind. Short term deprivation through the use of blindfolds shows that cortical excitability of the visual cortex is likely to show rapid modulatory changes after few minutes of light deprivation and therefore changes are possible in adulthood. However, reorganization remains more pronounced in the congenitally blind. Cortico-cortical pathways between visual areas and the areas of preserved sensory modalities are inhibited in the presence of vision, but are unmasked after loss of vision or blindfolding as a mechanism likely to drive cross-modal information to the deafferented visual cortex. Plasticity in the blind is also accompanied with neurochemical and morphological changes; both intrinsic connectivity and functional coupling at rest are altered but are likewise dependent on different sensory

  9. Mesocycles in conserving plastics

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2016-01-01

    driven by the need to balance the requirements for reversibility in conservation practices with the artist’s intent and significance. Developments within each of the three mesocycles from the 1990s to date are discussed in this article. Environmental science and toxicology of waste plastics offer a novel...... source of information about real time degradation in terrestrial and marine microenvironments that seems likely to contribute to the conservation of similar materials in contemporary artworks....

  10. Plastic footwear for leprosy.

    Science.gov (United States)

    Antia, N H

    1990-03-01

    The anaesthetic foot in leprosy poses the most major problem in the rehabilitation of its patients. Various attempts have been made to produce protective footwear such as the microcellular rubber-car-tyre sandals. Unfortunately these attempts have had little success on a large scale because of the inability to produce them in large numbers and the stigma attached to such unusual footwear. While such footwear may be superior to the 'tennis' shoe in protecting the foot from injury by the penetration of sharp objects, it fails to distribute the weight-bearing forces which is the major cause of plantar damage and ulceration in the anaesthetic foot. This can be achieved by providing rigidity to the sole, as demonstrated by the healing of ulcers in plaster of paris casts or the rigid wooden clog. A new type of moulded plastic footwear has been evolved in conjunction with the plastic footwear industry which provides footwear that can be mass produced at a low price and which overcomes the stigma of leprosy. Controlled rigidity is provided by the incorporation of a spring steel shank between the sponge insole and the hard wearing plastic sole. Trials have demonstrated both the acceptability of the footwear and its protective effects as well as its hard wearing properties.

  11. Plastic waste disposal apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Kito, S

    1972-05-01

    A test plant plastic incinerator was constructed by the Takuma Boiler Manufacturing Co. for Sekisui Chemical Industries, and the use of a continuous feed spreader was found to be most effective for prevention of black smoke, and the use of a venturi scrubber proved to be effective for elimination of hydrogen chloride gas. The incinerator was designed for combustion of polyvinyl chloride exclusively, but it is also applicable for combustion of other plastics. When burning polyethylene, polypropylene, or polystyrene, (those plastics which do not produce toxic gases), the incinerator requires no scrubber for the combustion gas. The system may or may not have a pretreatment apparatus. For an incinerator with a pretreatment system, the flow chart comprises a pit, a supply crane, a vibration feeder, a metal eliminator, a rotation shredder, a continuous screw feeder with a quantitative supply hopper, a pretreatment chamber (300 C dry distillation), a quantitative supply hopper, and the incinerator. The incinerator is a flat non-grid type combustion chamber with an oil burner and many air nozzles. From the incinerator, ashes are sent by an ash conveyor to an ash bunker. The combustion gas goes to the boiler, and the water supplied the boiler water pump creates steam. The heat from the gas is sent back to the pretreatment system through a heat exchanger. The gas then goes to a venturi scrubber and goes out from a stack.

  12. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  13. Spacetime extensions Pt. 1

    International Nuclear Information System (INIS)

    Racz, I.

    1991-09-01

    The problem of the existence of local extensions of spacetime is considered. It is shown that for a spacetime including an incomplete inextendible non-coiling causal geodesic curve there exists a particular C k (resp. C k- ) local extension provided that the curvature and its covariant derivatives are well behaved up to order k + 1 (resp. k) along a family of causal geodetics (around the chosen one). (R.P.) 15 refs

  14. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

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

  15. New perspectives in plastic biodegradation.

    Science.gov (United States)

    Sivan, Alex

    2011-06-01

    During the past 50 years new plastic materials, in various applications, have gradually replaced the traditional metal, wood, leather materials. Ironically, the most preferred property of plastics--durability--exerts also the major environmental threat. Recycling has practically failed to provide a safe solution for disposal of plastic waste (only 5% out of 1 trillion plastic bags, annually produced in the US alone, are being recycled). Since the most utilized plastic is polyethylene (PE; ca. 140 million tons/year), any reduction in the accumulation of PE waste alone would have a major impact on the overall reduction of the plastic waste in the environment. Since PE is considered to be practically inert, efforts were made to isolate unique microorganisms capable of utilizing synthetic polymers. Recent data showed that biodegradation of plastic waste with selected microbial strains became a viable solution. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Performance of molded plastic scintillators

    International Nuclear Information System (INIS)

    Gen, N.S.; Leman, V.E.; Solomonov, V.M.

    1989-01-01

    The performance of molded plastic scintillators is studied. The plastic scintillators studied were formed by transfer molding and intrusion from a scintillation composition consisting of polystyrene and a standard system of luminescent additives: 2 mass % of paraterphenyl + 0.06 mass % 1,4-di-/2-[5-phenyloxazoyly]/benzene and a plasticizer. The combined effect of mechanical load and temperature was studied. The effect of radiation on molded plastic scintillators was studied using gamma radiation from a 60 Co source. The studies show that the main operating characteristics of molded plastic scintillators are on a par with those of polymerized plastic scintillators. At the same time, molded plastic scintillators are superior in thermal stability at temperatures below the glass transition temperature and with respect to their working temperature range

  17. Less extensive surgery compared to extensive surgery

    DEFF Research Database (Denmark)

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

    2014-01-01

    -up by hospital data files, general practitioner, death certificate, and autopsy report. Revision of histopathology by a single pathologist. Main outcome measures: Survival and relapse by clinical data, stage, and type of surgery. RESULTS: The incidence of AGCT was 1.37 per year per 100,000 women (95% CI: 1.08, 1.......68). The median follow-up time was 15 years and for the 79 surviving women 22 years. Stage I was found in 94% of cases. Relapse occurred in 24% of women in stage I and 100% of the other stages. Survival in stage I was 95%, 89% and 84% after 5, 10 and 20 years respectively. Increased survival of stage I......: The survival of women was better in AGCT than in epithelial ovarian tumor. Age and type of surgery, besides stage, influenced survival. Total abdominal hysterectomy and bilateral salpingo-oophorectomy is the recommended treatment with advancing age. At younger age less extensive surgery was associated...

  18. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  19. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  20. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2013-11-12

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  1. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  2. Unified creep-plasticity model for halite

    International Nuclear Information System (INIS)

    Krieg, R.D.

    1980-11-01

    There are two national energy programs which are considering caverns in geological salt (NaCl) as a storage repository. One is the disposal of nuclear wastes and the other is the storage of oil. Both short-time and long-time structural deformations and stresses must be predictable for these applications. At 300K, the nominal initial temperature for both applications, the salt is at 0.28 of the melting temperature and exhibits a significant time dependent behavior. A constitutive model has been developed which describes the behavior observed in an extensive set of triaxial creep tests. Analysis of these tests showed that a single deformation mechanism seems to be operative over the stress and temperature range of interest so that the secondary creep data can be represented by a power of the stress over the entire test range. This simple behavior allowed a new unified creep-plasticity model to be applied with some confidence. The resulting model recognizes no inherent difference between plastic and creep strains yet models the total inelastic strain reasonably well including primary and secondary creep and reverse loadings. A multiaxial formulation is applied with a back stress. A Bauschinger effect is exhibited as a consequence and is present regardless of the time scale over which the loading is applied. The model would be interpreted as kinematic hardening in the sense of classical plasticity. Comparisons are made between test data and model behavior

  3. Plastics in the Marine Environment.

    Science.gov (United States)

    Law, Kara Lavender

    2017-01-03

    Plastics contamination in the marine environment was first reported nearly 50 years ago, less than two decades after the rise of commercial plastics production, when less than 50 million metric tons were produced per year. In 2014, global plastics production surpassed 300 million metric tons per year. Plastic debris has been detected worldwide in all major marine habitats, in sizes from microns to meters. In response, concerns about risks to marine wildlife upon exposure to the varied forms of plastic debris have increased, stimulating new research into the extent and consequences of plastics contamination in the marine environment. Here, I present a framework to evaluate the current understanding of the sources, distribution, fate, and impacts of marine plastics. Despite remaining knowledge gaps in mass budgeting and challenges in investigating ecological impacts, the increasing evidence of the ubiquity of plastics contamination in the marine environment, the continued rapid growth in plastics production, and the evidence-albeit limited-of demonstrated impacts to marine wildlife support immediate implementation of source-reducing measures to decrease the potential risks of plastics in the marine ecosystem.

  4. Plastics in the Marine Environment

    Science.gov (United States)

    Law, Kara Lavender

    2017-01-01

    Plastics contamination in the marine environment was first reported nearly 50 years ago, less than two decades after the rise of commercial plastics production, when less than 50 million metric tons were produced per year. In 2014, global plastics production surpassed 300 million metric tons per year. Plastic debris has been detected worldwide in all major marine habitats, in sizes from microns to meters. In response, concerns about risks to marine wildlife upon exposure to the varied forms of plastic debris have increased, stimulating new research into the extent and consequences of plastics contamination in the marine environment. Here, I present a framework to evaluate the current understanding of the sources, distribution, fate, and impacts of marine plastics. Despite remaining knowledge gaps in mass budgeting and challenges in investigating ecological impacts, the increasing evidence of the ubiquity of plastics contamination in the marine environment, the continued rapid growth in plastics production, and the evidence—albeit limited—of demonstrated impacts to marine wildlife support immediate implementation of source-reducing measures to decrease the potential risks of plastics in the marine ecosystem.

  5. 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.

  6. Pseudo Boolean Programming for Partially Ordered Genomes

    Science.gov (United States)

    Angibaud, Sébastien; Fertin, Guillaume; Thévenin, Annelyse; Vialette, Stéphane

    Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to different maps with some unordered genes. Starting from a partial order between genes of a genome, one method to find a total order consists in optimizing a given measure between a linear extension of this partial order and a given total order of a close and well-known genome. However, for most common measures, the problem turns out to be NP-hard. In this paper, we propose a (0,1)-linear programming approach to compute a linear extension of one genome that maximizes the number of common intervals (resp. the number of adjacencies) between this linear extension and a given total order. Next, we propose an algorithm to find linear extensions of two partial orders that maximize the number of adjacencies.

  7. Improving Public Health and Environment through Plastic Waste Management in Mumbai Metropolitan Region

    Directory of Open Access Journals (Sweden)

    Sanjay RODE

    2015-12-01

    Full Text Available The Mumbai Metropolitan Region is growing in terms of population, industry, educational and commercial units. The daily requirements of commodities and services by all units have increased fast. Plastic is used extensively for packing, protection and service of various commodities. The use of plastic is much higher by industry and households in region. In Brihan Mumbai Municipal Corporation, the density of population is higher. The concentration of small and large industries is more. Therefore the plastic use is much higher for different purposes. It leads to more waste of plastic. In Ulhasnagar Municipal Corporation, the population and industrial units are less. Therefore plastic waste is less generated. Theaters are generating less plastic waste in metropolitan region. The Brihan Mumbai Municipal Corporation (BMC and municipal corporations in Thane district will continuously generate more plastic waste in future. The Tobit regression model shows that plastic waste is positively co-related and statistically significant with pollution and industry in region. Therefore the comprehensive policies are required to reduce plastic waste. This is because plastic waste is affecting on the health of human being. It also affects negatively on soil, air and water. The entire food supply chain gets affected due to plastic waste. The water logging is common due to plastic waste in region. It chock ups the drainage system and it becomes the ground for mosquitoes. It further leads to dengue, malaria and other diseases in region. Municipal corporations must collect plastic in separate bins and process it. The plastic and e-waste can be utilized for road construction in region. All the policies will certainly help to reduce the plastic waste and maintain the clean environment in region.

  8. 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.

  9. Chromosome copy analysis by single-cell comparative genomic hybridization technique based on primer extension preamplification and degenerate oligonucleotide primed-PCR%引物延伸预扩增结合简并引物PCR在单细胞比较基因组杂交分析染色体异常中的应用

    Institute of Scientific and Technical Information of China (English)

    谭珂; 狄玉芬; 程德华; 徐芳; 卢光绣; 谭跃球

    2010-01-01

    Objective To establish a single-cell whole genome amplification (WGA) technique, in combination with comparative genomic hybridization (CGH), for analyzing chromosomal copy number changes, and to explore its clinical application in preimplantation genetic diagnosis (PGD). Methods Twelve single cell samples with known karyotypes, including 5 chorionic villus samples, 4 human embryonic stem cell (hESC) samples and 3 peripheral lymphocyte samples, and 4 single blastomere samples carrying chromosomal abnormalities detected by PGD, were collected for whole genome amplification by combining primer extension preamplification (PEP) with degenerate oligonucleotide primed-PCR (DOP-PCR)amplification. The amplified products labeled by red fluorescence were mixed with control DNA labeled by green fluorescence, and then the mixture was analyzed by CGH. As a comparison, 10 single cell samples were amplified by DOP-PCR only and then CGH analysis was performed. Results The amplification using PEP-DOP-PCR was more stable than traditional DOP-PCR. The products of PEP-DOP-PCR range from 100 bp to 1000 bp, with the mean size being about 400 bp. The CGH results were consistent with analyses by other methods. However, only 6 out of 10 single cell samples were successfully amplified by DOP-PCR,and CGH analysis showed a high background and 2 samples showed inconsistent results from other methods. Conclusion PEP-DOP-PCR can effectively amplify the whole genome DNA of single cell.Combined with CGH, this WGA method can successfully detect single-cell chromosomal copy number changes, while DOP-PCR was easy to fail to amplify and amplify inhomogeneousty, and CGH analysis using this PCR product usually showed high background. These results suggest that PEP-DOP-CGH is a promising method for preimplantation genetic diagnosis.%目的 建立一种可信的单细胞全基因组扩增(whole genome amplification.WGA)技术,结合比较基因组杂交(comparative genomic hybridization,CGH)分析单细

  10. Plastics pipe couplings

    International Nuclear Information System (INIS)

    Glover, J.B.

    1980-07-01

    A method is described of making a pipe coupling of the type comprising a plastics socket and a resilient annular sealing member secured in the mouth thereof, in which the material of at least one component of the coupling is subjected to irradiation with high energy radiation whereby the material is caused to undergo cross-linking. As examples, the coupling may comprise a polyethylene or plasticised PVC socket the material of which is subjected to irradiation, and the sealing member may be moulded from a thermoplastic elastomer which is subjected to irradiation. (U.K.)

  11. Android Access Control Extension

    Directory of Open Access Journals (Sweden)

    Anton Baláž

    2015-12-01

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

  12. Life extension economic analysis

    International Nuclear Information System (INIS)

    Smithling, A.P.

    1992-01-01

    Life extension economic analyses of fossil fueled power plants need the development of consistent methods which consider the capital costs associated with component replacement or repair and estimates of normal station capital expenditures over the units remaining life. In order to link capital and production costs, Niagra Mohawk Power Corp. develops most and worst cases. A most case includes capital components that would definitely need replacement or modification for life extension. The worst case scenario contains must case capital costs plus various components which may need replacement or modification. In addition, two forecasted conditions are used, base case capacity and low capacity

  13. Plastic pollutants in water environment

    Directory of Open Access Journals (Sweden)

    Mrowiec Bożena

    2017-12-01

    Full Text Available Nowadays, wide applications of plastics result in plastic waste being present in the water environment in a wide variety of sizes. Plastic wastes are in water mainly as microplastics (the size range of 1 nm to < 5 mm. Microplastics have been recognized as an emerging threat, as well as ecotoxicological and ecological risk for water ecosystems. In this review are presented some of the physicochemical properties of plastic materials that determine their toxic effect on the aquatic environment. Wastewater treatment plants (WWTPs are mentioned as one of main sources of microplastics introduced into fresh water, and rivers are the pathways for the transportation of the pollutants to seas and oceans. But, effluents from tertiary wastewater treatment facilities can contain only minimally microplastic loads. The issue of discharge reduction of plastic pollutants into water environment needs activities in the scope of efficient wastewater treatment, waste disposal, recycling of plastic materials, education and public involvement.

  14. Methodology for plastic fracture. A progress report

    International Nuclear Information System (INIS)

    Wilkinson, J.P.D.; Hahn, G.T.; Smith, R.E.E.

    1977-01-01

    The initiation and growth of flaws in pressure vessels under overload conditions is distinguished by a number of unique features, such as large scale yielding, three-dimensional structural and flaw configurations, and failure instabilities that may be controlled by either toughness or plastic flow. In order to develop a broadly applicable methodology of plastic fracture, these features require the following analytical and experimental studies: development of criteria for crack initiation and growth under large scale yielding; the use of the finite element method to describe elastic-plastic behavior of both the structure and the crack tip region; and extensive experimental studies on laboratory scale and large scale specimens, which attempt to reproduce the pertinent plastic flow and crack growth phenomena. A variety of candidate criteria for crack initiation and growth are examined. For the case of crack initiation, these criteria include the J-integral, crack opening displacement, and strain amplitude. In the case of crack growth, the criteria examined include in addition the strain amplitude at the crack tip, work done in a crack tip process zone, and a generalized energy release-rate approach. Each test specimen configuration is analyzed through the finite element method in order to predict its experimental behavior. Specimens include the compact tension specimen and center cracked panels. The basic materials used in the program are a single heat of reactor grade A533 Grade B Class 1 steel, purchased in the form of a plate of size 4.5 m (178 in.) square and 0.2 m (8 in.) thick, and two alloys with yield strength-to-roughness ratios about five times

  15. Plastic food packaging and health

    Directory of Open Access Journals (Sweden)

    Raika Durusoy

    2011-02-01

    Full Text Available Plastics have a wide usage in our daily lives. One of their uses is for food packaging and food containers. The aim of this review is to introduce different types of chemicals that can leach from food packaging plastics into foods and cause human exposure and to mention their effects on health. The types of plastics were reviewed under the 13 headings in Turkish Codex Alimentarius and plastics recycling symbols were provided to enable the recognition of the type of plastic when applicable. Chemicals used during the production and that can cause health risks are investigated under the heading of the relevant type of plastic. The most important chemicals from plastic food packaging that can cause toxicity are styrene, 1,3-butadiene, melamine, formaldehyde, acrylamide, di-2-ethylhexyl phthalate, di-2-ethylhexyl adipate, vinyl chloride and bisphenol A. These chemicals have endocrine disrupting, carcinogenic and/or development disrupting effects. These chemicals may leach into foods depending on the chemical properties of the plastic or food, temperature during packaging, processing and storage, exposure to UV and duration of storage. Contact with fatty/oily or acidic foods, heating of the food inside the container, or drinking hot drinks from plastic cups, use of old and scratched plastics and some detergents increase the risk of leaching. The use of plastic containers and packaging for food and beveradges should be avoided whenever possible and when necessary, less harmful types of plastic should be preferred. [TAF Prev Med Bull 2011; 10(1.000: 87-96

  16. Extensive mapping of PPAR binding to genomic DNA

    DEFF Research Database (Denmark)

    Nielsen, Ronni; Pedersen, Thomas Åskov; Trindade, Luisa

    processes such as adaptation to fasting and cold, muscle isotype switching and adipogenesis, underscoring the metabolic importance of these transcription factors. Although the PPARs have been subject to intensive studies for almost two decades, far from all PPAR target genes are known. In addition, only few...... analysis of the regulatory networks controlled by PPAR transcription factors, thereby allowing for a better understanding of PPAR biology. - Adenoviral expression PPARg2 and RXR induce transcription from a wide range of hepatocyte as well as non-hepatocyte PPAR target genes in the murine AML-12 hepatoma...... cell line. Only very few PPAR target genes are not induced by PPARg2/RXR. - ChIP-on-chip analysis shows ~1200 peaks on chr. 7 & 8 by peak detection software. 80% of selected peaks were positive in single ChIP experiments.   - PPARg2/RXR are recruited to DNA elements near several genes on chr. 7 & 8...

  17. New polyvinylchloride plasticizers

    Directory of Open Access Journals (Sweden)

    MAZITOVA Aliya Karamovna

    2017-11-01

    Full Text Available One of the main large-capacity polymers of modern chemical industry is polyvinylchloride (PVC. Polyvinylchloride is characterized by many useful engineering properties – chemical firmness in different environments, good electric properties, etc. It explains immensely various use of materials on the basis of PVC in different engineering industries. It is cable, building, light industries, mechanical engineering and automotive industry where PVC is widely applied. One of the reasons why PVC production is dramatically growing is that there is no yet other polymer which could be subjected to such various modifying as it is done with PVC. However under normal temperature this polymer is fragile and isn't elastic that limits the field of its application. Rapid growth of production of polyvinylchloride is explained by its ability to modify properties, due to introduction of special additives when processing. Introduction of plasticizers – mostlly esters of organic and inorganic acids – into PVC allows significant changing properties of polymer. Plasticizers facilitate process of receiving polymeric composition, increase flexibility and elasticity of the final polymeric product due to internal modification of polymeric molecule.

  18. Mobile Applications for Extension

    Science.gov (United States)

    Drill, Sabrina L.

    2012-01-01

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

  19. Brain Plasticity and Motor Practice in Cognitive Aging

    Directory of Open Access Journals (Sweden)

    Liuyang eCai

    2014-03-01

    Full Text Available For more than two decades, there have been extensive studies of experience-based neural plasticity exploring effective applications of brain plasticity for cognitive and motor development. Research suggests that human brains continuously undergo structural reorganization and functional changes in response to stimulations or training. From a developmental point of view, the assumption of lifespan brain plasticity has been extended to older adults in terms of the benefits of cognitive training and physical therapy. To summarize recent developments, first, we introduce the concept of neural plasticity from a developmental perspective. Secondly, we note that motor learning often refers to deliberate practice and the resulting performance enhancement and adaptability. We discuss the close interplay between neural plasticity, motor learning and cognitive aging. Thirdly, we review research on motor skill acquisition in older adults with, and without, impairments relative to aging-related cognitive decline. Finally, to enhance future research and application, we highlight the implications of neural plasticity in skills learning and cognitive rehabilitation for the aging population.

  20. Americium behaviour in plastic vessels

    International Nuclear Information System (INIS)

    Legarda, F.; Herranz, M.; Idoeta, R.; Abelairas, A.

    2010-01-01

    The adsorption of 241 Am dissolved in water in different plastic storage vessels was determined. Three different plastics were investigated with natural and distilled waters and the retention of 241 Am by these plastics was studied. The same was done by varying vessel agitation time, vessel agitation speed, surface/volume ratio of water in the vessels and water pH. Adsorptions were measured to be between 0% and 70%. The adsorption of 241 Am is minimized with no water agitation, with PET or PVC plastics, and by water acidification.

  1. Americium behaviour in plastic vessels

    Energy Technology Data Exchange (ETDEWEB)

    Legarda, F.; Herranz, M. [Departamento de Ingenieria Nuclear y Mecanica de Fluidos, Escuela Tecnica Superior de Ingenieria de Bilbao, Universidad del Pais Vasco (UPV/EHU), Alameda de Urquijo s/n, 48013 Bilbao (Spain); Idoeta, R., E-mail: raquel.idoeta@ehu.e [Departamento de Ingenieria Nuclear y Mecanica de Fluidos, Escuela Tecnica Superior de Ingenieria de Bilbao, Universidad del Pais Vasco (UPV/EHU), Alameda de Urquijo s/n, 48013 Bilbao (Spain); Abelairas, A. [Departamento de Ingenieria Nuclear y Mecanica de Fluidos, Escuela Tecnica Superior de Ingenieria de Bilbao, Universidad del Pais Vasco (UPV/EHU), Alameda de Urquijo s/n, 48013 Bilbao (Spain)

    2010-07-15

    The adsorption of {sup 241}Am dissolved in water in different plastic storage vessels was determined. Three different plastics were investigated with natural and distilled waters and the retention of {sup 241}Am by these plastics was studied. The same was done by varying vessel agitation time, vessel agitation speed, surface/volume ratio of water in the vessels and water pH. Adsorptions were measured to be between 0% and 70%. The adsorption of {sup 241}Am is minimized with no water agitation, with PET or PVC plastics, and by water acidification.

  2. Americium behaviour in plastic vessels.

    Science.gov (United States)

    Legarda, F; Herranz, M; Idoeta, R; Abelairas, A

    2010-01-01

    The adsorption of (241)Am dissolved in water in different plastic storage vessels was determined. Three different plastics were investigated with natural and distilled waters and the retention of (241)Am by these plastics was studied. The same was done by varying vessel agitation time, vessel agitation speed, surface/volume ratio of water in the vessels and water pH. Adsorptions were measured to be between 0% and 70%. The adsorption of (241)Am is minimized with no water agitation, with PET or PVC plastics, and by water acidification. Copyright 2009 Elsevier Ltd. All rights reserved.

  3. GenColors-based comparative genome databases for small eukaryotic genomes.

    Science.gov (United States)

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

  4. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  5. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

    Science.gov (United States)

    Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

    2014-08-21

    Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

  6. 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

  7. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  8. Plastics recycling: challenges and opportunities.

    Science.gov (United States)

    Hopewell, Jefferson; Dvorak, Robert; Kosior, Edward

    2009-07-27

    Plastics are inexpensive, lightweight and durable materials, which can readily be moulded into a variety of products that find use in a wide range of applications. As a consequence, the production of plastics has increased markedly over the last 60 years. However, current levels of their usage and disposal generate several environmental problems. Around 4 per cent of world oil and gas production, a non-renewable resource, is used as feedstock for plastics and a further 3-4% is expended to provide energy for their manufacture. A major portion of plastic produced each year is used to make disposable items of packaging or other short-lived products that are discarded within a year of manufacture. These two observations alone indicate that our current use of plastics is not sustainable. In addition, because of the durability of the polymers involved, substantial quantities of discarded end-of-life plastics are accumulating as debris in landfills and in natural habitats worldwide. Recycling is one of the most important actions currently available to reduce these impacts and represents one of the most dynamic areas in the plastics industry today. Recycling provides opportunities to reduce oil usage, carbon dioxide emissions and the quantities of waste requiring disposal. Here, we briefly set recycling into context against other waste-reduction strategies, namely reduction in material use through downgauging or product reuse, the use of alternative biodegradable materials and energy recovery as fuel. While plastics have been recycled since the 1970s, the quantities that are recycled vary geographically, according to plastic type and application. Recycling of packaging materials has seen rapid expansion over the last decades in a number of countries. Advances in technologies and systems for the collection, sorting and reprocessing of recyclable plastics are creating new opportunities for recycling, and with the combined actions of the public, industry and governments it

  9. Plastics recycling: challenges and opportunities

    Science.gov (United States)

    Hopewell, Jefferson; Dvorak, Robert; Kosior, Edward

    2009-01-01

    Plastics are inexpensive, lightweight and durable materials, which can readily be moulded into a variety of products that find use in a wide range of applications. As a consequence, the production of plastics has increased markedly over the last 60 years. However, current levels of their usage and disposal generate several environmental problems. Around 4 per cent of world oil and gas production, a non-renewable resource, is used as feedstock for plastics and a further 3–4% is expended to provide energy for their manufacture. A major portion of plastic produced each year is used to make disposable items of packaging or other short-lived products that are discarded within a year of manufacture. These two observations alone indicate that our current use of plastics is not sustainable. In addition, because of the durability of the polymers involved, substantial quantities of discarded end-of-life plastics are accumulating as debris in landfills and in natural habitats worldwide. Recycling is one of the most important actions currently available to reduce these impacts and represents one of the most dynamic areas in the plastics industry today. Recycling provides opportunities to reduce oil usage, carbon dioxide emissions and the quantities of waste requiring disposal. Here, we briefly set recycling into context against other waste-reduction strategies, namely reduction in material use through downgauging or product reuse, the use of alternative biodegradable materials and energy recovery as fuel. While plastics have been recycled since the 1970s, the quantities that are recycled vary geographically, according to plastic type and application. Recycling of packaging materials has seen rapid expansion over the last decades in a number of countries. Advances in technologies and systems for the collection, sorting and reprocessing of recyclable plastics are creating new opportunities for recycling, and with the combined actions of the public, industry and governments it

  10. Sustainable reverse logistics for household plastic waste

    NARCIS (Netherlands)

    Bing, X.

    2014-01-01

    Summary of the thesis titled “Sustainable Reverse Logistics for Household Plastic Waste”

    PhD Candidate: Xiaoyun Bing

    Recycled plastic can be used in the manufacturing of plastic products to reduce the use of virgin plastics material. The cost of recycled plastics is usually lower

  11. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  12. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.

    Science.gov (United States)

    Palermo, Giulia; Miao, Yinglong; Walker, Ross C; Jinek, Martin; McCammon, J Andrew

    2016-10-26

    The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system recently emerged as a transformative genome-editing technology that is innovating basic bioscience and applied medicine and biotechnology. The endonuclease Cas9 associates with a guide RNA to match and cleave complementary sequences in double stranded DNA, forming an RNA:DNA hybrid and a displaced non-target DNA strand. Although extensive structural studies are ongoing, the conformational dynamics of Cas9 and its interplay with the nucleic acids during association and DNA cleavage are largely unclear. Here, by employing multi-microsecond time scale molecular dynamics, we reveal the conformational plasticity of Cas9 and identify key determinants that allow its large-scale conformational changes during nucleic acid binding and processing. We show how the "closure" of the protein, which accompanies nucleic acid binding, fundamentally relies on highly coupled and specific motions of the protein domains, collectively initiating the prominent conformational changes needed for nucleic acid association. We further reveal a key role of the non-target DNA during the process of activation of the nuclease HNH domain, showing how the nontarget DNA positioning triggers local conformational changes that favor the formation of a catalytically competent Cas9. Finally, a remarkable conformational plasticity is identified as an intrinsic property of the HNH domain, constituting a necessary element that allows for the HNH repositioning. These novel findings constitute a reference for future experimental studies aimed at a full characterization of the dynamic features of the CRISPR-Cas9 system, and-more importantly-call for novel structure engineering efforts that are of fundamental importance for the rational design of new genome-engineering applications.

  13. Plastics for corrosion inhibition

    CERN Document Server

    Goldade, Victor A; Makarevich, Anna V; Kestelman, Vladimir N

    2005-01-01

    The development of polymer composites containing inhibitors of metal corrosion is an important endeavour in modern materials science and technology. Corrosion inhibitors can be located in a polymer matrix in the solid, liquid or gaseous phase. This book details the thermodynamic principles for selecting these components, their compatibility and their effectiveness. The various mechanisms of metal protection – barrier, inhibiting and electromechanical – are considered, as are the conflicting requirements placed on the structure of the combined material. Two main classes of inhibited materials (structural and films/coatings) are described in detail. Examples are given of structural plastics used in friction units subjected to mechano-chemical wear and of polymer films/coatings for protecting metal objects against corrosion.

  14. Extension without Cut

    OpenAIRE

    Straßburger , Lutz

    2012-01-01

    International audience; In proof theory one distinguishes sequent proofs with cut and cut-free sequent proofs, while for proof complexity one distinguishes Frege-systems and extended Frege-systems. In this paper we show how deep inference can provide a uniform treatment for both classifications, such that we can define cut-free systems with extension, which is neither possible with Frege-systems, nor with the sequent calculus. We show that the propositional pigeon-hole principle admits polyno...

  15. Pyrolysis of plastic waste for liquid fuel production as prospective energy resource

    Science.gov (United States)

    Sharuddin, S. D. A.; Abnisa, F.; Daud, W. M. A. W.; Aroua, M. K.

    2018-03-01

    The worldwide plastic generation expanded over years because of the variety applications of plastics in numerous sectors that caused the accumulation of plastic waste in the landfill. The growing of plastics demand definitely affected the petroleum resources availability as non-renewable fossil fuel since plastics were the petroleum-based material. A few options that have been considered for plastic waste management were recycling and energy recovery technique. Nevertheless, several obstacles of recycling technique such as the needs of sorting process that was labour intensive and water pollution that lessened the process sustainability. As a result, the plastic waste conversion into energy was developed through innovation advancement and extensive research. Since plastics were part of petroleum, the oil produced through the pyrolysis process was said to have high calorific value that could be used as an alternative fuel. This paper reviewed the thermal and catalytic degradation of plastics through pyrolysis process and the key factors that affected the final end product, for instance, oil, gaseous and char. Additionally, the liquid fuel properties and a discussion on several perspectives regarding the optimization of the liquid oil yield for every plastic were also included in this paper.

  16. Dimension and extensions

    CERN Document Server

    Aarts, JM

    1993-01-01

    Two types of seemingly unrelated extension problems are discussed in this book. Their common focus is a long-standing problem of Johannes de Groot, the main conjecture of which was recently resolved. As is true of many important conjectures, a wide range of mathematical investigations had developed, which have been grouped into the two extension problems. The first concerns the extending of spaces, the second concerns extending the theory of dimension by replacing the empty space with other spaces. The problem of de Groot concerned compactifications of spaces by means of an adjunction of a set of minimal dimension. This minimal dimension was called the compactness deficiency of a space. Early success in 1942 lead de Groot to invent a generalization of the dimension function, called the compactness degree of a space, with the hope that this function would internally characterize the compactness deficiency which is a topological invariant of a space that is externally defined by means of compact extensions of a...

  17. Nigerian Journal of Plastic Surgery

    African Journals Online (AJOL)

    The Nigerian Journal of Plastic Surgery has its objectives in publishing original articles about developments in all areas related to plastic and reconstructive surgery as well as to trauma surgery. It also serves as a means of providing a forum for correspondence, information and discussion. It also accepts review articles that ...

  18. Architecture of European Plastic Surgery

    NARCIS (Netherlands)

    Nicolai, J. -P. A.; Banic, A.; Molea, G.; Mazzola, R.; Poell, J. G.

    2006-01-01

    The architecture of European Plastic Surgery was published in 1996 [Nicolai JPA, Scuderi N. Plastic surgical Europe in an organogram. Eur J Plast Surg 1996; 19: 253-6.] It is the objective of this paper to update information of that article. Continuing medical education (CME), science, training,

  19. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

    DEFF Research Database (Denmark)

    Simola, Daniel F.; Wissler, Lothar; Donahue, Greg

    2013-01-01

    Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contain...

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

    Science.gov (United States)

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

    2017-01-25

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

  1. 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.

  2. Size effects in crystal plasticity

    DEFF Research Database (Denmark)

    Borg, Ulrik

    2007-01-01

    Numerical analyses of plasticity size effects have been carried out for different problems using a developed strain gradient crystal plasticiy theory. The theory employs higher order stresses as work conjugates to slip gradients and uses higher order boundary conditions. Problems on localization...... of plastic flow in a single crystal, grain boundary effects in a bicrystal, and grain size effects in a polycrystal are studied. Single crystals containing micro-scale voids have also been analyzed at different loading conditions with focus on the stress and deformation fields around the voids, on void...... growth and interaction between neighboring voids, and on a comparison between the developed strain gradient crystal plasticity theory and a discrete dislocation plasticity theory. Furthermore, voids and rigid inclusions in isotropic materials have been studied using a strain gradient plasticity theory...

  3. Computational strain gradient crystal plasticity

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Kysar, Jeffrey W.

    2014-01-01

    A numerical method for viscous strain gradient crystal plasticity theory is presented, which incorporates both energetic and dissipative gradient effects. The underlying minimum principles are discussed as well as convergence properties of the proposed finite element procedure. Three problems...... of plane crystal plasticity are studied: pure shear of a single crystal between rigid platens as well as plastic deformation around cylindrical voids in hexagonal close packed and face centered cubic crystals. Effective in-plane constitutive slip parameters for plane strain deformation of specifically...... oriented face centered cubic crystals are developed in terms of the crystallographic slip parameters. The effect on geometrically necessary dislocation structures introduced by plastic deformation is investigated as a function of the ratio of void radius to plasticity length scale....

  4. Grain Interactions in Crystal Plasticity

    International Nuclear Information System (INIS)

    Boyle, K.P.; Curtin, W.A.

    2005-01-01

    The plastic response of a sheet metal is governed by the collective response of the underlying grains. Intragranular plasticity depends on intrinsic variables such as crystallographic orientation and on extrinsic variables such as grain interactions; however, the role of the latter is not well understood. A finite element crystal plasticity formulation is used to investigate the importance of grain interactions on intragranular plastic deformation in initially untextured polycrystalline aggregates. A statistical analysis reveals that grain interactions are of equal (or more) importance for determining the average intragranular deviations from the applied strain as compared to the orientation of the grain itself. Furthermore, the influence of the surrounding grains is found to extend past nearest neighbor interactions. It is concluded that the stochastic nature of the mesoscale environment must be considered for a proper understanding of the plastic response of sheet metals at the grain-scale

  5. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  6. 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.

  7. Extensive translational regulation during seed germination revealed by polysomal profiling

    NARCIS (Netherlands)

    Bai, Bing; Peviani, Alessia; Horst, van der Sjors; Gamm, Magdalena; Snel, Berend; Bentsink, Leónie; Hanson, Johannes

    2017-01-01

    This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed

  8. Dr Jerome Pierce Webster (1888-1974): Surgeon, historian, campaigner, and 'the father of plastic surgery education'.

    Science.gov (United States)

    Wigley, Catrin H

    2016-09-28

    Dr Jerome Pierce Webster is best remembered as the 'founder of plastic surgery education in the United States' on the basis of developing his nation's first plastic surgery residency programme, his role in the founding of the American Board of Plastic Surgery, and, more generally, his influence in professionalising this subspecialty. He also deserves to be remembered for his extensive missionary work in China, his publications as a successful bibliographer, and as an accomplished historian. © The Author(s) 2016.

  9. Plasticity and beyond microstructures, crystal-plasticity and phase transitions

    CERN Document Server

    Hackl, Klaus

    2014-01-01

    The book presents the latest findings in experimental plasticity, crystal plasticity, phase transitions, advanced mathematical modeling of finite plasticity and multi-scale modeling. The associated algorithmic treatment is mainly based on finite element formulations for standard (local approach) as well as for non-standard (non-local approach) continua and for pure macroscopic as well as for directly coupled two-scale boundary value problems. Applications in the area of material design/processing are covered, ranging from grain boundary effects in polycrystals and phase transitions to deep-drawing of multiphase steels by directly taking into account random microstructures.

  10. Effect of notch and alloying on steel properties during extension

    International Nuclear Information System (INIS)

    Vinokur, B.B.; Pilyushenko, U.L.; Kasatkin, O.G.

    1985-01-01

    A study was made on change of strength and plastic characteristics during extension of notched steel samples of 15 compositions containing often-used alloying elements in various amounts and combinations. The notch causes increase of strength and decrease of plastic properties of structural steels during extension. The most pronounced change of properties takes place for the notched sample with expansion angle close to 180 deg. Reduction of notch expansion angle below 150 deg causes slower decrease of the rate of property change. Nickel alloying and vanadium, titanium microalloying assist the improvement of steel plasticity despite the increase of strength properties. Introduction of these elements in steel compensate partially for the negative notch effect. Alloying by silicon, molybdenum and tungsten results in steel strengthening and chromium alloying causes some loss of strength. Manse, chromium, silicon, molybdenum and tungsten cause decrease of plasticity, which intensifies the negative notch effect. When determining concentration ranges of carbon and alloying elements within the limits of quality composition it is necessary to consider both technology and possibility of sufficient change of properties especially in the case of stress concentrator presence in structures

  11. Continuous multivariate exponential extension

    International Nuclear Information System (INIS)

    Block, H.W.

    1975-01-01

    The Freund-Weinman multivariate exponential extension is generalized to the case of nonidentically distributed marginal distributions. A fatal shock model is given for the resulting distribution. Results in the bivariate case and the concept of constant multivariate hazard rate lead to a continuous distribution related to the multivariate exponential distribution (MVE) of Marshall and Olkin. This distribution is shown to be a special case of the extended Freund-Weinman distribution. A generalization of the bivariate model of Proschan and Sullo leads to a distribution which contains both the extended Freund-Weinman distribution and the MVE

  12. Extensive air showers

    CERN Document Server

    Rao, M V S

    1997-01-01

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

  13. The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation

    NARCIS (Netherlands)

    Cózar, Andrés; Martí, Elisa; Duarte, Carlos M; García-de-Lomas, Juan; van Sebille, Erik|info:eu-repo/dai/nl/304831921; Ballatore, Thomas J; Eguíluz, Victor M; González-Gordillo, J Ignacio; Pedrotti, Maria L; Echevarría, Fidel; Troublè, Romain; Irigoien, Xabier

    The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively

  14. International policies to reduce plastic marine pollution from single-use plastics (plastic bags and microbeads): A review.

    Science.gov (United States)

    Xanthos, Dirk; Walker, Tony R

    2017-05-15

    Marine plastic pollution has been a growing concern for decades. Single-use plastics (plastic bags and microbeads) are a significant source of this pollution. Although research outlining environmental, social, and economic impacts of marine plastic pollution is growing, few studies have examined policy and legislative tools to reduce plastic pollution, particularly single-use plastics (plastic bags and microbeads). This paper reviews current international market-based strategies and policies to reduce plastic bags and microbeads. While policies to reduce microbeads began in 2014, interventions for plastic bags began much earlier in 1991. However, few studies have documented or measured the effectiveness of these reduction strategies. Recommendations to further reduce single-use plastic marine pollution include: (i) research to evaluate effectiveness of bans and levies to ensure policies are having positive impacts on marine environments; and (ii) education and outreach to reduce consumption of plastic bags and microbeads at source. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Water Vapor Permeation in Plastics

    Energy Technology Data Exchange (ETDEWEB)

    Keller, Paul E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kouzes, Richard T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2017-01-01

    Polyvinyl toluene (PVT) and polystyrene (PS) (referred to as “plastic scintillator”) are used for gamma ray detectors. A significant decrease in radiation detection performance has been observed in some PVT-based gamma-ray detectors in systems in outdoor environments as they age. Recent studies have revealed that plastic scintillator can undergo an environmentally related material degradation that adversely affects gamma ray detection performance under certain conditions and histories. A significant decrease in sensitivity has been seen in some gamma-ray detectors in some systems as they age. The degradation of sensitivity of plastic scintillator over time is due to a variety of factors, and the term “aging” is used to encompass all factors. Some plastic scintillator samples show no aging effects (no significant change in sensitivity over more than 10 years), while others show severe aging (significant change in sensitivity in less than 5 years). Aging effects arise from weather (variations in heat and humidity), chemical exposure, mechanical stress, light exposure, and loss of volatile components. The damage produced by these various causes can be cumulative, causing observable damage to increase over time. Damage may be reversible up to some point, but becomes permanent under some conditions. The objective of this report is to document the phenomenon of permeability of plastic scintillator to water vapor and to derive the relationship between time, temperature, humidity and degree of water penetration in plastic. Several conclusions are documented about the properties of water permeability of plastic scintillator.

  16. 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

  17. Space Plastic Recycling System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Techshot's proposed Space Plastic Recycler (SPR) is an automated closed loop plastic recycling system that allows the automated conversion of disposable ISS...

  18. Concepts in local treatment of extensive paediatric burns

    Science.gov (United States)

    Ungureanu, M

    2014-01-01

    Abstract There is a wide variety of local therapeutical methods for extensive burns. This article aims to be a general overview of the most common methods used in the local treatment for extensive burns, both in our clinic and globally. Clinical examples are shown from our clinic; cases of the last 8 years. None of the less there is no such thing as the "perfect method of treatment" but a thin balance between the clinical experience of plastic surgeons, every case particularities and specified characteristics, meaning advantages, disadvantages and limited indications of local topics or methods of skin covering. PMID:25408723

  19. Durability of wood plastic composites manufactured from recycled plastic

    Directory of Open Access Journals (Sweden)

    Irina Turku

    2018-03-01

    Full Text Available The influence of accelerated weathering, xenon-arc light and freeze-thaw cycling on wood plastic composites extruded from a recycled plastic was studied. The results showed that, in general, weathering had a stronger impact on samples made from plastic waste compared to a sample made from virgin material. After weathering, the mechanical properties, tensile and flexural, were reduced by 2–30%, depending on the plastic source. Wettability of the samples was shown to play a significant role in their stability. Chemical analysis with infrared spectroscopy and surface observation with a scan electron microscope confirmed the mechanical test results. Incorporation of carbon black retained the properties during weathering, reducing the wettability of the sample, diminishing the change of mechanical properties, and improving color stability. Keywords: Environmental science, Mechanical engineering, Materials science

  20. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  1. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  2. Developmental plasticity: Friend or foe?

    Science.gov (United States)

    Michels, Karin B

    2017-01-01

    Developmental plasticity - the concept that adaptation to changing and unfavorable environmental conditions are possible but may come at the price of compromised health potentials - has evolutionary grounding as it facilitates survival but dissents with fundamental evolutionary principles in that it may advance the lesser fit. It is an important cornerstone of the Developmental Origins of Health and Disease (DOHaD). Unlike evolutionary adaptation developmental plasticity may be short-lived and restricted to one or few generations and inheritance is uncertain. Potential mechanisms include epigenetic modifications adopted in utero which may not transmit to the next generation; future insights may allow adjustments of the outcomes of developmental plasticity.

  3. Radiation damage in plastic scintillators

    International Nuclear Information System (INIS)

    Majewski, S.

    1990-01-01

    Results of radiation damage studies in plastic scintillators are reviewed and critically analyzed from the point of view of applications of plastic scintillators in calorimetric detectors for the SSC. Damage to transmission and to fluorescent yield in different conditions is discussed. New directions in R ampersand D are outlined. Several examples are given of the most recent data on the new scintillating materials made with old and new plastics and fluors, which are exhibiting significantly improved radiation resistance. With a present rate of a vigorous R D programme, the survival limits in the vicinity of 100 MRad seem to be feasible within a couple of years

  4. Plastics recycling: challenges and opportunities

    OpenAIRE

    Hopewell, Jefferson; Dvorak, Robert; Kosior, Edward

    2009-01-01

    Plastics are inexpensive, lightweight and durable materials, which can readily be moulded into a variety of products that find use in a wide range of applications. As a consequence, the production of plastics has increased markedly over the last 60 years. However, current levels of their usage and disposal generate several environmental problems. Around 4 per cent of world oil and gas production, a non-renewable resource, is used as feedstock for plastics and a further 3–4% is expended to pro...

  5. Recycling of Reinforced Plastics

    Science.gov (United States)

    Adams, R. D.; Collins, Andrew; Cooper, Duncan; Wingfield-Digby, Mark; Watts-Farmer, Archibald; Laurence, Anna; Patel, Kayur; Stevens, Mark; Watkins, Rhodri

    2014-02-01

    This work has shown is that it is possible to recycle continuous and short fibre reinforced thermosetting resins while keeping almost the whole of the original material, both fibres and matrix, within the recyclate. By splitting, crushing hot or cold, and hot forming, it is possible to create a recyclable material, which we designate a Remat, which can then be used to remanufacture other shapes, examples of plates and tubes being demonstrated. Not only can remanufacturing be done, but it has been shown that over 50 % of the original mechanical properties, such as the E modulus, tensile strength, and interlaminar shear strength, can be retained. Four different forms of composite were investigated, a random mat Glass Fibre Reinforced Plastic (GFRP) bathroom component and boat hull, woven glass and carbon fibre cloth impregnated with an epoxy resin, and unidirectional carbon fibre pre-preg. One of the main factors found to affect composite recyclability was the type of resin matrix used in the composite. Thermoset resins tested were shown to have a temperature range around the Glass Transition Temperature (Tg) where they exhibit ductile behaviour, hence aiding reforming of the material. The high-grade carbon fibre prepreg was found to be less easy to recycle than the woven of random fibre laminates. One method of remanufacturing was by heating the Remat to above its glass transition temperature, bending it to shape, and then cooling it. However, unless precautions are taken, the geometric form may revert. This does not happen with the crushed material.

  6. Wood plastic combination

    International Nuclear Information System (INIS)

    Cunanan, S.A.; Bonoan, L.S.; Verceluz, F.P.; Azucena, E.A.

    1976-03-01

    The purpose of this study is to improve the physical and mechaniproperties of local inferior quality wood species by radiation-induced graft polymerization with plastic monomers. The process involves the following: 1) Preparation of sample; 2) Impregnation of sample with the monomers; 3) Irradiation of the impregnated sample with the use of 20,000 curie Co-60 as gamma-source; 4) Drying of irradiated sample to remove the unpolymerized monomer. Experimentation on different wood species were undertaken and the results given. From the results obtained, it can be concluded that the monomers systems MMA, MMA-USP, and styrene-USP are suitable for graft polymerization with the wood species almon, apitong, bagtikan, mayapis, red lauan, and tanguile. This is shown by their maximum conversion value which range from 86% to 96% with the optimum dose range of 1 to 2 Mrads. However, in the application of WPC process, properties that are required in a given wood product must be considered, thus aid in the selection of the monomer system to be used with a particular wood species. Some promising applications of WPC is in the manufacture of picker sticks, shuttles, and bobbins for the textile industry. However, there is a need for a pilot plant scale study so that an economic assessment of the commercial feasibility of this process can be made

  7. Helene: A Plastic Model

    Science.gov (United States)

    Umurhan, O. M.; Moore, J. M.; Howard, A. D.; Schenk, P.; White, O. L.

    2014-12-01

    Helene, the Saturnian L4 Trojan satellite co-orbiting Dionne and sitting within the E-ring, possesses an unusual morphology characteristic of broad km-scale basins and depressions and a generally smooth surface patterned with streaks and grooves which are indicative of non-typical mass transport. Elevation angles do not appear to exceed 10o at most. The nature and origin of the surface materials forming these grooved patterns is unknown. Given the low surface gravity (plastic-like flow like a Bingham fluid, we setup and test a number of likely scenarios to explain the observations. The numerical results qualitatively indicate that treating the mass-wasting materials as a Bingham material reproduces many of the qualitative features observed. We also find that in those simulations in which accretion is concomitant with Bingham mass-wasting, the long time-evolution of the surface flow shows intermittency in the total surface activity (defined as total surface integral of the absolute magnitude of the mass-flux). Detailed analyses identify the locations where this activity is most pronounced and we will discuss these and its implications in further detail.

  8. Spike-Timing Dependent Plasticity and the Cognitive Map

    OpenAIRE

    Bush, Daniel; Philippides, Andrew; Husbands, Phil; O'Shea, Michael

    2010-01-01

    Since the discovery of place cells – single pyramidal neurons that encode spatial location – it has been hypothesized that the hippocampus may act as a cognitive map of known environments. This putative function has been extensively modeled using auto-associative networks, which utilize rate-coded synaptic plasticity rules in order to generate strong bi-directional connections between concurrently active place cells that encode for neighboring place fields. However, empirical studies using hi...

  9. 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 ...

  10. 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

  11. Life cycle assessment of post-consumer plastics production from waste electrical and electronic equipment (WEEE) treatment residues in a Central European plastics recycling plant.

    Science.gov (United States)

    Wäger, Patrick A; Hischier, Roland

    2015-10-01

    Plastics play an increasingly important role in reaching the recovery and recycling rates defined in the European WEEE Directive. In a recent study we have determined the life cycle environmental impacts of post-consumer plastics production from mixed, plastics-rich WEEE treatment residues in the Central European plant of a market-leading plastics recycler, both from the perspective of the customers delivering the residues and the customers buying the obtained post-consumer recycled plastics. The results of our life cycle assessments, which were extensively tested with sensitivity analyses, show that from both perspectives plastics recycling is clearly superior to the alternatives considered in this study (i.e. municipal solid waste incineration (MSWI) and virgin plastics production). For the three ReCiPe endpoint damage categories, incineration in an MSWI plant results in an impact exceeding that of the examined plastics recycling facility each by about a factor of 4, and the production of virgin plastics has an impact exceeding that of the post-consumer recycled (PCR) plastics production each by a factor of 6-10. On a midpoint indicator level the picture is more differentiated, showing that the environmental impacts of the recycling options are lower by 50% and more for almost all impact factors. While this provides the necessary evidence for the environmental benefits of plastics recycling compared to existing alternatives, it can, however, not be taken as conclusive evidence. To be conclusive, future research will have to address the fate of hazardous substances in the outputs of such recycling systems in more detail. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Ground System Extensibility Considerations

    Science.gov (United States)

    Miller, S. W.; Greene, E.

    2017-12-01

    The National Oceanic and Atmospheric Administration (NOAA) and National Aeronautics and Space Administration (NASA) are jointly acquiring the next-generation civilian weather and environmental satellite system: the Joint Polar Satellite System (JPSS). The Joint Polar Satellite System will replace the afternoon orbit component and ground processing system of the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA. The JPSS satellites will carry a suite of sensors designed to collect meteorological, oceanographic, climatological and geophysical observations of the Earth. The ground processing system for JPSS is known as the JPSS Common Ground System (JPSS CGS). Developed and maintained by Raytheon Intelligence, Information and Services (IIS), the CGS is a multi-mission enterprise system serving NOAA, NASA and their national and international partners, such as NASA's Earth Observation System (EOS), NOAA's current POES, the Japan Aerospace Exploration Agency's (JAXA) Global Change Observation Mission - Water (GCOM-W1), and DoD's Defense Meteorological Satellite Program (DMSP). The CGS provides a wide range of support to a number of national and international missions, including command and control, mission management, data acquisition and routing, and environmental data processing and distribution. The current suite of CGS-supported missions has demonstrated the value of interagency and international partnerships to address global observation needs. With its established infrastructure and existing suite of missions, the CGS is extensible to a wider array of potential new missions. This paper will describe how the inherent scalability and extensibility of the CGS enables the addition of these new missions, with an eye on global enterprise needs in the 2020's and beyond.

  13. Energy recovery from plastic wastes

    Energy Technology Data Exchange (ETDEWEB)

    Baur, A; Atzger, J

    1983-07-01

    The conversion of plastic wastes to energy is suggested as a practicable and advantageous alternative to recycling. A two-stage pilot gasification plant for the pyrolysis of wastes is described and the utilization of the resulting fuel gas discussed.

  14. Plasticity and creep of metals

    CERN Document Server

    Rusinko, Andrew

    2011-01-01

    Here is a systematic presentation of the postulates, theorems and principles of mathematical theories of plasticity and creep in metals, and their applications. Special attention is paid to analysis of the advantages and shortcomings of the classical theories.

  15. Neuromodulation, development and synaptic plasticity.

    Science.gov (United States)

    Foehring, R C; Lorenzon, N M

    1999-03-01

    We discuss parallels in the mechanisms underlying use-dependent synaptic plasticity during development and long-term potentiation (LTP) and long-term depression (LTD) in neocortical synapses. Neuromodulators, such as norepinephrine, serotonin, and acetylcholine have also been implicated in regulating both developmental plasticity and LTP/LTD. There are many potential levels of interaction between neuromodulators and plasticity. Ion channels are substrates for modulation in many cell types. We discuss examples of modulation of voltage-gated Ca2+ channels and Ca(2+)-dependent K+ channels and the consequences for neocortical pyramidal cell firing behaviour. At the time when developmental plasticity is most evident in rat cortex, the substrate for modulation is changing as the densities and relative proportions of various ion channels types are altered during ontogeny. We discuss examples of changes in K+ and Ca2+ channels and the consequence for modulation of neuronal activity.

  16. WEATHERABILITY OF ENHANCED DEGRADABLE PLASTICS

    Science.gov (United States)

    The main objective of this study was to assess the performance and the asociated variability of several selected enhanced degradable plastic materials under a variety of different exposure conditions. Other objectives were to identify the major products formed during degradation ...

  17. Computational materials science: Nanoscale plasticity

    DEFF Research Database (Denmark)

    Jacobsen, Karsten Wedel; Schiøtz, Jakob

    2002-01-01

    How does plastic deformation of polycrystalline materials with grain sizes less than 100 nm look at the atomic scale? A large-scale molecular dynamics simulation of nanocrystalline alluminium reveals some surprising behaviour.......How does plastic deformation of polycrystalline materials with grain sizes less than 100 nm look at the atomic scale? A large-scale molecular dynamics simulation of nanocrystalline alluminium reveals some surprising behaviour....

  18. Biocide Usage in Plastic Products

    OpenAIRE

    Kavak, Nergizhan; Çakır, Ayşegül; Koltuk, Fatmagül; Uzun, Utku

    2015-01-01

    People’s demand of improving their life quality caused to the term of hygiene become popular and increased the tendency to use more reliable and healthy products. This tendency makes the continuous developments in the properties of the materials used in manufactured goods compulsory. It is possible to create anti-bacterial plastic products by adding biocidal additives to plastic materials which have a wide-range of application in the areas such as health (medicine), food and many other indust...

  19. Interhemispheric plasticity in humans.

    Science.gov (United States)

    Hortobágyi, Tibor; Richardson, Sarah Pirio; Lomarev, Mikhael; Shamim, Ejaz; Meunier, Sabine; Russman, Heike; Dang, Nguyet; Hallett, Mark

    2011-07-01

    Chronic unimanual motor practice increases the motor output not only in the trained but also in the nonexercised homologous muscle in the opposite limb. We examined the hypothesis that adaptations in motor cortical excitability of the nontrained primary motor cortex (iM1) and in interhemispheric inhibition from the trained to the nontrained M1 mediate this interlimb cross education. Healthy, young volunteers (n=12) performed 1000 submaximal voluntary contractions (MVC) of the right first dorsal interosseus (FDI) at 80% MVC during 20 sessions. Trained FDI's MVC increased 49.9%, and the untrained FDI's MVC increased 28.1%. Although corticospinal excitability in iM1, measured with transcranial magnetic stimulation (TMS) before and after every fifth session, increased 6% at rest, these changes, as those in intracortical inhibition and facilitation, did not correlate with cross education. When weak and strong TMS of iM1 were delivered on a background of a weak and strong muscle contraction, respectively, of the right FDI, excitability of iM1 increased dramatically after 20 sessions. Interhemispheric inhibition decreased 8.9% acutely within sessions and 30.9% chronically during 20 sessions and these chronic reductions progressively became more strongly associated with cross education. There were no changes in force or TMS measures in the trained group's left abductor minimi digiti and there were no changes in the nonexercising control group (n=8). The findings provide the first evidence for plasticity of interhemispheric connections to mediate cross education produced by a simple motor task.

  20. Turning an Extension Aide into an Extension Agent

    Science.gov (United States)

    Seevers, Brenda; Dormody, Thomas J.

    2010-01-01

    For any organization to remain sustainable, a renewable source of faculty and staff needs to be available. The Extension Internship Program for Juniors and Seniors in High School is a new tool for recruiting and developing new Extension agents. Students get "hands on" experience working in an Extension office and earn college credit…

  1. Remote memory and cortical synaptic plasticity require neuronal CCCTC-binding factor (CTCF).

    Science.gov (United States)

    Kim, Somi; Yu, Nam-Kyung; Shim, Kyu-Won; Kim, Ji-Il; Kim, Hyopil; Han, Dae Hee; Choi, Ja Eun; Lee, Seung-Woo; Choi, Dong Il; Kim, Myung Won; Lee, Dong-Sung; Lee, Kyungmin; Galjart, Niels; Lee, Yong-Seok; Lee, Jae-Hyung; Kaang, Bong-Kiun

    2018-04-30

    The molecular mechanism of long-term memory has been extensively studied in the context of the hippocampus-dependent recent memory examined within several days. However, months-old remote memory maintained in the cortex for long-term has not been investigated much at the molecular level yet. Various epigenetic mechanisms are known to be important for long-term memory, but how the three-dimensional (3D) chromatin architecture and its regulator molecules contribute to neuronal plasticity and systems consolidation are still largely unknown. CCCTC-binding factor (CTCF) is an eleven-zinc finger protein well known for its role as a genome architecture molecule. Male conditional knockout (cKO) mice in which CTCF is lost in excitatory neurons during adulthood showed normal recent memory in the contextual fear conditioning and spatial water maze tasks. However, they showed remarkable impairments in remote memory in both tasks. Underlying the remote memory-specific phenotypes, we observed that female CTCF cKO mice exhibit disrupted cortical long-term potentiation (LTP), but not hippocampal LTP. Similarly, we observed that CTCF deletion in inhibitory neurons caused partial impairment of remote memory. Through RNA-sequencing, we observed that CTCF knockdown in cortical neuron culture caused altered expression of genes that are highly involved in cell adhesion, synaptic plasticity, and memory. These results suggest that remote memory storage in the cortex requires CTCF-mediated gene regulation in neurons while recent memory formation in the hippocampus does not. SIGNIFICANCE STATEMENT CTCF is a well-known 3D genome architectural protein that regulates gene expression. Here, we use two different CTCF conditional knockout mouse lines and reveal for the first time that CTCF is critically involved in the regulation of remote memory. We also show that CTCF is necessary for appropriate expression of genes, many of which we found to be involved in the learning and memory related

  2. A Genome-Wide Landscape of Retrocopies in Primate Genomes.

    Science.gov (United States)

    Navarro, Fábio C P; Galante, Pedro A F

    2015-07-29

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Improving Public Health and Environment through Plastic Waste Management in Mumbai Metropolitan Region

    OpenAIRE

    Sanjay RODE

    2015-01-01

    The Mumbai Metropolitan Region is growing in terms of population, industry, educational and commercial units. The daily requirements of commodities and services by all units have increased fast. Plastic is used extensively for packing, protection and service of various commodities. The use of plastic is much higher by industry and households in region. In Brihan Mumbai Municipal Corporation, the density of population is higher. The concentration of small and large industries is more. Therefor...

  4. Neutron-diffraction measurement of the evolution of strain for non-uniform plastic deformation

    CERN Document Server

    Rogge, R B; Boyce, D

    2002-01-01

    Neutrons are particularly adept for the validation of modeling predictions of stress and strain. In recent years, there has been a significant effort to model the evolution of both the macroscopic stresses and the intergranular stress during plastic deformation. These have had broad implications with regard to understanding the evolution of residual stress and to diffraction-based measurements of strain. Generally the modeling and associated measurements have been performed for simple uniaxial tension, leaving questions with regard to plastic deformation under multi-axial stress and non-uniform stress. Extensive measurements of the strain profile across a plastic hinge for each of a series of loading and unloading cycles to progressively higher degrees of plastic deformation are presented. These measurements are used to assess multiple-length-scale finite-element modeling (FEM) of the plastic hinge, in which the elements will range in size from single crystallites (as used in successful simulations of uniaxia...

  5. Plasticity dependent damage evolution in composites with strain-gradient effects

    DEFF Research Database (Denmark)

    Legarth, Brian Nyvang

    2015-01-01

    . (2013). In this study the reinforcement is assumed perfectly stiff and consequently only one new cohesive material parameter is introduced. Results are shown for both conventional isotropy as well as plastic anisotropy with higher-order material behavior. Due to fiber-matrix decohesion a sudden stress......A unit cell approach is adopted to numerically analyze the effect of reinforcement size on fracture evolution in metal matrix composites. The matrix material shows plastic size-effects and is modeled by an anisotropic version of the single parameter strain-gradient (higher-order) plasticity model...... by Fleck and Hutchinson (2001). The fracture process along the fiber-matrix interface is modeled using a recently proposed cohesive law extension, where plasticity affects the fracture process as both the average as well as the jump in plastic strain across the interface are accounted for Tvergaard et al...

  6. Genomic definition of species. Revision 2

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  7. Punctuated evolution of prostate cancer genomes.

    Science.gov (United States)

    Baca, Sylvan C; Prandi, Davide; Lawrence, Michael S; Mosquera, Juan Miguel; Romanel, Alessandro; Drier, Yotam; Park, Kyung; Kitabayashi, Naoki; MacDonald, Theresa Y; Ghandi, Mahmoud; Van Allen, Eliezer; Kryukov, Gregory V; Sboner, Andrea; Theurillat, Jean-Philippe; Soong, T David; Nickerson, Elizabeth; Auclair, Daniel; Tewari, Ashutosh; Beltran, Himisha; Onofrio, Robert C; Boysen, Gunther; Guiducci, Candace; Barbieri, Christopher E; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L; Saksena, Gordon; Voet, Douglas; Ramos, Alex H; Winckler, Wendy; Cipicchio, Michelle; Ardlie, Kristin; Kantoff, Philip W; Berger, Michael F; Gabriel, Stacey B; Golub, Todd R; Meyerson, Matthew; Lander, Eric S; Elemento, Olivier; Getz, Gad; Demichelis, Francesca; Rubin, Mark A; Garraway, Levi A

    2013-04-25

    The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. ARE PLASTIC GROCERY BAGS SACKING THE ENVIRONMENT?

    OpenAIRE

    Mangal Gogte

    2009-01-01

    This paper is oriented on analysis impacts of plastic bags on environment. In this paper is analyzed did plastic bags are so harmful, and what are the main ingredients of it. One part of this paper is oriented on effects of plastic bags and management of their usage. There is also made comparative analysis between impacts of plastic and paper bags on environment.

  9. Experiments with elasto-plastic oscillator

    DEFF Research Database (Denmark)

    Randrup-thomsen, Søren; Ditlevsen, Ove Dalager

    1996-01-01

    Plastic displacements of a Gaussian white noise excited three degrees of freedom non-ideal elasto-plastic oscillator are measured in laboratory experiments and the plastic displacements are compared to computer simulated results for the corresponding ideal elasto-plastic oscillator. The comparative...

  10. Experiments with elasto-plastic oscillator

    DEFF Research Database (Denmark)

    Randrup-Thomsen, S.; Ditlevsen, Ove Dalager

    1999-01-01

    Plastic displacements of a Gaussian white noise excited three degrees of freedom non-ideal elasto-plastic oscillator are measured in laboratory experiments and the plastic displacements are compared to computer simulated results for the corresponding ideal elasto-plastic oscillator. The comparative...

  11. Conformational plasticity of the Ebola virus matrix protein.

    Science.gov (United States)

    Radzimanowski, Jens; Effantin, Gregory; Weissenhorn, Winfried

    2014-11-01

    Filoviruses are the causative agents of a severe and often fatal hemorrhagic fever with repeated outbreaks in Africa. They are negative sense single stranded enveloped viruses that can cross species barriers from its natural host bats to primates including humans. The small size of the genome poses limits to viral adaption, which may be partially overcome by conformational plasticity. Here we review the different conformational states of the Ebola virus (EBOV) matrix protein VP40 that range from monomers, to dimers, hexamers, and RNA-bound octamers. This conformational plasticity that is required for the viral life cycle poses a unique opportunity for development of VP40 specific drugs. Furthermore, we compare the structure to homologous matrix protein structures from Paramyxoviruses and Bornaviruses and we predict that they do not only share the fold but also the conformational flexibility of EBOV VP40. © 2014 The Protein Society.

  12. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  13. Spacetime extensions II

    Energy Technology Data Exchange (ETDEWEB)

    Racz, Istvan, E-mail: iracz@rmki.kfki.h [RMKI, H-1121 Budapest, Konkoly Thege Miklos ut 29-33 (Hungary)

    2010-08-07

    The global extendibility of smooth causal geodesically incomplete spacetimes is investigated. Denote by {gamma} one of the incomplete non-extendible causal geodesics of a causal geodesically incomplete spacetime (M, g{sub ab}). First, it is shown that it is always possible to select a synchronized family of causal geodesics {Gamma} and an open neighbourhood U of a final segment of {gamma} in M such that U comprises members of {Gamma}, and suitable local coordinates can be defined everywhere on U provided that {gamma} does not terminate either on a tidal force tensor singularity or on a topological singularity. It is also shown that if, in addition, the spacetime (M, g{sub ab}) is globally hyperbolic, and the components of the curvature tensor, and its covariant derivatives up to order k - 1 are bounded on U, and also the line integrals of the components of the kth-order covariant derivatives are finite along the members of {Gamma}-where all the components are meant to be registered with respect to a synchronized frame field on U-then there exists a C{sup k-} extension {Phi} : (M,g{sub ab}) {yields}(M,g{sub ab}) so that for each {gamma}-bar from {Gamma}, which is inextendible in (M, g{sub ab}), the image, {Phi}{gamma}-bar, is extendible in (M,g{sub ab}). Finally, it is also proved that whenever {gamma} does terminate on a topological singularity (M, g{sub ab}) cannot be generic.

  14. Web Extensible Display Manager

    Energy Technology Data Exchange (ETDEWEB)

    Slominski, Ryan [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Larrieu, Theodore L. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2018-02-01

    Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a web gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.

  15. A Research Needs Assessment for waste plastics recycling: Volume 1, Executive summary. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-01

    This first volume provides a summary of the entire project. The study utilized the talents of a large number of participants, including a significant number of peer reviewers from industrial companies, government agencies, and research institutes. in addition, an extensive analysis of relevant literature was carried out. In considering the attractiveness of recycling technologies that are alternatives to waste-to-energy combustion units, a systems approach was utilized. Collection of waste streams containing plastics, sortation, and reclamation of plastics and plastic mixtures, reprocessing or chemical conversion of the reclaimed polymers, and the applicability of the products to specific market segments have been analyzed in the study.

  16. Revisiting the Corticomotor Plasticity in Low Back Pain: Challenges and Perspectives

    Directory of Open Access Journals (Sweden)

    Hugo Massé-Alarie

    2016-09-01

    Full Text Available Chronic low back pain (CLBP is a recurrent debilitating condition that costs billions to society. Refractoriness to conventional treatment, lack of improvement, and associated movement disorders could be related to the extensive brain plasticity present in this condition, especially in the sensorimotor cortices. This narrative review on corticomotor plasticity in CLBP will try to delineate how interventions such as training and neuromodulation can improve the condition. The review recommends subgrouping classification in CLBP owing to brain plasticity markers with a view of better understanding and treating this complex condition.

  17. Plastic zonder olie : lesmodule voor nieuwe scheikunde

    OpenAIRE

    Langejan, B.; Klein Douwel, C.; Horst, ter, J.J.; Tijdink, K.; Marle, van, N.; Klaasen, P.; Coolen, R.; Assenbergh, van, P.; Sijbers, J.P.J.; Mast, A.

    2013-01-01

    Lesmodule voor nieuwe scheikunde voor leerlingen uit 5 en 6 vwo. Bioplastics worden gemaakt uit natuurlijke grondstoffen. Als ze de synthetische plastics vervangen kan de voorraad aardolie ontzien worden. Omdat veel bioplastics afbreekbaar zijn, kan ook de berg plastic afval krimpen. Maar zijn bioplastics in staat om ons de reguliere plastics te doen vergeten? Hoe maken we bioplastics met dezelfde veelzijdige eigenschappen als plastic? Waar komen de uiteenlopende eigenschappen van plastics ei...

  18. Elimination of Plastic Polymers in Natural Environments

    OpenAIRE

    Ramirez-Ekner, Sofia; Bidstrup, Marie Juliane Svea; Brusen, Nicklas Hald; Rugaard-Morgan, Zsa-Zsa Sophie Oona Ophelia

    2017-01-01

    Plastic production and consumption continues to rise and subsequently plastic waste continues to accumulates in natural environments, causing harm to ecosystems.The aim of this paper was to come up with a way to utilize organisms, that have been identified to produce plastic degrading enzymes, as a waste disposal technology. This review includes accounts of plastic production rates, the occurrence of plastic in natural environments and the current waste management systems to create an underst...

  19. A public resource facilitating clinical use of genomes.

    NARCIS (Netherlands)

    Ball, M.P.; Thakuria, J.V.; Zaranek, A.W.; Clegg, T.; Rosenbaum, A.M.; Wu, X.; Angrist, M.; Bhak, J.; Bobe, J.; Callow, M.J.; Cano, C.; Chou, M.F.; Chung, W.K.; Douglas, S.M.; Estep, P.W.; Gore, A.; Hulick, P.; Labarga, A.; Lee, J.-H.; Lunshof, J.E.; Kim, B.C.; Kim, J.L.; Li, Z.; Murray, M.F.; Nilsen, G.B.; Peters, B.A.; Raman, A.M.; Rienhoff, H.Y.; Robasky, K.; Wheeler, M.T.; Vandewege, W.; Vorhaus, D.B.; Yang, Y.L.; Yang, L.; Aach, J.; Ashley, E.A.; Drmanac, R.; Kim, S.-J.; Li, J.B.; Peshkin, L.; Seidman, S.E.; Seo, J.-S.; Zhang, K.; Rehm, H.L.; Church, G.M.

    2012-01-01

    Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the

  20. Avalanches and plastic flow in crystal plasticity: an overview

    Science.gov (United States)

    Papanikolaou, Stefanos; Cui, Yinan; Ghoniem, Nasr

    2018-01-01

    Crystal plasticity is mediated through dislocations, which form knotted configurations in a complex energy landscape. Once they disentangle and move, they may also be impeded by permanent obstacles with finite energy barriers or frustrating long-range interactions. The outcome of such complexity is the emergence of dislocation avalanches as the basic mechanism of plastic flow in solids at the nanoscale. While the deformation behavior of bulk materials appears smooth, a predictive model should clearly be based upon the character of these dislocation avalanches and their associated strain bursts. We provide here a comprehensive overview of experimental observations, theoretical models and computational approaches that have been developed to unravel the multiple aspects of dislocation avalanche physics and the phenomena leading to strain bursts in crystal plasticity.

  1. Design extension conditions

    Energy Technology Data Exchange (ETDEWEB)

    Bujor, A.; Harwood, C.; Lei, Q.; Viktorov, A., E-mail: christopher.harwood@cnsc-ccsn.gc.ca [Canadian Nuclear Safety Commission, Ottawa, Ontario (Canada)

    2013-07-01

    The CNSC has introduced the term Design Extension Conditions (DEC) in regulatory document RD-337 version 2, 'Design of New Nuclear Power Plants' which was issued for public consultation in July 2012. The primary drivers for this change compared with the earlier version of RD-337 are to maintain alignment with the equivalent International Atomic Energy Agency (IAEA) safety standard and to introduce changes resulting from lessons learned from the Fukushima Daiichi accident. RD-337 version 2 and the accompanying guidance document GD-337 establish high level design requirements and expectations for new Nuclear Power Plants (NPPs), including those pertaining to DEC. Other regulatory documents provide requirements for safety analysis and accident management as well as other aspect relevant to DEC. Nevertheless, the currently available guidance specific to DEC is not comprehensive, while the practices just begin to emerge. CNSC and industry stakeholders are actively discussing how the high level requirements and expectations will be applied in various fields. This paper is a summary of a CNSC discussion paper that is being developed to encourage substantive stakeholder discussions. The topic of DEC is being advanced rapidly both nationally and internationally. With this in mind, this paper does not intend to provide a final established position, but rather to stimulate discussion on the subject of DEC. This paper provides the definition of DEC, gives background information relating to the adoption of the term, describes the identification of DECs and the underlying principles associated with design, analysis, operational and procedural requirements. As described in this paper, DEC and associated requirements apply to new NPPs. Applicability to existing NPPs is also discussed. (author)

  2. A Classification of BPEL Extensions

    Directory of Open Access Journals (Sweden)

    Oliver Kopp

    2011-10-01

    Full Text Available The Business Process Execution Language (BPEL has emerged as de-facto standard for business processes implementation. This language is designed to be extensible for including additional valuable features in a standardized manner. There are a number of BPEL extensions available. They are, however, neither classified nor evaluated with respect to their compliance to the BPEL standard. This article fills this gap by providing a framework for classifying BPEL extensions, a classification of existing extensions, and a guideline for designing BPEL extensions.

  3. Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence

    DEFF Research Database (Denmark)

    Wan, Ni; Delorenzo, Drew M.; He, Lian

    2017-01-01

    Synechocystis sp. strain PCC 6803 has been widely used as a photo-biorefinery chassis. Based on its genome annotation, this species contains a complete TCA cycle, an Embden-Meyerhof-Parnas pathway (EMPP), an oxidative pentose phosphate pathway (OPPP), and an Entner-Doudoroff pathway (EDP). To eva...... the ability to regulate their fluxes under various growth conditions (plastic), whereas its TCA cycle always maintains at low levels (rigid). This work also demonstrates how genetic profiles do not always reflect actual metabolic flux through native or heterologous pathways....

  4. Plasticity characteristic obtained by indentation

    International Nuclear Information System (INIS)

    Milman, Yu V

    2008-01-01

    A dimensionless parameter δ H = ε p /ε t (where ε p and ε t are the average values of plastic and total deformation of material on the contact area indenter-specimen) may be used as the plasticity characteristic of materials, which made it possible to characterize the plasticity of materials that are brittle in standard mechanical tests. δ H may be calculated from the values of microhardness HM, Young's modulus E and Poisson's ratio ν. In instrumented indentation the plasticity characteristic δ A = A p /A t (A p and A t are the work of plastic and total deformation during indentation) may be calculated. δ A ∼ δ H for materials with δ H > 0.5, i.e. for all metals and the majority of ceramic materials. In this case, the theoretical equation δ A ∼ δ H = 1-10.2 · (1 - ν - 2ν 2 )(HM/E) is satisfied in experiments with the Berkovich indenter. The influence of the temperature and structural parameters (dislocation density and grain size including nanostructured materials) on δ H is discussed

  5. Mechanisms of GABAergic Homeostatic Plasticity

    Directory of Open Access Journals (Sweden)

    Peter Wenner

    2011-01-01

    Full Text Available Homeostatic plasticity ensures that appropriate levels of activity are maintained through compensatory adjustments in synaptic strength and cellular excitability. For instance, excitatory glutamatergic synapses are strengthened following activity blockade and weakened following increases in spiking activity. This form of plasticity has been described in a wide array of networks at several different stages of development, but most work and reviews have focussed on the excitatory inputs of excitatory neurons. Here we review homeostatic plasticity of GABAergic neurons and their synaptic connections. We propose a simplistic model for homeostatic plasticity of GABAergic components of the circuitry (GABAergic synapses onto excitatory neurons, excitatory connections onto GABAergic neurons, cellular excitability of GABAergic neurons: following chronic activity blockade there is a weakening of GABAergic inhibition, and following chronic increases in network activity there is a strengthening of GABAergic inhibition. Previous work on GABAergic homeostatic plasticity supports certain aspects of the model, but it is clear that the model cannot fully account for some results which do not appear to fit any simplistic rule. We consider potential reasons for these discrepancies.

  6. Smartphones and the plastic surgeon.

    Science.gov (United States)

    Al-Hadithy, Nada; Ghosh, Sudip

    2013-06-01

    Surgical trainees are facing limited training opportunities since the introduction of the European Working Time Directive. Smartphone sales are increasing and have usurped computer sales for the first time. In this context, smartphones are an important portable reference and educational tool, already in the possession of the majority of surgeons in training. Technology in the palm of our hands has led to a revolution of accessible information for the plastic surgery trainee and surgeon. This article reviews the uses of smartphones and applications for plastic surgeons in education, telemedicine and global health. A comprehensive guide to existing and upcoming learning materials and clinical tools for the plastic surgeon is included. E-books, podcasts, educational videos, guidelines, work-based assessment tools and online logbooks are presented. In the limited resource setting of modern clinical practice, savvy plastic surgeons can select technological tools to democratise access to education and best clinical care. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

  7. Generalizing genetical genomics: getting added value from environmental perturbation.

    Science.gov (United States)

    Li, Yang; Breitling, Rainer; Jansen, Ritsert C

    2008-10-01

    Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across multiple environments. We propose a generalization of genetical genomics, which combines genetic and sensibly chosen environmental perturbations, to study the plasticity of molecular networks. This strategy forms a crucial step toward understanding why individuals respond differently to drugs, toxins, pathogens, nutrients and other environmental influences. Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach.

  8. Building the sequence map of the human pan-genome

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Zheng, Hancheng

    2010-01-01

    analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing...

  9. The genome of Tetranychus urticae reveals herbivorous pest adaptations

    NARCIS (Netherlands)

    Grbić, M.; Van Leeuwen, T.; Clark, R.M.; Rombauts, S.; Grbić, V.; Osborne, E.J.; Dermauw, W.; Phuong, C.T.N.; Ortego, F.; Hernández-Crespo, P.; Diaz, I.; Martinez, M.; Navajas, M.; Sucena, E.; Magalhães, S.; Nagy, L.; Pace, R.M.; Djuranović, S.; Smagghe, G.; Iga, M.; Christiaens, O.; Veenstra, J.A.; Ewer, J.; Villalobos, R.M.; Hutter, J.L.; Hudson, S.D.; Velez, M.; Yi, S.V.; Zeng, J.; Pires-dasilva, A.; Roch, F.; Cazaux, M.; Navarro, M.; Zhurov, V.; Acevedo, G.; Bjelica, A.; Fawcett, J.A.; Bonnet, E.; Martens, C.; Baele, G.; Wissler, L.; Sanchez-Rodriguez, A.; Tirry, L.; Blais, C.; Demeestere, K.; Henz, S.R.; Gregory, T.R.; Mathieu, J.; Verdon, L.; Farinelli, L.; Schmutz, J.; Lindquist, E.; Feyereisen, R.; Van de Peer, Y.

    2011-01-01

    The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T.

  10. Exercise and plasticize the brain

    DEFF Research Database (Denmark)

    Mala, Hana; Wilms, Inge

    Neuroscientific studies continue to shed light on brain’s plasticity and its innate mechanisms to recover. The recovery process includes re-wiring of the existing circuitry, establishment of new connections, and recruitment of peri-lesional and homologous areas in the opposite hemisphere....... The plasticity of the brain can be stimulated and enhanced through training, which serves as a fundamental element of neurorehabilitative strategies. For instance, intensive cognitive and physical training promote the activation of processes that may help the brain to adapt to new conditions and needs. However...... neurorehabilitation is to understand and define how to stimulate the injured brain to elicit the desired adaptation. Research focuses on uncovering specific elements relevant for training planning and execution in order to create an environment that stimulates and maximizes the exploitation of the brain’s plastic...

  11. Surface properties of beached plastics.

    Science.gov (United States)

    Fotopoulou, Kalliopi N; Karapanagioti, Hrissi K

    2015-07-01

    Studying plastic characteristics in the marine environment is important to better understand interaction between plastics and the environment. In the present study, high-density polyethylene (HDPE), polyethylene terephalate (PET), and polyvinyl chloride (PVC) samples were collected from the coastal environment in order to study their surface properties. Surface properties such as surface functional groups, surface topography, point of zero charge, and color change are important factors that change during degradation. Eroded HDPE demonstrated an altered surface topography and color and new functional groups. Eroded PET surface was uneven, yellow, and occasionally, colonized by microbes. A decrease in Fourier transform infrared (FTIR) peaks was observed for eroded PET suggesting that degradation had occurred. For eroded PVC, its surface became more lamellar and a new FTIR peak was observed. These surface properties were obtained due to degradation and could be used to explain the interaction between plastics, microbes, and pollutants.

  12. The Prism Plastic Calorimeter (PPC)

    CERN Multimedia

    2002-01-01

    This proposal supports two goals: \\\\ \\\\ First goal:~~Demonstrate that current, widely used plastic technologies allow to design Prism Plastic Calorimeter~(PPC) towers with a new ``liquid crystal'' type plastic called Vectra. It will be shown that this technique meets the requirements for a LHC calorimeter with warm liquids: safety, hermeticity, hadronic compensation, resolution and time response. \\\\ \\\\ Second goal:~~Describe how one can design a warm liquid calorimeter integrated into a LHC detector and to list the advantages of the PPC: low price, minimum of mechanical structures, minimum of dead space, easiness of mechanical assembly, accessibility to the electronics, possibility to recirculate the liquid. The absorber and the electronic being outside of the liquid and easily accessible, one has maximum flexibility to define them. \\\\ \\\\ The R&D program, we define here aims at showing the feasibility of these new ideas by building nine towers of twenty gaps and exposing them to electron and hadron beams.

  13. Plastic solidification of radioactive wastes

    International Nuclear Information System (INIS)

    Moriyama, Noboru

    1981-01-01

    Over 20 years have elapsed after the start of nuclear power development, and the nuclear power generation in Japan now exceeds the level of 10,000 MW. In order to meet the energy demands, the problem of the treatment and disposal of radioactive wastes produced in nuclear power stations must be solved. The purpose of the plastic solidification of such wastes is to immobilize the contained radionuclides, same as other solidification methods, to provide the first barrier against their move into the environment. The following matters are described: the nuclear power generation in Japan, the radioactive wastes from LWR plants, the position of plastic solidification, the status of plastic solidification in overseas countries and in Japan, the solidification process for radioactive wastes with polyethylene, and the properties of solidified products, and the leachability of radionuclides in asphalt solids. (J.P.N.)

  14. Thermal image analysis of plastic deformation and fracture behavior by a thermo-video measurement system

    International Nuclear Information System (INIS)

    Ohbuchi, Yoshifumi; Sakamoto, Hidetoshi; Nagatomo, Nobuaki

    2016-01-01

    The visualization of the plastic region and the measurement of its size are necessary and indispensable to evaluate the deformation and fracture behavior of a material. In order to evaluate the plastic deformation and fracture behavior in a structural member with some flaws, the authors paid attention to the surface temperature which is generated by plastic strain energy. The visualization of the plastic deformation was developed by analyzing the relationship between the extension of the plastic deformation range and the surface temperature distribution, which was obtained by an infrared thermo-video system. Furthermore, FEM elasto-plastic analysis was carried out with the experiment, and the effectiveness of this non-contact measurement system of the plastic deformation and fracture process by a thermography system was discussed. The evaluation method using an infrared imaging device proposed in this research has a feature which does not exist in the current evaluation method, i.e. the heat distribution on the surface of the material has been measured widely by noncontact at 2D at high speed. The new measuring technique proposed here can measure the macroscopic plastic deformation distribution on the material surface widely and precisely as a 2D image, and at high speed, by calculation from the heat generation and the heat propagation distribution. (paper)

  15. Constraints on the evolution of phenotypic plasticity

    DEFF Research Database (Denmark)

    Murren, Courtney J; Auld, Josh R.; Callahan, Hilary S

    2015-01-01

    Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce...... an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits...... to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently...

  16. Low Abundance of Plastic Fragments in the Surface Waters of the Red Sea

    KAUST Repository

    Martí, Elisa

    2017-11-08

    The floating plastic debris along the Arabian coast of the Red Sea was sampled by using surface-trawling plankton nets. A total of 120 sampling sites were spread out over the near-shore waters along 1,500 km of coastline during seven cruises performed during 2016 and 2017. Plastic debris, dominated by millimeter-sized pieces, was constituted mostly of fragments of rigid objects (73%) followed by pieces of films (17%), fishing lines (6%), and foam (4%). These fragments were mainly made up by polyethylene (69%) and polypropylene (21%). Fibers, likely released from synthetic textiles, were ubiquitous and abundant, although were analyzed independently due to the risk of including non-plastic fibers and airborne contamination of samples in spite of the precautions taken. The plastic concentrations (excluding possible plastic fibers) contrasts with those found in other semi-closed seas, such as the neighboring Mediterranean. They were relatively low all over the Red Sea ( < 50,000 items km; mean ± SD = 3,546 ± 8,154 plastic item km, 1.1 ± 3.0 g km) showing no clear spatial relationship with the distribution of coastal population. Results suggests a low plastic waste input from land as the most plausible explanation for this relative shortage of plastic in the surface waters of the Red Sea; however, the additional intervention of particular processes of surface plastic removal by fish or the filtering activity of the extensive coral reefs along the coastline cannot be discarded. In addition, our study highlights the relevance of determining specific regional conversion rates of mismanaged plastic waste to marine debris, accounting for the role of near-shore activities (e.g., beach tourism, recreational navigation), in order to estimate plastic waste inputs into the ocean.

  17. Low Abundance of Plastic Fragments in the Surface Waters of the Red Sea

    Directory of Open Access Journals (Sweden)

    Elisa Martí

    2017-11-01

    Full Text Available The floating plastic debris along the Arabian coast of the Red Sea was sampled by using surface-trawling plankton nets. A total of 120 sampling sites were spread out over the near-shore waters along 1,500 km of coastline during seven cruises performed during 2016 and 2017. Plastic debris, dominated by millimeter-sized pieces, was constituted mostly of fragments of rigid objects (73% followed by pieces of films (17%, fishing lines (6%, and foam (4%. These fragments were mainly made up by polyethylene (69% and polypropylene (21%. Fibers, likely released from synthetic textiles, were ubiquitous and abundant, although were analyzed independently due to the risk of including non-plastic fibers and airborne contamination of samples in spite of the precautions taken. The plastic concentrations (excluding possible plastic fibers contrasts with those found in other semi-closed seas, such as the neighboring Mediterranean. They were relatively low all over the Red Sea (<50,000 items km−2; mean ± SD = 3,546 ± 8,154 plastic item km−2, 1.1 ± 3.0 g km−2 showing no clear spatial relationship with the distribution of coastal population. Results suggests a low plastic waste input from land as the most plausible explanation for this relative shortage of plastic in the surface waters of the Red Sea; however, the additional intervention of particular processes of surface plastic removal by fish or the filtering activity of the extensive coral reefs along the coastline cannot be discarded. In addition, our study highlights the relevance of determining specific regional conversion rates of mismanaged plastic waste to marine debris, accounting for the role of near-shore activities (e.g., beach tourism, recreational navigation, in order to estimate plastic waste inputs into the ocean.

  18. BGD: a database of bat genomes.

    Science.gov (United States)

    Fang, Jianfei; Wang, Xuan; Mu, Shuo; Zhang, Shuyi; Dong, Dong

    2015-01-01

    Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

  19. BGD: a database of bat genomes.

    Directory of Open Access Journals (Sweden)

    Jianfei Fang

    Full Text Available Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD. BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

  20. Plasticity Theory of Fillet Welds

    DEFF Research Database (Denmark)

    Hansen, Thomas

    2005-01-01

    a safe and statically admissible stress distribution is established. The plasticity solutions are compared with tests carried out at the Engineering Academy of Denmark, Lyngby, in the early nineties, and old fillet weld tests. The new failure conditions are in very good agreement with the yield load......This paper deals with simple methods for calculation of fillet welds based on the theory of plasticity. In developing the solutions the lower-bound theorem is used. The welding material and parts of the base material are subdivided into triangular regions with homogeneous stress fields; thereby...... tests, but not so good agreement with the old failure load tests....

  1. The Plastic Tension Field Method

    DEFF Research Database (Denmark)

    Hansen, Thomas

    2005-01-01

    This paper describes a calculation method for steel plate girders with transverse web stiffeners subjected to shear. It may be used for predicting the failure load or, as a design method, to determine the optimal amount of internal web stiffeners. The new method is called the plastic tension field...... method. The method is based on the theory of plasticity and is analogous to the so-called diagonal compression field method developed for reinforced concrete beams with transverse stirrups, which is adopted in the common European concrete code (Eurocode 2). Many other theories have been developed...

  2. Preparation of coloured wood plastics

    International Nuclear Information System (INIS)

    Lebedev, V.T.; Filippova, T.G.; Rajchuk, F.Z.

    1977-01-01

    A study has been made into the possibility of using fat, as well as alcohol- and water-soluble dyes for radiation-chemical dying of polymers and plastics filled with wood. The use of fat-soluble azo and anthraquinone dyes permits obtaining intensely colored wood-plastic materials based on methyl methacrylate by way of gamma radiation with doses of up to 3 Mrad. At a dose above 5 Mrad, a marked tarnishing of the dye or a change in color and stains are observed. Dyes in styrene withstand higher radiation doses without any significant destruction

  3. Pitfalls of nonstandardized photography in facial plastic surgery patients.

    Science.gov (United States)

    Sommer, Doron D; Mendelsohn, Martyn

    2004-07-01

    The authors tested the hypothesis that certain maneuvers (neck flexion/extension and head protrusion/retrusion) alter the appearance of the submental area, jawline, and melolabial groove. They used a questionnaire survey of 20 naïve judges who assessed a standardized photograph album of three subjects. The subjects' faces (frontal and lateral views) were photographed in neutral, neck flexion/extension, and head protrusion/retrusion positions. High Kendall coefficients of correlation were observed in 10 of 12 questions evaluating an improvement in jawline definition with neck extension or head protrusion, as well as in 11 of 12 questions assessing decreased submental soft tissue. All questions relating to the melolabial groove had a correlation coefficient of less than 0.70. Small changes in patient positioning during photodocumentation for facial plastic surgical procedures can cause dramatic changes in the appearance of certain parameters. Standardizing patient positioning for preoperative and postoperative photographs is imperative.

  4. Role of the plastic surgeon in a cancer hospital

    International Nuclear Information System (INIS)

    Sinclair, M.H.

    1979-01-01

    This paper discusses and illustrates the complicated problems faced by the plastic surgeon in a cancer hospital. His patients are often weakened, both physically and psychologically, not only by the cancer itself, but also by extensive ablative surgery. The goal of the plastic surgeon is rehabilitation of the patient after he is cured of cancer. Good planning with the cancer surgeon before the ablative operation is very important, as is immediate repair, whenever possible. The simplest procedure with the fewest stages that can accomplish satisfactory repair in the shortest time should be chosen, as we can never, even after the most extensive cancer operation, be sure that no recurrence will appear. Partial surgical repair and the use of a prosthesis should be considered for complicated defects in old and weak patients. Postoperative radiation therapy, if indicated, can be given after the flap has healed into the defect but before the pedicle is separated. The plastic surgeon should always be aware that his most important goal is speedy and satisfactory rehabilitation of the patient

  5. Project Muskan : Social responsibility of the plastic surgeon

    Directory of Open Access Journals (Sweden)

    Bhatt Yogesh

    2008-01-01

    Full Text Available Although exact statistics are not available, Indian plastic surgeons see around 7,00,000-8,00,000 burn admissions annually with around 10,00,000 cleft patients yet to be operated. In spite of this voluminous load, India does not have national health programs for the various deformities Indian plastic surgeons typically treat. As Plastic Surgeons, it is our social responsibility to treat these patients and bring ′ muskan ′ (smile in Hindi back into their lives. Project Muskan was initiated as an innovative model for targeting these patients and is probably one of its kind in the field of plastic surgery in our country. It is unique because it is a perfect collaboration of government institutions, a Non Government Organization (NGO, and cooperative sectors providing free health care at the doorstep. Identification of the patients was done with the help of the extensive milk dairy network in the state of Gujarat. Provision of transport and other facilities was done by the NGOs and quality health care provision was taken care of by the government hospital. Project Muskan started from a single village but now covers around 3000 villages and tribal areas of Gujarat. It is a system that can be easily reproducible in all hospitals and has reestablished the faith of the common man in government institutes.

  6. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

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

  8. A work criterion for plastic collapse

    International Nuclear Information System (INIS)

    Muscat, Martin; Mackenzie, Donald; Hamilton, Robert

    2003-01-01

    A new criterion for evaluating limit and plastic loads in pressure vessel design by analysis is presented. The proposed criterion is based on the plastic work dissipated in the structure as loading progresses and may be used for structures subject to a single load or a combination of multiple loads. Example analyses show that limit and plastic loads given by the plastic work criterion are robust and consistent. The limit and plastic loads are determined purely by the inelastic response of the structure and are not influenced by the initial elastic response: a problem with some established plastic criteria

  9. Molecular mechanisms of extensive mitochondrial gene rearrangementin plethodontid salamanders

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Rachel Lockridge; Boore, Jeffrey L.

    2005-06-01

    Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25 percent of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intra-molecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

  10. Think - Baltic Extension / Kalle Kask

    Index Scriptorium Estoniae

    Kask, Kalle

    2002-01-01

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

  11. Robotic hand with modular extensions

    Science.gov (United States)

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

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

  12. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  13. Genome-wide analysis of tandem repeats in plants and green algae

    Science.gov (United States)

    Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang

    2014-01-01

    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...

  14. Ecological Genomics of Marine Picocyanobacteria†

    Science.gov (United States)

    Scanlan, D. J.; Ostrowski, M.; Mazard, S.; Dufresne, A.; Garczarek, L.; Hess, W. R.; Post, A. F.; Hagemann, M.; Paulsen, I.; Partensky, F.

    2009-01-01

    Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level. PMID:19487728

  15. Genomic prediction when some animals are not genotyped

    Directory of Open Access Journals (Sweden)

    Lund Mogens S

    2010-01-01

    Full Text Available Abstract Background The use of genomic selection in breeding programs may increase the rate of genetic improvement, reduce the generation time, and provide higher accuracy of estimated breeding values (EBVs. A number of different methods have been developed for genomic prediction of breeding values, but many of them assume that all animals have been genotyped. In practice, not all animals are genotyped, and the methods have to be adapted to this situation. Results In this paper we provide an extension of a linear mixed model method for genomic prediction to the situation with non-genotyped animals. The model specifies that a breeding value is the sum of a genomic and a polygenic genetic random effect, where genomic genetic random effects are correlated with a genomic relationship matrix constructed from markers and the polygenic genetic random effects are correlated with the usual relationship matrix. The extension of the model to non-genotyped animals is made by using the pedigree to derive an extension of the genomic relationship matrix to non-genotyped animals. As a result, in the extended model the estimated breeding values are obtained by blending the information used to compute traditional EBVs and the information used to compute purely genomic EBVs. Parameters in the model are estimated using average information REML and estimated breeding values are best linear unbiased predictions (BLUPs. The method is illustrated using a simulated data set. Conclusions The extension of the method to non-genotyped animals presented in this paper makes it possible to integrate all the genomic, pedigree and phenotype information into a one-step procedure for genomic prediction. Such a one-step procedure results in more accurate estimated breeding values and has the potential to become the standard tool for genomic prediction of breeding values in future practical evaluations in pig and cattle breeding.

  16. Genomic footprinting in mammalian cells with ultraviolet light

    International Nuclear Information System (INIS)

    Becker, M.M.; Wang, Z.; Grossmann, G.; Becherer, K.A.

    1989-01-01

    A simple and accurate genomic primer extension method has been developed to detect ultraviolet footprinting patterns of regulatory protein-DNA interactions in mammalian genomic DNA. The technique can also detect footprinting or sequencing patterns introduced into genomic DNA by other methods. Purified genomic DNA, containing either damaged bases or strand breaks introduced by footprinting or sequencing reactions, is first cut with a convenient restriction enzyme to reduce its molecular weight. A highly radioactive single-stranded DNA primer that is complementary to a region of genomic DNA whose sequence or footprint one wishes to examine is then mixed with 50 micrograms of restriction enzyme-cut genomic DNA. The primer is approximately 100 bases long and contains 85 radioactive phosphates, each of specific activity 3000 Ci/mmol (1 Ci = 37 GBq). A simple and fast method for preparing such primers is described. Following brief heat denaturation at 100 degrees C, the solution of genomic DNA and primer is cooled to 74 degrees C and a second solution containing Taq polymerase (Thermus aquaticus DNA polymerase) and the four deoxynucleotide triphosphates is added to initiate primer extension of genomic DNA. Taq polymerase extends genomic hybridized primer until its polymerization reaction is terminated either by a damaged base or strand break in genomic DNA or by the addition of dideoxynucleotide triphosphates in the polymerization reaction. The concurrent primer hybridization-extension reaction is terminated after 5 hr and unhybridized primer is digested away by mung bean nuclease. Primer-extended genomic DNA is then denatured and electrophoresed on a polyacrylamide sequencing gel, and radioactive primer extension products are revealed by autoradiography

  17. Body dysmorphia and plastic surgery.

    Science.gov (United States)

    Kyle, Allison

    2012-01-01

    Body dysmorphic disorder is a mental disorder characterized by a preoccupation with some aspect of one's appearance. In cosmetic surgery, this preoccupation can be overlooked by practitioners resulting in a discrepancy between expected and realistic outcome. Identifying the characteristics of this disorder may be crucial to the practitioner-patient relationship in the plastic surgery setting.

  18. Ways of Viewing Pictorial Plasticity

    NARCIS (Netherlands)

    Wijntjes, M.W.A.

    2017-01-01

    The plastic effect is historically used to denote various forms of stereopsis. The vivid impression of depth often associated with binocular stereopsis can also be achieved in other ways, for example, using a synopter. Accounts of this go back over a hundred years. These ways of viewing all aim

  19. Ways of Viewing Pictorial Plasticity

    Directory of Open Access Journals (Sweden)

    Maarten W. A. Wijntjes

    2017-03-01

    Full Text Available The plastic effect is historically used to denote various forms of stereopsis. The vivid impression of depth often associated with binocular stereopsis can also be achieved in other ways, for example, using a synopter. Accounts of this go back over a hundred years. These ways of viewing all aim to diminish sensorial evidence that the picture is physically flat. Although various viewing modes have been proposed in the literature, their effects have never been compared. In the current study, we compared three viewing modes: monocular blur, synoptic viewing, and free viewing (using a placebo synopter. By designing a physical embodiment that was indistinguishable for the three experimental conditions, we kept observers naïve with respect to the differences between them; 197 observers participated in an experiment where the three viewing modes were compared by performing a rating task. Results indicate that synoptic viewing causes the largest plastic effect. Monocular blur scores lower than synoptic viewing but is still rated significantly higher than the baseline conditions. The results strengthen the idea that synoptic viewing is not due to a placebo effect. Furthermore, monocular blur has been verified for the first time as a way of experiencing the plastic effect, although the effect is smaller than synoptic viewing. We discuss the results with respect to the theoretical basis for the plastic effect. We show that current theories are not described with sufficient details to explain the differences we found.

  20. Ways of Viewing Pictorial Plasticity.

    Science.gov (United States)

    Wijntjes, Maarten W A

    2017-01-01

    The plastic effect is historically used to denote various forms of stereopsis. The vivid impression of depth often associated with binocular stereopsis can also be achieved in other ways, for example, using a synopter. Accounts of this go back over a hundred years. These ways of viewing all aim to diminish sensorial evidence that the picture is physically flat. Although various viewing modes have been proposed in the literature, their effects have never been compared. In the current study, we compared three viewing modes: monocular blur, synoptic viewing, and free viewing (using a placebo synopter). By designing a physical embodiment that was indistinguishable for the three experimental conditions, we kept observers naïve with respect to the differences between them; 197 observers participated in an experiment where the three viewing modes were compared by performing a rating task. Results indicate that synoptic viewing causes the largest plastic effect. Monocular blur scores lower than synoptic viewing but is still rated significantly higher than the baseline conditions. The results strengthen the idea that synoptic viewing is not due to a placebo effect. Furthermore, monocular blur has been verified for the first time as a way of experiencing the plastic effect, although the effect is smaller than synoptic viewing. We discuss the results with respect to the theoretical basis for the plastic effect. We show that current theories are not described with sufficient details to explain the differences we found.

  1. Electron beam micromachining of plastics

    Czech Academy of Sciences Publication Activity Database

    Dupák, Libor

    2014-01-01

    Roč. 49, 5-6 (2014), s. 310-314 ISSN 0861-4717 R&D Projects: GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01; GA MŠk EE.2.3.20.0103 Institutional support: RVO:68081731 Keywords : micromachining of plastics * Electron beam Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  2. Field based plastic contamination sensing

    Science.gov (United States)

    The United States has a long-held reputation of being a dependable source of high quality, contaminant-free cotton. Recently, increased incidence of plastic contamination from sources such as shopping bags, vegetable mulch, surface irrigation tubing, and module covers has threatened the reputation o...

  3. Recycling of plastics in Germany

    International Nuclear Information System (INIS)

    Thienen, N. von; Patel, M.

    1999-01-01

    This article deals with the waste management of post-consumer plastics in Germany and its potential to save fossil fuels and reduce CO 2 emissions. Since most experience is available for packaging, the paper first gives an overview of the legislative background and the material flows for this sector. Then recycling and recovery processes for plastics waste from all sectors are assessed in terms of their contribution to energy saving and CO 2 abatement. Practically all the options studied show a better performance than waste treatment in an average incinerator which has been chosen as the reference case. High ecological benefits can be achieved by mechanical recycling if virgin polymers are substituted. The paper then presents different scenarios for managing plastic waste in Germany in 1995: considerable savings can be made by strongly enhancing the efficiency of waste incinerators. Under these conditions the distribution of plastics waste among mechanical recycling, feedstock recycling and energy recovery has a comparatively mall impact on the overall results. The maximum savings amount to 74 PJ of energy, i.e, 9% of the chemical sector energy demand in 1995 and 7.0 Mt CO 2 , representing 13% of the sector's emissions. The assessment does not support a general recommendation of energy recovery due to the large difference between the German average and the best available municipal waste-to-energy facilities and also due to new technological developments in the field of mechanical recycling

  4. Transformation plasticity and hot pressing

    International Nuclear Information System (INIS)

    Chaklader, A.C.D.

    1975-01-01

    The transformation plasticity during the phase transition of quartz to cristobalite, monoclinic reversible tetragonal of zirconia, metakaolin to a spinel phase, and brucite to periclase was investigated by studying their compaction characteristics. Viscous flow was found to be the predominant mechanism of mass transport (after an initial particle rearrangement stage) in the case of quartz to cristobalite phase change where the transformation was associated with the formation of an intermediate amorphous silica phase. The results on the monoclinic reversible tetragonal transformation of zirconia indicated that it is most likely controlled by internal strain induced by the stress associated with the volume change (ΔV/V) and the flow stress of the weaker phase. Particle movement and deformation of the weaker phase (possibly tetragonal) may be the manifestation of this plasticity. The plasticity in the case of metakaolin to a spinel phase appeared to start before the exothermic reaction (generally encountered in a dta plot) and may be diffusion controlled. The plasticity encountered during brucite to periclase transformation may be the combined effect of disintegration of precursor particles, vapor-phase lubrication and some deformability of freshly formed very fine MgO particles

  5. Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence

    Directory of Open Access Journals (Sweden)

    Francis Delpeyroux

    2011-08-01

    Full Text Available Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV, an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of the same species. In particular, the interest for this mechanism of genetic plasticity was renewed with the emergence of pathogenic recombinant circulating vaccine-derived polioviruses (cVDPVs, which were implicated in poliomyelitis outbreaks in several regions of the world with insufficient vaccination coverage. Most of these cVDPVs had mosaic genomes constituted of mutated poliovaccine capsid sequences and part or all of the non-structural sequences from other human enteroviruses of species C (HEV-C, in particular coxsackie A viruses. A study in Madagascar showed that recombinant cVDPVs had been co-circulating in a small population of children with many different HEV-C types. This viral ecosystem showed a surprising and extensive biodiversity associated to several types and recombinant genotypes, indicating that intertypic genetic recombination was not only a mechanism of evolution for HEV-C, but an usual mode of genetic plasticity shaping viral diversity. Results suggested that recombination may be, in conjunction with mutations, implicated in the phenotypic diversity of enterovirus strains and in the emergence of new pathogenic strains. Nevertheless, little is known about the rules and mechanisms which govern genetic exchanges between HEV-C types, as well as about the importance of intertypic recombination in generating phenotypic variation. This review summarizes our current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs.

  6. Recombination between poliovirus and coxsackie A viruses of species C: a model of viral genetic plasticity and emergence.

    Science.gov (United States)

    Combelas, Nicolas; Holmblat, Barbara; Joffret, Marie-Line; Colbère-Garapin, Florence; Delpeyroux, Francis

    2011-08-01

    Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV), an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of the same species. In particular, the interest for this mechanism of genetic plasticity was renewed with the emergence of pathogenic recombinant circulating vaccine-derived polioviruses (cVDPVs), which were implicated in poliomyelitis outbreaks in several regions of the world with insufficient vaccination coverage. Most of these cVDPVs had mosaic genomes constituted of mutated poliovaccine capsid sequences and part or all of the non-structural sequences from other human enteroviruses of species C (HEV-C), in particular coxsackie A viruses. A study in Madagascar showed that recombinant cVDPVs had been co-circulating in a small population of children with many different HEV-C types. This viral ecosystem showed a surprising and extensive biodiversity associated to several types and recombinant genotypes, indicating that intertypic genetic recombination was not only a mechanism of evolution for HEV-C, but an usual mode of genetic plasticity shaping viral diversity. Results suggested that recombination may be, in conjunction with mutations, implicated in the phenotypic diversity of enterovirus strains and in the emergence of new pathogenic strains. Nevertheless, little is known about the rules and mechanisms which govern genetic exchanges between HEV-C types, as well as about the importance of intertypic recombination in generating phenotypic variation. This review summarizes our current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs.

  7. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T. B. K.; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R.; Eloe-Fadrosh, Emiley A.; Tringe, Susannah G.; Ivanova, Natalia N.; Copeland, Alex; Clum, Alicia; Becraft, Eric D.; Malmstrom, Rex R.; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M.; Garrity, George M.; Dodsworth, Jeremy A.; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O.; Gilbert, Jack A.; Nelson, William C.; Hallam, Steven J.; Jungbluth, Sean P.; Ettema, Thijs J. G.; Tighe, Scott; Konstantinidis, Konstantinos T.; Liu, Wen-Tso; Baker, Brett J.; Rattei, Thomas; Eisen, Jonathan A.; Hedlund, Brian; McMahon, Katherine D.; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W.; Rinke, Christian; Kyrpides, Nikos C.; Schriml, Lynn; Garrity, George M.; Hugenholtz, Philip; Sutton, Granger; Yilmaz, Pelin; Meyer, Folker; Glöckner, Frank O.; Gilbert, Jack A.; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H.; Eren, A. M.; Schriml, Lynn; Banfield, Jillian F.; Hugenholtz, Philip; Woyke, Tanja

    2017-08-08

    We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

  8. The research progress of genomic selection in livestock.

    Science.gov (United States)

    Li, Hong-wei; Wang, Rui-jun; Wang, Zhi-ying; Li, Xue-wu; Wang, Zhen-yu; Yanjun, Zhang; Rui, Su; Zhihong, Liu; Jinquan, Li

    2017-05-20

    With the development of gene chip and breeding technology, genomic selection in plants and animals has become research hotspots in recent years. Genomic selection has been extensively applied to all kinds of economic livestock, due to its high accuracy, short generation intervals and low breeding costs. In this review, we summarize genotyping technology and the methods for genomic breeding value estimation, the latter including the least square method, RR-BLUP, GBLUP, ssGBLUP, BayesA and BayesB. We also cover basic principles of genomic selection and compare their genetic marker ranges, genomic selection accuracy and operational speed. In addition, we list common indicators, methods and influencing factors that are related to genomic selection accuracy. Lastly, we discuss latest applications and the current problems of genomic selection at home and abroad. Importantly, we envision future status of genomic selection research, including multi-trait and multi-population genomic selection, as well as impact of whole genome sequencing and dominant effects on genomic selection. This review will provide some venues for other breeders to further understand genome selection.

  9. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  10. Epigenetic control of cell identity and plasticity

    KAUST Repository

    Orlando, Valerio

    2014-04-02

    The DNA centered dogma for genetic information and cell identity is now evolving into a much more complex and flexible dimension provided by the discovery of the Epigenome. This comprises those chromosome structural and topological components that complement DNA information and contribute to genome functional organization. Current concept is that the Epigenome constitutes the dynamic molecular interface allowing the Genome to interact with the Environment. Exploring how the genome interacts with the environment is a key to fully understand cellular and complex organism mechanisms of adaptation and plasticity. Our work focuses on the role of an essential, specialized group or chromatin associated proteins named Polycomb (PcG) that control maintenance of transcription programs during development and in adult life. In particular PcG proteins exert epigenetic “memory” function by modifying chromosome structures at various levels to maintain gene silencing in particular through cell division. While in the past decade substantial progress was made in understanding PcG mechanisms acting in development and partially during cell cycle, very little is known about their role in adult post-mitotic tissues and more in general the role of the epigenome in adaptation. To this, we studied the role of PcG in the context of mammalian skeletal muscle cell differentiation. We previously reported specific dynamics of PRC2 proteins in myoblasts and myotubes, in particular the dynamics of PcG Histone H3 K27 Methyl Transferases (HMT), EZH2 and EZH1, the latter apparently replacing for EZH2 in differentiated myotubes. Ezh1 protein, although almost identical to Ezh2, shows a weak H3K27 HMT activity and its primary function remains elusive. Recent ChIPseq studies performed in differentiating muscle cells revealed that Ezh1 associates with active and not repressed regulatory regions to control RNA pol II elongation. Since H3K27 tri-methylation levels are virtually steady in non

  11. Investigation on the toxic interaction of typical plasticizers with calf thymus DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xiaojing [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Zong, Wansong, E-mail: gaocz@sdu.edu.cn [College of Population, Resources and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan 250014 (China); Liu, Chunguang; Liu, Yang [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Gao, Canzhu, E-mail: rutaoliu@sdu.edu.cn [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Liu, Rutao [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China)

    2015-05-15

    The interactions of typical plasticizers dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP) with calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopic techniques and molecular modeling. Experimental results indicated that the characteristic fluorescence intensity of phthalic acid rose with the increase of DNA concentration; while the characteristic fluorescence intensities of plasticizers decreased with the increase of DNA concentration. Experiments on native and denatured DNA determined that plasticizers interacted with DNA both in groove and electrostatic binding mode. The molecular modeling results further illustrated that there is groove binding between them; hydrogen bonding and Van der Waals interactions were the main forces. With the extension of branched-chains, the binding effects between plasticizers and DNA were weakened, which could be related to the increased steric hindrance. - Highlights: • This work established the binding mode of plasticizers with DNA on molecular level. • The mechanism was explored by fluorescence spectroscopic and molecular docking methods. • There are two kinds of binding mode between DMP, DEP, DBP and DNA, electrostatic and groove. • With the branched chain extension, the binding effect of plasticizers and DNA has been weakened.

  12. Plastics and beaches: A degrading relationship

    International Nuclear Information System (INIS)

    Corcoran, Patricia L.; Biesinger, Mark C.; Grifi, Meriem

    2009-01-01

    Plastic debris in Earth's oceans presents a serious environmental issue because breakdown by chemical weathering and mechanical erosion is minimal at sea. Following deposition on beaches, plastic materials are exposed to UV radiation and physical processes controlled by wind, current, wave and tide action. Plastic particles from Kauai's beaches were sampled to determine relationships between composition, surface textures, and plastics degradation. SEM images indicated that beach plastics feature both mechanically eroded and chemically weathered surface textures. Granular oxidation textures were concentrated along mechanically weakened fractures and along the margins of the more rounded plastic particles. Particles with oxidation textures also produced the most intense peaks in the lower wavenumber region of FTIR spectra. The textural results suggest that plastic debris is particularly conducive to both chemical and mechanical breakdown in beach environments, which cannot be said for plastics in other natural settings on Earth

  13. Toward Modeling Limited Plasticity in Ceramic Materials

    National Research Council Canada - National Science Library

    Grinfeld, Michael; Schoenfeld, Scott E; Wright, Tim W

    2008-01-01

    The characteristic features of many armor-related ceramic materials are the anisotropy on the micro-scale level and the very limited, though non-vanishing, plasticity due to limited number of the planes for plastic slip...

  14. Antireflection coatings on plastics deposited by plasma ...

    Indian Academy of Sciences (India)

    In the ophthalmic industry, plastic lenses are rapidly displacing glass lenses ... Moreover, the plasma polymerization process allows deposition of optical films at room temperature, essential for plastics. ... Bulletin of Materials Science | News.

  15. Mechanical behaviour of nanoparticles: Elasticity and plastic ...

    Indian Academy of Sciences (India)

    2015-06-03

    Jun 3, 2015 ... Mechanical behaviour of nanoparticles: Elasticity and plastic deformation mechanisms ... The main results in terms of elasticity and plastic deformation mechanisms are then reported ... Pramana – Journal of Physics | News.

  16. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

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

  17. Frames and extension problems I

    DEFF Research Database (Denmark)

    Christensen, Ole

    2014-01-01

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

  18. Why Do Extension Agents Resign?

    Science.gov (United States)

    Manton, Linda Nunes; van Es, J. C.

    1985-01-01

    Past and current Illinois extension agents were surveyed via mail questionnaires as to reasons for staying or leaving extension programs. Reasons for leaving included family changes, family moves, opportunity to advance, better salary/benefits, dissatisfaction with administration, and too much time away from family. (CT)

  19. Quotient semigroups and extension semigroups

    Indian Academy of Sciences (India)

    Introduction. Abelian groups and semigroups play an important role in the classification of C. ∗. -algebras and their extensions. ... -algebra extension theory and K K-theory, it is crucial to study the theory of quotient semigroups from the ...

  20. Universal extensions to simulate specifications

    NARCIS (Netherlands)

    Hesselink, Wim H.

    A previous paper introduced eternity variables as an alternative to the prophecy variables of Abadi and Lamport and proved the formalism to be semantically complete: every simulation F. K -> L that preserves quiescence contains a composition of a history extension, an extension with eternity

  1. Genomic definition of species. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Dramanac, R.

    1992-06-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called (species) genome. The definition of species based on chromosomes, genes, or genome common to its member organisms has been implied or mentioned in passing numerous times. Some population biologists think that members of species have similar ``homeostatic genotypes,`` which are to a degree resistant to mutation or environmental change in the production of a basic phenotype.

  2. Recycling plastic bottles in a creative way

    OpenAIRE

    Pavlin, Suzana

    2016-01-01

    Beside other plastic products, plastic bottles represent a true environmental disaster in the last few years. We assume that hardly anyone asks what happens after they drink that last drop of water out of it. Just like most municipal waste, a plastic bottle can be reused, recycled, burned or deposited into landfill. When the Environment Protection Act is not respected, plastic bottle ends up in the nature, very often in the sea, where it decomposes very slowly and has negative influence on th...

  3. Plastic Accumulation in the Mediterranean Sea

    OpenAIRE

    C?zar, Andr?s; Sanz-Mart?n, Marina; Mart?, Elisa; Gonz?lez-Gordillo, J. Ignacio; Ubeda, B?rbara; G?lvez, Jos? ?.; Irigoien, Xabier; Duarte, Carlos M.

    2015-01-01

    Copyright: © 2015 Cózar et al. Concentrations of floating plastic were measured throughout the Mediterranean Sea to assess whether this basin can be regarded as a great accumulation region of plastic debris. We found that the average density of plastic (1 item per 4 m2), as well as its frequency of occurrence (100% of the sites sampled), are comparable to the accumulation zones described for the five subtropical ocean gyres. Plastic debris in the Mediterranean surface waters was dominated by ...

  4. ARE PLASTIC GROCERY BAGS SACKING THE ENVIRONMENT?

    Directory of Open Access Journals (Sweden)

    Mangal Gogte

    2009-12-01

    Full Text Available This paper is oriented on analysis impacts of plastic bags on environment. In this paper is analyzed did plastic bags are so harmful, and what are the main ingredients of it. One part of this paper is oriented on effects of plastic bags and management of their usage. There is also made comparative analysis between impacts of plastic and paper bags on environment.

  5. PLASTIC ANALYSIS OF STEEL FRAME STRUCTURE

    Directory of Open Access Journals (Sweden)

    M. Rogac

    2013-05-01

    Full Text Available This paper presents the plastic analysis of steel frame structure loaded by gravity loads. By applying the cinematic theorem of ultimate analysis, the ultimate load for the case of elastic - ideally plastic material is calculated. The identical structure was treated in the computer program SAP2000 where the zone of material reinforcement in the plastic area was covered. Keywords: Steel frame structure, plastic analysis, ultimate gravity load, material reinforcement.

  6. 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.

  7. 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.

  8. 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

  9. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  10. Functional nanostructures on injection molded plastic

    DEFF Research Database (Denmark)

    Johansson, Alicia Charlotte; Søgaard, Emil; Andersen, Nis Korsgaard

    Nanotechnology can be used to make inexpensive plastic parts with functional surfaces. The plastic parts can be molded using a standard injection molding process. The nanostructures are directly transferred from the surface of the molding tool to the surface of the molded plastic part during...

  11. 7 CFR 58.326 - Plastic cream.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Plastic cream. 58.326 Section 58.326 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Material § 58.326 Plastic cream. To produce plastic cream eligible for official certification, the quality...

  12. 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.

  13. The evolution of age-dependent plasticity

    NARCIS (Netherlands)

    Fischer, Barbara; van Doorn, G. Sander; Dieckmann, Ulf; Taborsky, Barbara

    2014-01-01

    When organisms encounter environments that are heterogeneous in time, phenotypic plasticity is often favored by selection. The degree of such plasticity can vary during an organism''s lifetime, but the factors promoting differential plastic responses at different ages or life stages remain poorly

  14. 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

  15. Repair of extensive radionecrosis of the thoracic wall using soft tissues from the paralyzed upper limb

    Energy Technology Data Exchange (ETDEWEB)

    Delacroix, R; Wallaert, C; Soulier, A; Delepoulle, E; Francois, C; Grignet, J P

    1975-04-01

    The authors report one case of extensive radionecrosis after postoperative radiotherapy for breast cancer, with overt pyothorax, deep axillary ulceration, and brachial paralysis. The plastic use of the musculo-aponeutrotic tissues of the paralysed upper limb resulted in spectacular success, complicated only by empyema of the hemithoracic cavity, for which treatment with neomycin is recommended.

  16. Plastic deformation and contact area of an elastic-plastic contact of ellipsoid bodies after unloading

    NARCIS (Netherlands)

    Jamari, Jamari; Schipper, Dirk J.

    2007-01-01

    This paper presents theoretical and experimental results of the residual or plastic deformation and the plastic contact area of an elastic–plastic contact of ellipsoid bodies after unloading. There are three regime responses of the deformation and contact area: elastic, elastic–plastic and fully

  17. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  18. Production Flexibility in Extensive Beef Farming Systems

    Directory of Open Access Journals (Sweden)

    Laura Astigarraga

    2011-03-01

    Full Text Available The aim of this work is to assess the flexibility of production allowed by extensive production conditions faced with variations in the environment, i.e., market variations and climatic fluctuations, of Limousin beef systems. The study used a case-based methodology in which seven beef farms with less than 1 LU/ha were chosen. Data collection was based on three interviews using a semistructured questionnaire and on the analysis of productive and economic results over a 15-year period (1991-2005. The main evolution of these farms is related to a rise in work productivity associated with an increase in herd size. Herd increase was made possible by enlarging the area, the margin of intensification being limited in these regions. To take advantage of the enlarged land area, females were reared for fattening or for reproduction instead of selling them at weaning. The Limousin female provides a wide product mix because of its plasticity, as has been studied by several researchers. This mix flexibility is achieved by delaying product differentiation, a form of production flexibility that can reduce the risk of under-producing or over-producing varied product configurations. On the other hand, calves sold to the Italian market after weaning are generic products, associated with a flexible production process to overcome fluctuations in forage availability due to climatic variations. The introduction of maize silage for feeding acts as an alternative route, actual and potential, through the system to overcome unexpected forage shortage from natural grasslands as a result of droughts. The study shows that extensive farming systems have developed types of flexibility to match different factors of uncertainty from the environment. Finally, the issue of farm system performance is thus not so much a question of whether a farm is fit at a specific moment in time, but whether it transforms into a less or more sustainable orientation.

  19. Forces shaping the fastest evolving regions in the human genome

    DEFF Research Database (Denmark)

    Pollard, Katherine S; Salama, Sofie R; King, Bryan

    2006-01-01

    Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202...... genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements...... contributed to accelerated evolution of the fastest evolving elements in the human genome....

  20. Journal of Agricultural Extension submitted to Agricultural Extension ...

    African Journals Online (AJOL)

    PROF. MADUKWE

    ... typically confront narrower range of labour markets than men, and lower wage ... capabilities of women and by extension the household, female household ..... gap in accessibility to productive resources between male and female heads of.

  1. Basic Strain Gradient Plasticity Theories with Application to Constrained Film Deformation

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Hutchinson, John W.

    2011-01-01

    films: the compression or extension of a finite layer joining rigid platens. Full elastic-plastic solutions are obtained for the same problem based on a finite element method devised for the new class of flow theories. Potential difficulties and open issues associated with the new class of flow theories......A family of basic rate-independent strain gradient plasticity theories is considered that generalize conventional J(2) deformation and flow theories of plasticity to include a dependence on strain gradients in a simple way. The theory builds on three recent developments: the work of Gudmundson (J....... Mech. Phys. Solids 52 (2004), 1379-1406) and Gurtin and Anand (J. Mech. Phys. Solids 57 (2009), 405-421), proposing constitutive relations for flow theories consistent with requirements of positive plastic dissipation; the work of Fleck and Willis (J. Mech. Phys. Solids 57 (2009), 161-177 and 1045...

  2. Elasto/visco-plastic analysis of moderately thick shells of revolution

    International Nuclear Information System (INIS)

    Takezono, S.; Tanoue, M.

    1981-01-01

    The analytical formulation on the elasto-visco-plastic problems of general, moderately thick shells of revolution subjected to axisymmetrical load is developed by extension of the Reissner theory in elastic shells where a consideration on the effect of shear deformations is given. The authors employ as constitutive relation of the shell materials Perzyna's equation where in the plastic range the viscosity of the material is considered. The criterion for yielding used in this analysis is the von Mises yield theory. The basic differential equations derived for elasto-visco-plastic problems are numerically solved by a finite difference method, and the solutions are obtained by integration of the incremental values. As a numerical example, the elasto/visco-plastic deformation of pressure vessels is analyzed, and the results are compared with those from the classical theory which neglects the effect of shear deformations. (orig.)

  3. Recycling of plastic waste: Presence of phthalates in plastics from households and industry

    DEFF Research Database (Denmark)

    Pivnenko, Kostyantyn; Eriksen, Marie Kampmann; Martín-Fernández, J. A.

    2016-01-01

    Plastics recycling has the potential to substitute virgin plastics partially as a source of raw materials in plastic product manufacturing. Plastic as a material may contain a variety of chemicals, some potentially hazardous. Phthalates, for instance, are a group of chemicals produced in large...... recognised, the influence of plastic recycling on phthalate content has been hypothesised but not well documented. In the present work we analysed selected phthalates (DMP, DEP, DPP, DiBP, DBP, BBzP, DEHP, DCHP and DnOP) in samples of waste plastics as well as recycled and virgin plastics. DBP, DiBP and DEHP...

  4. Recent activities in flame retardancy of wood-plastic composites at the Forest Products Laboratory

    Science.gov (United States)

    Robert H. White; Nicole M. Stark; Nadir Ayrilmis

    2011-01-01

    For a variety of reasons, wood-plastic composite (WPC) products are widely available for some building applications. In applications such as outdoor decking, WPCs have gained a significant share of the market. As an option to improve the efficient use of wood fiber, the USDA Forest Service, Forest Products Laboratory (FPL), has an extensive research program on WPCs....

  5. Phenological plasticity will not help all species adapt to climate change.

    Science.gov (United States)

    Duputié, Anne; Rutschmann, Alexis; Ronce, Ophélie; Chuine, Isabelle

    2015-08-01

    Concerns are rising about the capacity of species to adapt quickly enough to climate change. In long-lived organisms such as trees, genetic adaptation is slow, and how much phenotypic plasticity can help them cope with climate change remains largely unknown. Here, we assess whether, where and when phenological plasticity is and will be adaptive in three major European tree species. We use a process-based species distribution model, parameterized with extensive ecological data, and manipulate plasticity to suppress phenological variations due to interannual, geographical and trend climate variability, under current and projected climatic conditions. We show that phenological plasticity is not always adaptive and mostly affects fitness at the margins of the species' distribution and climatic niche. Under current climatic conditions, phenological plasticity constrains the northern range limit of oak and beech and the southern range limit of pine. Under future climatic conditions, phenological plasticity becomes strongly adaptive towards the trailing edges of beech and oak, but severely constrains the range and niche of pine. Our results call for caution when interpreting geographical variation in trait means as adaptive, and strongly point towards species distribution models explicitly taking phenotypic plasticity into account when forecasting species distribution under climate change scenarios. © 2015 John Wiley & Sons Ltd.

  6. Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes.

    Science.gov (United States)

    Murat, Claude; Zampieri, Elisa; Vallino, Marta; Daghino, Stefania; Perotto, Silvia; Bonfante, Paola

    2011-05-01

    Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  7. Learning Joomla! 3 extension development

    CERN Document Server

    Plummer, Tim

    2013-01-01

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

  8. Programming Reactive Extensions and LINQ

    CERN Document Server

    Liberty, Jesse

    2011-01-01

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

  9. Extensions of the Standard Model

    CERN Document Server

    Zwirner, Fabio

    1996-01-01

    Rapporteur talk at the International Europhysics Conference on High Energy Physics, Brussels (Belgium), July 27-August 2, 1995. This talk begins with a brief general introduction to the extensions of the Standard Model, reviewing the ideology of effective field theories and its practical implications. The central part deals with candidate extensions near the Fermi scale, focusing on some phenomenological aspects of the Minimal Supersymmetric Standard Model. The final part discusses some possible low-energy implications of further extensions near the Planck scale, namely superstring theories.

  10. Influence of a Double-Lumen Extension Tube on Drug Delivery: Examples of Isosorbide Dinitrate and Diazepam.

    Directory of Open Access Journals (Sweden)

    Aurélie Maiguy-Foinard

    Full Text Available Plastic materials such as polyurethane (PUR, polyethylene (PE, polypropylene (PP and polyvinyl chloride (PVC are widely used in double-lumen extension tubing. The purposes of our study were to 1 compare in vitro drug delivery through the double extension tubes available on the market 2 assess the plastic properties of PUR in infusion devices and their impact on drug delivery.The study compared eight double-lumen extension tubes in PUR, co-extruded (PE/PVC plastic and plasticised PVC from different manufacturers. Isosorbide dinitrate and diazepam were used as model compounds to evaluate their sorption on the internal surface of the infusion device. Control experiments were performed using norepinephrine known not to absorb to plastics. Drug concentrations delivered at the egress of extension tubes were determined over time by an analytical spectrophotometric UV-Vis method. The main characteristics of plastics were also determined.Significant differences in the sorption phenomenon were observed among the eight double-lumen extension tubes and between pairs of extension tubes. Mean concentrations of isosorbide dinitrate delivered at the egress of double-lumen extension tubes after a 150-minute infusion (mean values ± standard deviation in percentage of the initial concentrations in the prepared syringes ranged between 80.53 ± 1.66 (one of the PUR tubes and 92.84 ± 2.73 (PE/PVC tube. The same parameters measured during diazepam infusion ranged between 48.58 ± 2.88 (one of the PUR tubes and 85.06 ± 3.94 (PE/PVC tube. The double-lumen extension tubes in PUR were either thermosetting (resin or thermoplastic according to reference.Clinicians must be aware of potential drug interactions with extension tube materials and so must consider their nature as well as the sterilisation method used before selecting an infusion device.

  11. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

    Science.gov (United States)

    Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

    2016-01-01

    Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and

  12. Plastic waste as a resource. Strategies for reduction and utilization of plastic waste

    OpenAIRE

    Pasqual i Camprubí, Gemma

    2010-01-01

    Plastic materials have experienced a spectacular rate of growth in recent decades, consequently, production of plastics, and likewise their consumption, has increased markedly since 1950. Moreover, they are lightweight and durable, as well as can be moulded into a variety of products that can be manufactured in many different types of plastic and in a wide range of applications. Inevitably, continually increasing amounts of used plastic are originating daily, resulting in a plastic waste prob...

  13. Plasticity Approach to Shear Design

    DEFF Research Database (Denmark)

    Hoang, Cao Linh; Nielsen, Mogens Peter

    1998-01-01

    The paper presents some plastic models for shear design of reinforced concrete beams. Distinction is made between two shear failure modes, namely web crushing and crack sliding. The first mentioned mode is met in beams with large shear reinforcement degrees. The mode of crack sliding is met in non......-shear reinforced beams as well as in lightly shear reinforced beams. For such beams the shear strength is determined by the recently developed crack sliding model. This model is based upon the hypothesis that cracks can be transformed into yield lines, which have lower sliding resistance than yield lines formed...... in uncracked concrete. Good agree between theory and tests has been found.Keywords: dsign, plasticity, reinforced concrete, reinforcement, shear, web crushing....

  14. Computational Strain Gradient Crystal Plasticity

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Kysar, Jeffrey W.

    2011-01-01

    A model for strain gradient crystal visco-plasticity is formulated along the lines proposed by Fleck andWillis (2009) for isotropic plasticity. Size-effects are included in the model due to the addition of gradient terms in both the free energy as well as through a dissipation potential. A finite...... element solution method is presented, which delivers the slip-rate field and the velocity-field based on two minimum principles. Some plane deformation problems relevant for certain specific orientations of a face centered cubic crystal under plane loading conditions are studied, and effective in......-plane parameters are developed based on the crystallographic properties of the material. The problem of cyclic shear of a single crystal between rigid platens is studied as well as void growth of a cylindrical void....

  15. Alternative Diesel from Waste Plastics

    Directory of Open Access Journals (Sweden)

    Stella Bezergianni

    2017-10-01

    Full Text Available The long term ambition of energy security and solidarity, coupled with the environmental concerns of problematic waste accumulation, is addressed via the proposed waste-to-fuel technology. Plastic waste is converted into automotive diesel fuel via a two-step thermochemical process based on pyrolysis and hydrotreatment. Plastic waste was pyrolyzed in a South East Asia plant rendering pyrolysis oil, which mostly consisted of middle-distillate (naphtha and diesel hydrocarbons. The diesel fraction (170–370 °C was fractionated, and its further upgrade was assessed in a hydroprocessing pilot plant at the Centre for Research and Technology Hellas (CERTH in Greece. The final fuel was evaluated with respect to the diesel fuel quality specifications EN 590, which characterized it as a promising alternative diesel pool component with excellent ignition quality characteristics and low back end volatility.

  16. Polishing compound for plastic surfaces

    Science.gov (United States)

    Stowell, M.S.

    1991-01-01

    This invention is comprised of a polishing compound for plastic materials. The compound includes approximately by approximately by weight 25 to 80 parts at least one petroleum distillate lubricant, 1 to 12 parts mineral spirits, 50 to 155 parts abrasive paste, and 15 to 60 parts water. Preferably, the compound includes approximately 37 to 42 parts at least one petroleum distillate lubricant, up to 8 parts mineral spirits, 95 to 110 parts abrasive paste, and 50 to 55 parts water. The proportions of the ingredients are varied in accordance with the particular application. The compound is used on PLEXIGLAS{trademark}, LEXAN{trademark}, LUCITE{trademark}, polyvinyl chloride (PVC), and similar plastic materials whenever a smooth, clear polished surface is desired.

  17. Temperature dependence of plastic scintillators

    Science.gov (United States)

    Peralta, L.

    2018-03-01

    Plastic scintillator detectors have been studied as dosimeters, since they provide a cost-effective alternative to conventional ionization chambers. Several articles have reported undesired response dependencies on beam energy and temperature, which provides the motivation to determine appropriate correction factors. In this work, we studied the light yield temperature dependency of four plastic scintillators, BCF-10, BCF-60, BC-404, RP-200A and two clear fibers, BCF-98 and SK-80. Measurements were made using a 50 kVp X-ray beam to produce the scintillation and/or radioluminescence signal. The 0 to 40 °C temperature range was scanned for each scintillator, and temperature coefficients were obtained.

  18. Vascular plasticity in cerebrovascular disorders

    DEFF Research Database (Denmark)

    Edvinsson, Lars I H; Povlsen, Gro Klitgaard

    2011-01-01

    Cerebral ischemia remains a major cause of morbidity and mortality with little advancement in subacute treatment options. This review aims to cover and discuss novel insight obtained during the last decade into plastic changes in the vasoconstrictor receptor profiles of cerebral arteries and micr......Cerebral ischemia remains a major cause of morbidity and mortality with little advancement in subacute treatment options. This review aims to cover and discuss novel insight obtained during the last decade into plastic changes in the vasoconstrictor receptor profiles of cerebral arteries...... therapeutic target for prevention of vasoconstrictor receptor upregulation after stroke. Together, those findings provide new perspectives on the pathophysiology of ischemic stroke and point toward a novel way of reducing vasoconstriction, neuronal cell death, and thus neurologic deficits after stroke....

  19. Process for remediation of plastic waste

    Science.gov (United States)

    Pol, Vilas G [Westmont, IL; Thiyagarajan, Pappannan [Germantown, MD

    2012-04-10

    A single step process for degrading plastic waste by converting the plastic waste into carbonaceous products via thermal decomposition of the plastic waste by placing the plastic waste into a reactor, heating the plastic waste under an inert or air atmosphere until the temperature of 700.degree. C. is achieved, allowing the reactor to cool down, and recovering the resulting decomposition products therefrom. The decomposition products that this process yields are carbonaceous materials, and more specifically egg-shaped and spherical-shaped solid carbons. Additionally, in the presence of a transition metal compound, this thermal decomposition process produces multi-walled carbon nanotubes.

  20. Learning and plasticity in adolescence

    OpenAIRE

    Fuhrmann, Delia Ute Dorothea

    2017-01-01

    Adolescence is the period of life between puberty and relative independence. It is a time during which the human brain undergoes protracted changes - particularly in the frontal, parietal and temporal cortices. These changes have been linked to improvements in cognitive performance; and are thought to render adolescence a period of relatively high levels of plasticity, during which the environment has a heightened impact on brain development and behaviour. This thesis investigates learning an...

  1. Studies of novel plastic scintillators

    International Nuclear Information System (INIS)

    McInally, I.D.

    1979-08-01

    The general aim of this study was to synthesize fluorescent compounds which are capable of polymerisation, to prepare polymers and co-polymers from these compounds and to study the photophysical properties of these materials. In this way it is hoped to produce plastic scintillators exhibiting improved energy transfer efficiency. Materials studied included POS(2-phenyl-5-(p vinyl) phenyloxazole) vinyl naphthalene, methyl anthracene terminated poly vinyl toluene) and derivatives of BuPBD. (author)

  2. Ways of Viewing Pictorial Plasticity

    OpenAIRE

    Maarten W. A. Wijntjes

    2017-01-01

    The plastic effect is historically used to denote various forms of stereopsis. The vivid impression of depth often associated with binocular stereopsis can also be achieved in other ways, for example, using a synopter. Accounts of this go back over a hundred years. These ways of viewing all aim to diminish sensorial evidence that the picture is physically flat. Although various viewing modes have been proposed in the literature, their effects have never been compared. In the current study, we...

  3. The Plastic Surgery Hand Curriculum.

    Science.gov (United States)

    Silvestre, Jason; Levin, L Scott; Serletti, Joseph M; Chang, Benjamin

    2015-12-01

    Designing an effective hand rotation for plastic surgery residents is difficult. The authors address this limitation by elucidating the critical components of the hand curriculum during plastic surgery residency. Hand questions on the Plastic Surgery In-Service Training Exam for six consecutive years (2008 to 2013) were characterized by presence of imaging, vignette setting, question taxonomy, answer domain, anatomy, and topic. Answer references were quantified by source and year of publication. Two hundred sixty-six questions were related to hand surgery (22.7 percent of all questions; 44.3 per year) and 61 were accompanied by an image (22.9 percent). Vignettes tended to be clinic- (50.0 percent) and emergency room-based (35.3 percent) (p < 0.001). Questions required decision-making (60.5 percent) over interpretation (25.9 percent) and recall skills (13.5 percent) (p < 0.001). Answers focused on interventions (57.5 percent) over anatomy/pathology (25.2 percent) and diagnoses (17.3 percent) (p < 0.001). Nearly half of the questions focused on the digits. The highest yield topics were trauma (35.3 percent), reconstruction (24.4 percent), and aesthetic and functional problems (14.2 percent). The Journal of Hand Surgery (American volume) (20.5 percent) and Plastic and Reconstructive Surgery (18.0 percent) were the most-cited journals, and the median publication lag was 7 years. Green's Operative Hand Surgery was the most-referenced textbook (41.8 percent). These results will enable trainees to study hand surgery topics with greater efficiency. Faculty can use these results to ensure that tested topics are covered during residency training. Thus, a benchmark is established to improve didactic, clinical, and operative experiences in hand surgery.

  4. Processing of plastic track detectors

    International Nuclear Information System (INIS)

    Somogyi, G.

    1977-01-01

    A survey of some actual problems of the track processing methods available at this time for plastics is presented. In the case of the conventional chemical track-etching technique, mainly the etching situations related to detector geometry, and the relationship between registration sensitivity and the etching parameters are considered. Special attention is paid to the behaviour of track-revealing by means of electrochemical etching. Finally, some properties of a promising new track processing method based on graft polymerization are discussed. (author)

  5. Processing of plastic track detectors

    International Nuclear Information System (INIS)

    Somogyi, G.

    1976-01-01

    A survey of some actual problems of the track processing methods available at this time for plastics is presented. In the case of the conventional chemical track etching technique mainly the etching situations related to detector geometry and the relationship of registration sensitivity and the etching parameters are considered. A special attention is paid to the behaviour of track revealing by means of electrochemical etching. Finally, some properties of a promising new track processing method based on graft polymerization is discussed. (orig.) [de

  6. Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

    OpenAIRE

    Spradling, A C; Stern, D M; Kiss, I; Roote, J; Laverty, T; Rubin, G M

    1995-01-01

    Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and a...

  7. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  8. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  9. Vocal plasticity in a reptile.

    Science.gov (United States)

    Brumm, Henrik; Zollinger, Sue Anne

    2017-05-31

    Sophisticated vocal communication systems of birds and mammals, including human speech, are characterized by a high degree of plasticity in which signals are individually adjusted in response to changes in the environment. Here, we present, to our knowledge, the first evidence for vocal plasticity in a reptile. Like birds and mammals, tokay geckos ( Gekko gecko ) increased the duration of brief call notes in the presence of broadcast noise compared to quiet conditions, a behaviour that facilitates signal detection by receivers. By contrast, they did not adjust the amplitudes of their call syllables in noise (the Lombard effect), which is in line with the hypothesis that the Lombard effect has evolved independently in birds and mammals. However, the geckos used a different strategy to increase signal-to-noise ratios: instead of increasing the amplitude of a given call type when exposed to noise, the subjects produced more high-amplitude syllable types from their repertoire. Our findings demonstrate that reptile vocalizations are much more flexible than previously thought, including elaborate vocal plasticity that is also important for the complex signalling systems of birds and mammals. We suggest that signal detection constraints are one of the major forces driving the evolution of animal communication systems across different taxa. © 2017 The Author(s).

  10. Plastic buckling of cylindrical shells

    International Nuclear Information System (INIS)

    Bandyopadhyay, K.; Xu, J.; Shteyngart, S.; Eckert, H.

    1994-01-01

    Cylindrical shells exhibit buckling under axial loads at stresses much less than the respective theoretical critical stresses. This is due primarily to the presence of geometrical imperfections even though such imperfections could be very small (e.g., comparable to thickness). Under internal pressure, the shell regains some of its buckling strength. For a relatively large radius-to-thickness ratio and low internal pressure, the effect can be reasonably estimated by an elastic analysis. However, for low radius-to-thickness ratios and greater pressures, the elastic-plastic collapse controls the failure load. in order to quantify the elastic-plastic buckling capacity of cylindrical shells, an analysis program was carried out by use of the computer code BOSOR5 developed by Bushnell of Lockheed Missiles and Space Company. The analysis was performed for various radius-to-thickness ratios and imperfection amplitudes. The purpose of the analytical program was to compute the buckling strength of underground cylindrical tanks, that are used for storage of nuclear wastes, for realistic geometric imperfections and internal pressure loads. This paper presents the results of the elastic-plastic analyses and compares them with other available information for various pressure loads

  11. G-InforBIO: integrated system for microbial genomics

    Directory of Open Access Journals (Sweden)

    Abe Takashi

    2006-08-01

    Full Text Available Abstract Background Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. Results The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. Conclusion The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

  12. Plastic solid waste utilization technologies: A Review

    Science.gov (United States)

    Awasthi, Arun Kumar; Shivashankar, Murugesh; Majumder, Suman

    2017-11-01

    Plastics are used in more number of applications in worldwide and it becomes essential part of our daily life. In Indian cities and villages people use the plastics in buying vegetable as a carry bag, drinking water bottle, use of plastic furniture in home, plastics objects uses in kitchen, plastic drums in packing and storage of the different chemicals for industrial use, use plastic utensils in home and many more uses. After usage of plastics it will become part of waste garbage and create pollution due to presence of toxic chemicals and it will be spread diseases and give birth to uncontrolled issues in social society. In current scenario consumption of plastic waste increasing day by day and it is very difficult to manage the plastic waste. There are limited methodologies available for reutilization of plastic waste again. Such examples are recycling, landfill, incineration, gasification and hydrogenation. In this paper we will review the existing methodologies of utilization of plastic waste in current scenario

  13. Research-extension-farmer linkages

    African Journals Online (AJOL)

    agricultural research and extension services, Government in 1990 set up a number of ... charged with the role of articulating the most appropriate research and ... production of 1800 copies of NARO bulletin, 1000 copies of Uganda Journal of ...

  14. Journal of Environmental Extension: Submissions

    African Journals Online (AJOL)

    Journal of Environmental Extension is purely academic and accepts positional or ... and so responsibility for the content and macro formatting remain of the author. ... For research articles, the methodology, result analysis (statistical tests to be ...

  15. Applications and societal benefits of plastics.

    Science.gov (United States)

    Andrady, Anthony L; Neal, Mike A

    2009-07-27

    This article explains the history, from 1600 BC to 2008, of materials that are today termed 'plastics'. It includes production volumes and current consumption patterns of five main commodity plastics: polypropylene, polyethylene, polyvinyl chloride, polystyrene and polyethylene terephthalate. The use of additives to modify the properties of these plastics and any associated safety, in use, issues for the resulting polymeric materials are described. A comparison is made with the thermal and barrier properties of other materials to demonstrate the versatility of plastics. Societal benefits for health, safety, energy saving and material conservation are described, and the particular advantages of plastics in society are outlined. Concerns relating to littering and trends in recycling of plastics are also described. Finally, we give predictions for some of the potential applications of plastic over the next 20 years.

  16. The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation

    KAUST Repository

    Cózar, Andrés

    2017-04-20

    The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris.

  17. Boiler-turbine life extension

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-12-01

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

  18. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  19. Agricultural extension and mass media.

    Science.gov (United States)

    Perraton, H

    1983-12-01

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

  20. Extensions to a nonlinear finite-element axisymmetric shell model based on Reissner's shell theory

    International Nuclear Information System (INIS)

    Cook, W.A.

    1981-01-01

    Extensions to shell analysis not usually associated with shell theory are described in this paper. These extensions involve thick shells, nonlinear materials, a linear normal stress approximation, and a changing shell thickness. A finite element shell-of-revolution model has been developed to analyze nuclear material shipping containers under severe impact conditions. To establish the limits for this shell model, the basic assumptions used in its development were studied; these are listed in this paper. Several extensions were evident from the study of these limits: a thick shell, a plastic hinge, and a linear normal stress

  1. Is the holy grail plastic? Radiation identification from plastic scintillators

    International Nuclear Information System (INIS)

    Butchins, L. J. C.; Gosling, J. M.; Hogbin, M. R. W.; Jones, D. C.; Lacey, R. J.; Stearn, J. G.

    2009-01-01

    Thousands of shipping containers containing Naturally Occurring Radioactive Materials (NORM) made from ceramics, stoneware and other natural products are transported worldwide on a daily basis. Some of these NORM loads are sufficiently radioactive to trigger alarms from plastic scintillator detectors which have limited ability to also identify the radionuclides present thus necessitating secondary inspection which increases the operational overhead. Previous studies have been carried out to ascertain if radionuclide discrimination using plastic scintillators is possible with a variety of approaches including deconvolution and computer learning. In this paper, a two stage algorithm is described. An example implementation of the algorithm is presented, applied to operational data, and has been installed in real time operation on a polyvinyl-toluene (PVT) detector. The approach requires the collection of a large library of spectra using examples of the detectors to be deployed. In this study, data from both actual freight loads passing through a port and predefined freight containing various radionuclides were collected. The library represents freight loads that may contain industrial, medical, nuclear, and NORM radionuclides. The radionuclides in the predefined freight were placed in various orientations and in various amounts of shielding to mimic many different scenarios. Preliminary results on an initial subset of data containing industrial and NORM sources show the number of mis-classifications to be less than 1% of the total test data. Good initial results were obtained even for low energy radionuclides such as 241 Am. Where discrimination is not possible, and principle components overlap, this region or 'cloud' of the n-dimensional plot can be put aside. Those spectra that fall in the 'cloud' can be regarded as suspect and in these cases, some secondary screening will still be necessary. It is predicted that the algorithm will enable recognition of NORM loads

  2. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    KAUST Repository

    Liu, Huanle; Stephens, Timothy G.; Gonzá lez-Pech, Raú l; Beltran, Victor H.; Lapeyre, Bruno; Bongaerts, Pim; Cooke, Ira; Bourne, David G.; Forê t, Sylvain; Miller, David John; van Oppen, Madeleine J. H.; Voolstra, Christian R.; Ragan, Mark A.; Chan, Cheong Xin

    2017-01-01

    Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

  3. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    KAUST Repository

    Liu, Huanle

    2017-10-06

    Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world\\'s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

  4. Origins of the Human Genome Project.

    Science.gov (United States)

    Watson, J D; Cook-Deegan, R M

    1991-01-01

    Caenorhabditis elegans by a collaboration between Washington University and the Medical Research Council laboratory in Cambridge, U.K. This project is now turning to sequencing C. elegans DNA as a logical extension of this work. These are but the first fruits of the genome project. There is much more to come.

  5. 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.

  6. Developmental systems of plasticity and trans-generational epigenetic inheritance in nematodes.

    Science.gov (United States)

    Serobyan, Vahan; Sommer, Ralf J

    2017-08-01

    Several decades of research provided detailed insight into how genes control development and evolution, whereas recent studies have expanded this purely genetic perspective by presenting strong evidence for environmental and epigenetic influences. We summarize examples of phenotypic plasticity and trans-generational epigenetic inheritance in the nematode model organisms Pristionchus pacificus and Caenorhabditis elegans, which indicate that the response of developmental systems to environmental influences is hardwired into the organismś genome. We argue that genetic programs regulating these organismal-environmental interactions are themselves subject to natural selection. Indeed, macro-evolutionary studies of nematode feeding structures indicate evolutionary trajectories in which plasticity followed by genetic assimilation results in extreme diversity highlighting the role of plasticity as major facilitator of phenotypic diversification. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents.

    Science.gov (United States)

    Gilbert, Scott F; Bosch, Thomas C G; Ledón-Rettig, Cristina

    2015-10-01

    The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

  8. RURAL EXTENSION EPISTEMOLOGY AND THE TIME OF TOTAL EXTENSION

    Directory of Open Access Journals (Sweden)

    Silvio Calgaro Neto

    2016-09-01

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

  9. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  10. Elastic-plastic analysis of tube expansion in tubesheets

    International Nuclear Information System (INIS)

    Kasraie, B.; O'Donnell, W.J.; Porowski, J.S.; Selz, A.

    1983-01-01

    Conditions for expansion of tubes in tubesheets are often determined by the test. The tightness of the joint and pull out force are used as criteria for evaluation of the results. For closely spaced tubes, it is also necessary to control development of the plastic regions in the ligaments surrounding the tube being expanded. High local strains may occur and excessive distortion may result if the expansion of the tube is continued beyond the admissible limits. Elastic-plastic finite element analyses are performed herein in order to establish conditions for rolling of the tubes in tubesheets of low ligament efficiency. Such penetration patterns are often required in the design of tubular reactors for catalytic processes. The model considered includes individual tube expansion in tubesheets with triangular penetration patterns. The effect of prior expansion of the neighboring tubes is also evaluated. Gap elements are used to model the initial clearance of the tube in the hole. Development of the plastic zones and distortion of the ligaments is monitored during radial expansion of the tube diameter. The residual stresses between the tube and the hole surface and the history of gap closing after removal of the expansion tool are determined. The effect of axial extension of the tube on the tube thinning is determined. Tube thinning is often used as a measure of tube expansion in manufacturing processes. For the analyzed ligament efficiency, reliable joints are obtained for a thinning range within 2% to 3%

  11. The Mediterranean Plastic Soup: synthetic polymers in Mediterranean surface waters

    Science.gov (United States)

    Suaria, Giuseppe; Avio, Carlo G.; Mineo, Annabella; Lattin, Gwendolyn L.; Magaldi, Marcello G.; Belmonte, Genuario; Moore, Charles J.; Regoli, Francesco; Aliani, Stefano

    2016-11-01

    The Mediterranean Sea has been recently proposed as one of the most impacted regions of the world with regards to microplastics, however the polymeric composition of these floating particles is still largely unknown. Here we present the results of a large-scale survey of neustonic micro- and meso-plastics floating in Mediterranean waters, providing the first extensive characterization of their chemical identity as well as detailed information on their abundance and geographical distribution. All particles >700 μm collected in our samples were identified through FT-IR analysis (n = 4050 particles), shedding for the first time light on the polymeric diversity of this emerging pollutant. Sixteen different classes of synthetic materials were identified. Low-density polymers such as polyethylene and polypropylene were the most abundant compounds, followed by polyamides, plastic-based paints, polyvinyl chloride, polystyrene and polyvinyl alcohol. Less frequent polymers included polyethylene terephthalate, polyisoprene, poly(vinyl stearate), ethylene-vinyl acetate, polyepoxide, paraffin wax and polycaprolactone, a biodegradable polyester reported for the first time floating in off-shore waters. Geographical differences in sample composition were also observed, demonstrating sub-basin scale heterogeneity in plastics distribution and likely reflecting a complex interplay between pollution sources, sinks and residence times of different polymers at sea.

  12. 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

  13. A review of plastic waste biodegradation.

    Science.gov (United States)

    Zheng, Ying; Yanful, Ernest K; Bassi, Amarjeet S

    2005-01-01

    With more and more plastics being employed in human lives and increasing pressure being placed on capacities available for plastic waste disposal, the need for biodegradable plastics and biodegradation of plastic wastes has assumed increasing importance in the last few years. This review looks at the technological advancement made in the development of more easily biodegradable plastics and the biodegradation of conventional plastics by microorganisms. Additives, such as pro-oxidants and starch, are applied in synthetic materials to modify and make plastics biodegradable. Recent research has shown that thermoplastics derived from polyolefins, traditionally considered resistant to biodegradation in ambient environment, are biodegraded following photo-degradation and chemical degradation. Thermoset plastics, such as aliphatic polyester and polyester polyurethane, are easily attacked by microorganisms directly because of the potential hydrolytic cleavage of ester or urethane bonds in their structures. Some microorganisms have been isolated to utilize polyurethane as a sole source of carbon and nitrogen source. Aliphatic-aromatic copolyesters have active commercial applications because of their good mechanical properties and biodegradability. Reviewing published and ongoing studies on plastic biodegradation, this paper attempts to make conclusions on potentially viable methods to reduce impacts of plastic waste on the environment.

  14. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  15. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  16. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    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 MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  17. Improved airline-type supplied-air plastic suit. [For personnel protection against inhalation of airborne plutonium and tritium

    Energy Technology Data Exchange (ETDEWEB)

    Jolley, L. Jr.; Zippler, D.B.; Cofer, C.H.; Harper, J.A.

    1978-06-01

    Two piece supplied-air plastic suits are used extensively at the Savannah River Plant for personnel protection against inhalation of airborne plutonium and tritium. Worker comfort and noise level problems gave impetus to development of an improved suit and aid distribution system. The resulting plastic suit and development work are discussed. The plastic suit unit cost is less than $20, the hearing zone noise level is less than 75 dBA, protection factors exceed 10,000, and user comfort is approved. This suit is expected to meet performance requirements for unrestricted use.

  18. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  19. Recycling of plastic waste: Presence of phthalates in plastics from households and industry

    DEFF Research Database (Denmark)

    Pivnenko, Kostyantyn; Eriksen, Marie Kampmann; Martín-Fernández, J. A.

    2016-01-01

    recognised, the influence of plastic recycling on phthalate content has been hypothesised but not well documented. In the present work we analysed selected phthalates (DMP, DEP, DPP, DiBP, DBP, BBzP, DEHP, DCHP and DnOP) in samples of waste plastics as well as recycled and virgin plastics. DBP, DiBP and DEHP...... product manufacturing (labelling, gluing, etc.) and were not removed following recycling of household waste plastics. Furthermore, DEHP was identified as a potential indicator for phthalate contamination of plastics. Close monitoring of plastics intended for phthalates-sensitive applications...

  20. Characterization of plastic blends made from mixed plastics waste of different sources.

    Science.gov (United States)

    Turku, Irina; Kärki, Timo; Rinne, Kimmo; Puurtinen, Ari

    2017-02-01

    This paper studies the recyclability of construction and household plastic waste collected from local landfills. Samples were processed from mixed plastic waste by injection moulding. In addition, blends of pure plastics, polypropylene and polyethylene were processed as a reference set. Reference samples with known plastic ratio were used as the calibration set for quantitative analysis of plastic fractions in recycled blends. The samples were tested for the tensile properties; scanning electron microscope-energy-dispersive X-ray spectroscopy was used for elemental analysis of the blend surfaces and Fourier transform infrared (FTIR) analysis was used for the quantification of plastics contents.