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

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

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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

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

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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.

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

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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.

Radiation crosslinking of highly plasticized PVC

Science.gov (United States)

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

1996-02-01

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

Radiation crosslinking of highly plasticized PVC

International Nuclear Information System (INIS)

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

1996-01-01

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

High-speed and high-ratio referential genome compression.

Science.gov (United States)

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

2017-11-01

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

Neurogenomic mechanisms of social plasticity.

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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.

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.

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.

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

Science.gov (United States)

Helmer Pedersen, Thomas; Conti, Federica

2017-10-01

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

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.

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.

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.

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

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

Machado, Henrique; Gram, Lone

2017-01-01

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

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

DEFF Research Database (Denmark)

Machado, Henrique; Gram, Lone

2017-01-01

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

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

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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.

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.

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

Science.gov (United States)

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

2013-03-01

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

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....

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

Science.gov (United States)

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

2010-12-15

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

Temperature-dependent plastic hysteresis in highly confined polycrystalline Nb films

Science.gov (United States)

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

2018-02-01

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

High order curvilinear finite elements for elastic–plastic Lagrangian dynamics

International Nuclear Information System (INIS)

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

2014-01-01

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

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

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 ...

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

Directory of Open Access Journals (Sweden)

Keeling Patrick J

2007-09-01

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

Recovery of Porosity and Permeability for High Plasticity Clays

DEFF Research Database (Denmark)

Krogsbøll, Anette; Foged, Niels Nielsen

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

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.

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.

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.

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.

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.

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 ...

High Rate Plastic Deformation and Failure of Tungsten-Sintered Metals

National Research Council Canada - National Science Library

Bjerke, Todd

2004-01-01

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

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

Science.gov (United States)

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

2018-02-14

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

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

DEFF Research Database (Denmark)

Zhan, Bujie; Fadista, João; Thomsen, Bo

2011-01-01

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

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

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

Directory of Open Access Journals (Sweden)

Rodolphe François

2006-08-01

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

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

Science.gov (United States)

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

2007-05-01

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

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

Science.gov (United States)

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

2007-05-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-10-15

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

International Nuclear Information System (INIS)

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

1999-01-01

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

Whole-genome shotgun optical mapping of rhodospirillumrubrum

Energy Technology Data Exchange (ETDEWEB)

Reslewic, Susan; Zhou, Shiguo; Place, Mike; Zhang, Yaoping; Briska, Adam; Goldstein, Steve; Churas, Chris; Runnheim, Rod; Forrest,Dan; Lim, Alex; Lapidus, Alla; Han, Cliff S.; Roberts, Gary P.; Schwartz,David C.

2004-07-01

Rhodospirillum rubrum is a phototrophic purple non-sulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems, and as a source of hydrogen and biodegradable plastics production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction maps (Xba I, Nhe I, and Hind III) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction maps from randomly sheared genomic DNA molecules extracted directly from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the Hind III map acted as a scaffold for high resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and validation of genome sequence, our work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a ''molecular cytogenetics'' approach to solving problems in genomic analysis.

Exceptionally high levels of recombination across the honey bee genome.

Science.gov (United States)

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

2006-11-01

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

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.

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

Science.gov (United States)

2013-08-01

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

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

Science.gov (United States)

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

2014-01-01

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

Scrutinizing virus genome termini by high-throughput sequencing.

Directory of Open Access Journals (Sweden)

Shasha Li

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

High-temperature discrete dislocation plasticity

Science.gov (United States)

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

2015-09-01

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

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...

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

DEFF Research Database (Denmark)

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

2011-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1997-12-31

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

Whole-genome shotgun optical mapping of Rhodospirillum rubrum

Energy Technology Data Exchange (ETDEWEB)

Reslewic, S. [Univ. Wisc.-Madison; Zhou, S. [Univ. Wisc.-Madison; Place, M. [Univ. Wisc.-Madison; Zhang, Y. [Univ. Wisc.-Madison; Briska, A. [Univ. Wisc.-Madison; Goldstein, S. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Forrest, D. [Univ. Wisc.-Madison; Lim, A. [Univ. Wisc.-Madison; Lapidus, A. [Univ. Wisc.-Madison; Han, C. S. [Univ. Wisc.-Madison; Roberts, G. P. [Univ. Wisc.-Madison; Schwartz, D. C. [Univ. Wisc.-Madison

2005-09-01

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a "molecular cytogenetics" approach to solving problems in genomic analysis.

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

NARCIS (Netherlands)

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

2010-01-01

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

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

Science.gov (United States)

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

2014-06-01

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

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

Science.gov (United States)

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

2013-10-15

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-07-01

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

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

International Nuclear Information System (INIS)

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

1994-01-01

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

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

Directory of Open Access Journals (Sweden)

Matthew R Henn

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

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

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

International Nuclear Information System (INIS)

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

1994-01-01

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

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

Science.gov (United States)

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

2018-05-01

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

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

Science.gov (United States)

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

2018-06-01

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

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.

High pressure studies of fluorenone emission in plastic media

International Nuclear Information System (INIS)

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

1977-01-01

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

Elastic-plastic behaviour of thick-walled containers considering plastic compressibility

International Nuclear Information System (INIS)

Betten, J.; Frosch, H.G.

1983-01-01

In this paper the elastic-plastic behaviour of thick-walled pressure vessels with internal and external pressure is studied. To describe the mechanical behaviour of isotropic, plastic compressible materials we use a plastic potential which is a single-valued function of the principle stresses. For cylinders and spheres an analytic expression for the computation of stresses and residual stresses is specified. Afterwards the strains are calculated by using the finite difference method. Some examples will high-light the influence of the plastic compressibility on the behaviour of pressure vessels. (orig.) [de

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

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

Directory of Open Access Journals (Sweden)

Magness Charles L

2007-01-01

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-15

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

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.

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

Science.gov (United States)

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

2012-01-01

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

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

Directory of Open Access Journals (Sweden)

César D Petroli

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

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

Directory of Open Access Journals (Sweden)

Tercio Goes

2014-10-01

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

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.

Quantitative high-resolution genomic analysis of single cancer cells.

Science.gov (United States)

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

2011-01-01

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

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

International Nuclear Information System (INIS)

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

2010-12-01

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

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.

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

High Genomic Instability Predicts Survival in Metastatic High-Risk Neuroblastoma

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Sara Stigliani

2012-09-01

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

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.

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.

Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

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Charu Tripathi

2017-07-01

Full Text Available Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C using PacBio RSII SMRT technique. The small genome (2.01 Mbp comprises a chromosome (1.87 Mbp and a plasmid (143 Kbp, designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%. We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI, conserved marker genes (31 and 400, pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5 by recruiting raw metagenomic data (from the same niche against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

Quantitative high-resolution genomic analysis of single cancer cells.

Directory of Open Access Journals (Sweden)

Juliane Hannemann

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

A Primer on High-Throughput Computing for Genomic Selection

Directory of Open Access Journals (Sweden)

Xiao-Lin eWu

2011-02-01

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

The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

Energy Technology Data Exchange (ETDEWEB)

Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

2009-04-01

Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have

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...

A primer on high-throughput computing for genomic selection.

Science.gov (United States)

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

2011-01-01

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

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

Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

Energy Technology Data Exchange (ETDEWEB)

Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

2014-03-14

Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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.

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

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

International Nuclear Information System (INIS)

Wasserbaech, W.; Thompson, E.

2001-01-01

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

The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens.

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Anja Voigt

Full Text Available Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis.A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins.This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.

The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens.

Science.gov (United States)

Voigt, Anja; Schöfl, Gerhard; Saluz, Hans Peter

2012-01-01

Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.

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

Science.gov (United States)

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

2012-05-01

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

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

Directory of Open Access Journals (Sweden)

Jinchuan Xing

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

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

Science.gov (United States)

Yu, Peng; Hochholdinger, Frank; Li, Chunjian

2015-10-01

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

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

Science.gov (United States)

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

2017-05-01

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

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

OpenAIRE

Henrique Machado; Henrique Machado; Lone Gram

2017-01-01

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

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

Science.gov (United States)

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

2016-07-06

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

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...

Diffusion and plasticity at high temperature

Science.gov (United States)

Philibert, J.

1991-06-01

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

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.

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

Science.gov (United States)

2011-01-01

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

High-carbon chromium steel resistance to small plastic deformation

International Nuclear Information System (INIS)

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

1978-01-01

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

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

Science.gov (United States)

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

2015-07-01

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

Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction

Directory of Open Access Journals (Sweden)

Issei Nishimura

2017-07-01

Full Text Available Genome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics of growth and mutation. In the present study, we analyzed a small collection of W3110 Escherichia coli derivatives containing either the wild-type genome or reduced genomes of various lengths to examine whether the mutation rate, a global parameter representing genomic plasticity, was affected by genome reduction. We found that the mutation rates of these cells increased with genome reduction. The correlation between genome length and mutation rate, which has been reported for the evolution of bacteria, was also identified, intriguingly, for genome reduction. Gene function enrichment analysis indicated that the deletion of many of the genes encoding membrane and transport proteins play a role in the mutation rate changes mediated by genome reduction. Furthermore, the increase in the mutation rate with genome reduction was highly associated with a decrease in the growth rate in a nutrition-dependent manner; thus, poorer media showed a larger change that was of higher significance. This negative correlation was strongly supported by experimental evidence that the serial transfer of the reduced genome improved the growth rate and reduced the mutation rate to a large extent. Taken together, the global parameters corresponding to the genome, growth, and mutation showed a coordinated relationship, which might be an essential working principle for balancing the cellular dynamics appropriate to the environment.

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

Science.gov (United States)

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

2016-05-01

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

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.

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.

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

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

International Nuclear Information System (INIS)

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

1998-01-01

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

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...

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...

Genomic Islands: an overview of current software tools and future improvements

Directory of Open Access Journals (Sweden)

Soares Siomar de Castro

2016-03-01

Full Text Available Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.

Genomic Islands: an overview of current software tools and future improvements.

Science.gov (United States)

Soares, Siomar de Castro; Oliveira, Letícia de Castro; Jaiswal, Arun Kumar; Azevedo, Vasco

2016-03-01

Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth's biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.

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

The genomic signatures of Shigella evolution, adaptation and geographical spread.

Science.gov (United States)

The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

2016-04-01

Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.

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

Science.gov (United States)

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

2011-11-01

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

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Science.gov (United States)

Martino, Maria Elena; Bayjanov, Jumamurat R; Caffrey, Brian E; Wels, Michiel; Joncour, Pauline; Hughes, Sandrine; Gillet, Benjamin; Kleerebezem, Michiel; van Hijum, Sacha A F T; Leulier, François

2016-12-01

The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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

Directory of Open Access Journals (Sweden)

Mark Ravinet

2018-05-01

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

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

Science.gov (United States)

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

2018-05-01

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

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

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Varala Kranthi

2007-05-01

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

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

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

2017-11-01

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

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

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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.

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

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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.

Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

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Ana Carolina Vieira Araujo

2016-10-01

Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

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

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

2014-01-01

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

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

International Nuclear Information System (INIS)

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

1989-01-01

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

The yak genome and adaptation to life at high altitude

DEFF Research Database (Denmark)

Qiu, Qiang; Zhang, Guojie; Ma, Tao

2012-01-01

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

Bacterial production of the biodegradable plastics polyhydroxyalkanoates.

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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.

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

DEFF Research Database (Denmark)

Pedersen, Thomas Helmer; Conti, Federica

2017-01-01

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

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

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Claus, Robert; And Others

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

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

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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.

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)

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...

The loci controlling plasticity in flax

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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 

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

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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

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

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

2015-10-07

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

Optical Communication over Plastic Optical Fibers Integrated Optical Receiver Technology

CERN Document Server

Atef, Mohamed

2013-01-01

This book presents high-performance data transmission over plastic optical fibers (POF) using integrated optical receivers having good properties with multilevel modulation, i.e. a higher sensitivity and higher data rate transmission over a longer plastic optical fiber length. Integrated optical receivers and transmitters with high linearity are introduced for multilevel communication. For binary high-data rate transmission over plastic optical fibers, an innovative receiver containing an equalizer is described leading also to a high performance of a plastic optical fiber link. The cheap standard PMMA SI-POF (step-index plastic optical fiber) has the lowest bandwidth and the highest attenuation among multimode fibers. This small bandwidth limits the maximum data rate which can be transmitted through plastic optical fibers. To overcome the problem of the plastic optical fibers high transmission loss, very sensitive receivers must be used to increase the transmitted length over POF. The plastic optical fiber li...

Genomic characterization of recurrent high-grade astroblastoma.

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

2016-01-01

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

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

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Wenqin Wang

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

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

Science.gov (United States)

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

2013-12-01

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

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

Directory of Open Access Journals (Sweden)

Georgio eKfoury

2013-12-01

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

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

Science.gov (United States)

2017-04-01

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

Testing the effect of paraquat exposure on genomic recombination rates in queens of the western honey bee, Apis mellifera.

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Langberg, Kurt; Phillips, Matthew; Rueppell, Olav

2018-04-01

The rate of genomic recombination displays evolutionary plasticity and can even vary in response to environmental factors. The western honey bee (Apis mellifera L.) has an extremely high genomic recombination rate but the mechanistic basis for this genome-wide upregulation is not understood. Based on the hypothesis that meiotic recombination and DNA damage repair share common mechanisms in honey bees as in other organisms, we predicted that oxidative stress leads to an increase in recombination rate in honey bees. To test this prediction, we subjected honey bee queens to oxidative stress by paraquat injection and measured the rates of genomic recombination in select genome intervals of offspring produced before and after injection. The evaluation of 26 genome intervals in a total of over 1750 offspring of 11 queens by microsatellite genotyping revealed several significant effects but no overall evidence for a mechanistic link between oxidative stress and increased recombination was found. The results weaken the notion that DNA repair enzymes have a regulatory function in the high rate of meiotic recombination of honey bees, but they do not provide evidence against functional overlap between meiotic recombination and DNA damage repair in honey bees and more mechanistic studies are needed.

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

Science.gov (United States)

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

2017-11-03

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

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

Science.gov (United States)

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

2016-01-01

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

Review of the partitioning of chemicals into different plastics: Consequences for the risk assessment of marine plastic debris

International Nuclear Information System (INIS)

O'Connor, Isabel A.; Golsteijn, Laura; Hendriks, A. Jan

2016-01-01

Marine plastic debris are found worldwide in oceans and coastal areas. They degrade only slowly and contain chemicals added during manufacture or absorbed from the seawater. Therefore, they can pose a long-lasting contaminant source and potentially transfer chemicals to marine organisms when ingested. In order to assess their risk, the contaminant concentration in the plastics needs to be estimated and differences understood. We collected from literature plastic water partition coefficients of various organic chemicals for seven plastic types: polydimethylsiloxane (PDMS), high-density, low-density and ultra-high molecular weight polyethylene (LDPE, HDPE, UHMWPE), polystyrene (PS), polypropylene (PP), and polyvinyl chloride (PVC). Most data was available for PDMS (1060) and LDPE (220), but much less for the remaining plastics (73). Where possible, regression models were developed and the partitioning was compared between the different plastic types. The partitioning of chemicals follows the order of LDPE ≈ HDPE ≥ PP > PVC ≈ PS. Data describing the impact of weathering are urgently needed. - Highlights: • Comparison of organic chemicals partitioning into seven plastic types • Linear correlation between plastic-water partition coefficient K pw and K ow • More data is needed for polypropylene, polystyrene and polyvinyl chloride. • In all plastic types, most K pw were similar to/smaller than the corresponding K ow .

Plastic condoms.

Science.gov (United States)

1968-01-01

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

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.

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

Technology update on fast plastic scintillators for medical applications

International Nuclear Information System (INIS)

Lyons, P.B.

1977-01-01

Plastic scintillators appear to have potential utility in three research areas related to nuclear medicine: (1) high count rate applications in general, (2) positron camera applications, and (3) positron source localization through measurement of relative arrival times of annihilation quanta at two co-linear detectors. These three areas of applicability depend on improvement in three specific areas of plastic scintillator technology: (a) development of plastics with very fast decay times, (b) development of plastics with greatly improved high energy photon detection efficiencies (high-Z loaded plastics), and (c) improvement of fast timing system capabilities. The three preceding areas of improvement are discussed

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.

Seabirds, gyres and global trends in plastic pollution

International Nuclear Information System (INIS)

Franeker, Jan A. van; Law, Kara Lavender

2015-01-01

Fulmars are effective biological indicators of the abundance of floating plastic marine debris. Long-term data reveal high plastic abundance in the southern North Sea, gradually decreasing to the north at increasing distance from population centres, with lowest levels in high-arctic waters. Since the 1980s, pre-production plastic pellets in North Sea fulmars have decreased by ∼75%, while user plastics varied without a strong overall change. Similar trends were found in net-collected floating plastic debris in the North Atlantic subtropical gyre, with a ∼75% decrease in plastic pellets and no obvious trend in user plastic. The decreases in pellets suggest that changes in litter input are rapidly visible in the environment not only close to presumed sources, but also far from land. Floating plastic debris is rapidly “lost” from the ocean surface to other as-yet undetermined sinks in the marine environment. - Highlights: • Seabirds are effective biological monitors of floating plastic marine debris. • Plastics in fulmar stomachs and in the North Atlantic gyre show similar trends. • Pre-production plastic pellets show strong decreases in fulmars and in the gyre. • These data show that floating plastics rapidly disappear from the ocean surface. - Long term studies give evidence that reduced input of plastic debris into the ocean becomes rapidly visible. Floating plastics disappear to as-yet undetermined sinks

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

Science.gov (United States)

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

2013-09-01

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

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

Science.gov (United States)

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

2017-11-01

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

One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.

Science.gov (United States)

Mueller, Linda; Bertelli, Claire; Pillonel, Trestan; Salamin, Nicolas; Greub, Gilbert

2017-06-01

Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species.

Science.gov (United States)

Watanabe, Takayasu; Shibasaki, Masaki; Maruyama, Fumito; Sekizaki, Tsutomu; Nakagawa, Ichiro

2017-01-01

The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.

Seabirds, gyres and global trends in plastic pollution.

Science.gov (United States)

van Franeker, Jan A; Law, Kara Lavender

2015-08-01

Fulmars are effective biological indicators of the abundance of floating plastic marine debris. Long-term data reveal high plastic abundance in the southern North Sea, gradually decreasing to the north at increasing distance from population centres, with lowest levels in high-arctic waters. Since the 1980s, pre-production plastic pellets in North Sea fulmars have decreased by ∼75%, while user plastics varied without a strong overall change. Similar trends were found in net-collected floating plastic debris in the North Atlantic subtropical gyre, with a ∼75% decrease in plastic pellets and no obvious trend in user plastic. The decreases in pellets suggest that changes in litter input are rapidly visible in the environment not only close to presumed sources, but also far from land. Floating plastic debris is rapidly "lost" from the ocean surface to other as-yet undetermined sinks in the marine environment. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Marine microbe with potential to adhere and degrade plastic structures

Directory of Open Access Journals (Sweden)

Alka Kumari

2017-10-01

different plastics and dictates the need for the further studies on the underlying biological process. We planned to explore the genes encoding the enzymes involved in degradation of plastic through whole genome study and metabolic profiling to investigate any phenotypic changes [5]. Establishing microbial resources for the degradation of plastics is an ecofriendly approach which could be useful in reduction of its accumulation.

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.

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

Directory of Open Access Journals (Sweden)

Qianli Huang

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

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.

Validation of a Crystal Plasticity Model Using High Energy Diffraction Microscopy

Science.gov (United States)

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

2012-01-01

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

Plastic crystal phases of simple water models

International Nuclear Information System (INIS)

Aragones, J. L.; Vega, C.

2009-01-01

We report the appearance of two plastic crystal phases of water at high pressure and temperature using computer simulations. In one of them the oxygen atoms form a body centered cubic structure (bcc) and in the other they form a face centered cubic structure (fcc). In both cases the water molecules were able to rotate almost freely. We have found that the bcc plastic crystal transformed into a fcc plastic crystal via a Martensitic phase transition when heated at constant pressure. We have performed the characterization and localization in the phase diagram of these plastic crystal phases for the SPC/E, TIP4P, and TIP4P/2005 water potential models. For TIP4P/2005 model free energy calculations were carried out for the bcc plastic crystal and fcc plastic crystal using a new method (which is a slight variation of the Einstein crystal method) proposed for these types of solid. The initial coexistence points for the SPC/E and TIP4P models were obtained using Hamiltonian Gibbs–Duhem integration. For all of these models these two plastic crystal phases appear in the high pressure and temperature region of the phase diagram. It would be of interest to study if such plastic crystal phases do indeed exist for real water. This would shed some light on the question of whether these models can describe satisfactorily the high pressure part of the phase diagram of water, and if not, where and why they fail.

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

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

Science.gov (United States)

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

2017-11-16

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

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

Science.gov (United States)

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

2017-08-01

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

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

Science.gov (United States)

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

2012-10-01

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

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

The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics

Directory of Open Access Journals (Sweden)

Levasseur Anthony

2011-02-01

Full Text Available Abstract Understanding the evolutionary plasticity of the genome requires a global, comparative approach in which genetic events are considered both in a phylogenetic framework and with regard to population genetics and environmental variables. In the mechanisms that generate adaptive and non-adaptive changes in genomes, segmental duplications (duplication of individual genes or genomic regions and polyploidization (whole genome duplications are well-known driving forces. The probability of fixation and maintenance of duplicates depends on many variables, including population sizes and selection regimes experienced by the corresponding genes: a combination of stochastic and adaptive mechanisms has shaped all genomes. A survey of experimental work shows that the distinction made between fixation and maintenance of duplicates still needs to be conceptualized and mathematically modeled. Here we review the mechanisms that increase or decrease the probability of fixation or maintenance of duplicated genes, and examine the outcome of these events on the adaptation of the organisms. Reviewers This article was reviewed by Dr. Etienne Joly, Dr. Lutz Walter and Dr. W. Ford Doolittle.

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

Directory of Open Access Journals (Sweden)

Yingqin Luo

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

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

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.

Genomics of Aspergillus oryzae: Learning from the History of Koji Mold and Exploration of Its Future

Science.gov (United States)

Machida, Masayuki; Yamada, Osamu; Gomi, Katsuya

2008-01-01

At a time when the notion of microorganisms did not exist, our ancestors empirically established methods for the production of various fermentation foods: miso (bean curd seasoning) and shoyu (soy sauce), both of which have been widely used and are essential for Japanese cooking, and sake, a magical alcoholic drink consumed at a variety of ritual occasions, are typical examples. A filamentous fungus, Aspergillus oryzae, is the key organism in the production of all these traditional foods, and its solid-state cultivation (SSC) has been confirmed to be the secret for the high productivity of secretory hydrolases vital for the fermentation process. Indeed, our genome comparison and transcriptome analysis uncovered mechanisms for effective degradation of raw materials in SSC: the extracellular hydrolase genes that have been found only in the A. oryzae genome but not in A. fumigatus are highly induced during SSC but not in liquid cultivation. Also, the temperature reduction process empirically adopted in the traditional soy-sauce fermentation processes has been found to be important to keep strong expression of the A. oryzae-specific extracellular hydrolases. One of the prominent potentials of A. oryzae is that it has been successfully applied to effective degradation of biodegradable plastic. Both cutinase, responsible for the degradation of plastic, and hydrophobin, which recruits cutinase on the hydrophobic surface to enhance degradation, have been discovered in A. oryzae. Genomic analysis in concert with traditional knowledge and technology will continue to be powerful tools in the future exploration of A. oryzae. PMID:18820080

Recent advances in high performance poly(lactide): from “green” plasticization to super-tough materials via (reactive) compounding

Science.gov (United States)

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

2013-01-01

Due to its origin from renewable resources, its biodegradability, and recently, its industrial implementation at low costs, poly(lactide) (PLA) is considered as one of the most promising ecological, bio-sourced and biodegradable plastic materials to potentially and increasingly replace traditional petroleum derived polymers in many commodity and engineering applications. Beside its relatively high rigidity [high tensile strength and modulus compared with many common thermoplastics such as poly(ethylene terephthalate) (PET), high impact poly(styrene) (HIPS) and poly(propylene) (PP)], PLA suffers from an inherent brittleness, which can limit its applications especially where mechanical toughness such as plastic deformation at high impact rates or elongation is required. Therefore, the curve plotting stiffness vs. impact resistance and ductility must be shifted to higher values for PLA-based materials, while being preferably fully bio-based and biodegradable upon the application. This review aims to establish a state of the art focused on the recent progresses and preferably economically viable strategies developed in the literature for significantly improve the mechanical performances of PLA. A particular attention is given to plasticization as well as to impact resistance modification of PLA in the case of (reactive) blending PLA-based systems. PMID:24790960

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

Science.gov (United States)

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

2017-07-01

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

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

Science.gov (United States)

Shukla, Avi; Chatterjee, Anirvan

2018-01-01

Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

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

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

International Nuclear Information System (INIS)

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

1987-01-01

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

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.

Charge carrier dynamics in PMMA-LiClO4 based polymer electrolytes plasticized with different plasticizers

Science.gov (United States)

Pal, P.; Ghosh, A.

2017-07-01

We have studied the charge carrier dynamics in poly(methylmethacrylate)-LiClO4 polymer electrolytes plasticized with different plasticizers such as ethylene carbonate (EC), propylene carbonate (PC), polyethylene glycol (PEG), and dimethyl carbonate (DMC). We have measured the broadband complex conductivity spectra of these electrolytes in the frequency range of 0.01 Hz-3 GHz and in the temperature range of 203 K-363 K and analyzed the conductivity spectra in the framework of the random barrier model by taking into account the contribution of the electrode polarization observed at low frequencies and/or at high temperatures. It is observed that the temperature dependences of the ionic conductivity and relaxation time follow the Vogel-Tammann-Fulcher relation for all plasticized electrolytes. We have also performed the scaling of the conductivity spectra, which indicates that the charge carrier dynamics is almost independent of temperature and plasticizers in a limited frequency range. The existence of nearly constant loss in these electrolytes has been observed at low temperatures and/or high frequencies. We have studied the dielectric relaxation in these electrolytes using electric modulus formalism and obtained the stretched exponent and the decay function. We have observed less cooperative ion dynamics in electrolytes plasticized with DMC compared to electrolytes plasticized with EC, PC, and PEG.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

Science.gov (United States)

Cook, Deborah H.

2014-01-01

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

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....

Moving through the stressed genome: Emerging regulatory roles for transposons in plant stress tolerance

Directory of Open Access Journals (Sweden)

Negi Pooja

2016-10-01

Full Text Available The recognition of a positive correlation between organism genome size with its transposable element (TE content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock’s original ’Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences which project TEs as distributed genomic control modules. According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution and function, and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response.

Science.gov (United States)

Negi, Pooja; Rai, Archana N; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

Science.gov (United States)

Negi, Pooja; Rai, Archana N.; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement. PMID:27777577

Plastic accumulation in the Mediterranean sea.

Directory of Open Access Journals (Sweden)

Andrés Cózar

Full Text Available 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 millimeter-sized fragments, but showed a higher proportion of large plastic objects than that present in oceanic gyres, reflecting the closer connection with pollution sources. The accumulation of floating plastic in the Mediterranean Sea (between 1,000 and 3,000 tons is likely related to the high human pressure together with the hydrodynamics of this semi-enclosed basin, with outflow mainly occurring through a deep water layer. Given the biological richness and concentration of economic activities in the Mediterranean Sea, the affects of plastic pollution on marine and human life are expected to be particularly frequent in this plastic accumulation region.

Plastic Accumulation in the Mediterranean Sea

KAUST Repository

Có zar, André s; Sanz-Martí n, Marina; Martí , Elisa; Gonzá lez-Gordillo, J. Ignacio; Ubeda, Bá rbara; Gá lvez, José Á .; Irigoien, Xabier; Duarte, Carlos M.

2015-01-01

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 millimeter-sized fragments, but showed a higher proportion of large plastic objects than that present in oceanic gyres, reflecting the closer connection with pollution sources. The accumulation of floating plastic in the Mediterranean Sea (between 1,000 and 3,000 tons) is likely related to the high human pressure together with the hydrodynamics of this semi-enclosed basin, with outflow mainly occurring through a deep water layer. Given the biological richness and concentration of economic activities in the Mediterranean Sea, the affects of plastic pollution on marine and human life are expected to be particularly frequent in this plastic accumulation region.

Nano-plastics in the aquatic environment.

Science.gov (United States)

Mattsson, K; Hansson, L-A; Cedervall, T

2015-10-01

The amount of plastics released to the environment in modern days has increased substantially since the development of modern plastics in the early 1900s. As a result, concerns have been raised by the public about the impact of plastics on nature and on, specifically, aquatic wildlife. Lately, much attention has been paid to macro- and micro-sized plastics and their impact on aquatic organisms. However, micro-sized plastics degrade subsequently into nano-sizes whereas nano-sized particles may be released directly into nature. Such particles have a different impact on aquatic organisms than larger pieces of plastic due to their small size, high surface curvature, and large surface area. This review describes the possible sources of nano-sized plastic, its distribution and behavior in nature, the impact of nano-sized plastic on the well-being of aquatic organisms, and the difference of impact between nano- and micro-sized particles. We also identify research areas which urgently need more attention and suggest experimental methods to obtain useful data.

Plastic Accumulation in the Mediterranean Sea

KAUST Repository

Cózar, Andrés

2015-04-01

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 millimeter-sized fragments, but showed a higher proportion of large plastic objects than that present in oceanic gyres, reflecting the closer connection with pollution sources. The accumulation of floating plastic in the Mediterranean Sea (between 1,000 and 3,000 tons) is likely related to the high human pressure together with the hydrodynamics of this semi-enclosed basin, with outflow mainly occurring through a deep water layer. Given the biological richness and concentration of economic activities in the Mediterranean Sea, the affects of plastic pollution on marine and human life are expected to be particularly frequent in this plastic accumulation region.

Plastic accumulation in the Mediterranean sea.

Science.gov (United States)

Cózar, Andrés; Sanz-Martín, Marina; Martí, Elisa; González-Gordillo, J Ignacio; Ubeda, Bárbara; Gálvez, José Á; Irigoien, Xabier; Duarte, Carlos M

2015-01-01

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 millimeter-sized fragments, but showed a higher proportion of large plastic objects than that present in oceanic gyres, reflecting the closer connection with pollution sources. The accumulation of floating plastic in the Mediterranean Sea (between 1,000 and 3,000 tons) is likely related to the high human pressure together with the hydrodynamics of this semi-enclosed basin, with outflow mainly occurring through a deep water layer. Given the biological richness and concentration of economic activities in the Mediterranean Sea, the affects of plastic pollution on marine and human life are expected to be particularly frequent in this plastic accumulation region.

Plastic Accumulation in the Mediterranean Sea

Science.gov (United States)

Cózar, Andrés; Sanz-Martín, Marina; Martí, Elisa; González-Gordillo, J. Ignacio; Ubeda, Bárbara; Gálvez, José Á.; Irigoien, Xabier; Duarte, Carlos M.

2015-01-01

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 millimeter-sized fragments, but showed a higher proportion of large plastic objects than that present in oceanic gyres, reflecting the closer connection with pollution sources. The accumulation of floating plastic in the Mediterranean Sea (between 1,000 and 3,000 tons) is likely related to the high human pressure together with the hydrodynamics of this semi-enclosed basin, with outflow mainly occurring through a deep water layer. Given the biological richness and concentration of economic activities in the Mediterranean Sea, the affects of plastic pollution on marine and human life are expected to be particularly frequent in this plastic accumulation region. PMID:25831129

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.

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.

Clay membrane made of natural high plasticity clay

DEFF Research Database (Denmark)

Foged, Niels; Baumann, Jens

1998-01-01

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

Clay membrane made of natural high plasticity clay:

DEFF Research Database (Denmark)

Foged, Niels; Baumann, Jens

1999-01-01

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

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

Science.gov (United States)

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

2015-01-01

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

Plastic and Non-plastic Debris Ingestion in Three Gull Species Feeding in an Urban Landfill Environment.

Science.gov (United States)

Seif, S; Provencher, J F; Avery-Gomm, S; Daoust, P-Y; Mallory, M L; Smith, P A

2018-04-01

Plastic debris is recognized as a widespread, common and problematic environmental pollutant. An important consequence of this pollution is the ingestion of plastic debris by wildlife. Assessing the degree to which different species ingest plastics, and the potential effects of these plastics on their health are important research needs for understanding the impacts of plastic pollution. We examined debris (plastic and other types) ingestion in three sympatric overwintering gull species (Herring gulls Larus smithsonianus, Great Black-backed Gulls Larus marinus, and Iceland Gulls Larus glaucoides) to understand how debris ingestion differs among species, age classes and sexes in gulls. We also assessed how plastic burdens were associated with body condition to investigate how gulls may be affected by debris ingestion. There were no differences among the species, age classes or sexes in the incidence of debris ingestion (plastic or otherwise), the mass or number of debris pieces ingested. We found no correlation between ingested plastics burdens and individual condition. Gulls ingested plastic debris, but also showed high levels of other debris types as well, including metal, glass and building materials, including a metal piece of debris found within an abscess in the stomach. Thus, when the health effects of debris ingestion on gulls, and other species that ingest debris, is of interest, either from a physical or chemical perspective, it may be necessary to consider all debris types and not just plastic burdens as is often currently done for seabirds.

The neurophysiologist perspective into MS plasticity

Directory of Open Access Journals (Sweden)

Elise eHoudayer

2015-09-01

Full Text Available Multiple sclerosis (MS is a frequent, highly debilitating inflammatory demyelinating disease, starting to manifest in early adulthood and presenting a wide variety of symptoms which are often resistant to pharmacological treatments. Cortical dysfunctions have been demonstrated to be key components of MS condition, and plasticity of the corticospinal motor system is highly involved in major MS symptoms, such as fatigue, spasticity or pain. Cortical dysfunction in MS can be studied with neurophysiological tools such as electroencephalography (EEG and related techniques (evoked potentials – EPs or transcranial magnetic stimulation (TMS. These techniques are now widely used to provide essential elements of MS diagnosis and can also be used to modulate plasticity. Indeed the recent development of non-invasive brain stimulation (NIBS techniques able to induce cortical plasticity, such as repetitive TMS or transcranial direct current stimulation (tDCS, has brought promising results as add-on treatments.In this review we will focus on the use of these tools (EEG, TMS to study plasticity in MS and on the major techniques used to modulate plasticity in MS.

The Neurophysiologist Perspective into MS Plasticity.

Science.gov (United States)

Houdayer, Elise; Comi, Giancarlo; Leocani, Letizia

2015-01-01

Multiple sclerosis (MS) is a frequent, highly debilitating inflammatory demyelinating disease, starting to manifest in early adulthood and presenting a wide variety of symptoms, which are often resistant to pharmacological treatments. Cortical dysfunctions have been demonstrated to be key components of MS condition, and plasticity of the corticospinal motor system is highly involved in major MS symptoms, such as fatigue, spasticity, or pain. Cortical dysfunction in MS can be studied with neurophysiological tools, such as electroencephalography (EEG) and related techniques (evoked potentials) or transcranial magnetic stimulation (TMS). These techniques are now widely used to provide essential elements of MS diagnosis and can also be used to modulate plasticity. Indeed, the recent development of non-invasive brain stimulation techniques able to induce cortical plasticity, such as repetitive TMS or transcranial direct current stimulation, has brought promising results as add-on treatments. In this review, we will focus on the use of these tools (EEG and TMS) to study plasticity in MS and on the major techniques used to modulate plasticity in MS.

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

Science.gov (United States)

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

2016-01-06

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

Genome variations associated with viral susceptibility and calcification in Emiliania huxleyi.

Science.gov (United States)

Kegel, Jessica U; John, Uwe; Valentin, Klaus; Frickenhaus, Stephan

2013-01-01

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.

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.

High throughput platforms for structural genomics of integral membrane proteins.

Science.gov (United States)

Mancia, Filippo; Love, James

2011-08-01

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

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

Directory of Open Access Journals (Sweden)

Gounder Kamini

2011-11-01

of an oligotrophic lifestyle. Conclusions The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.

Whole-genome sequencing of a laboratory-evolved yeast strain

Directory of Open Access Journals (Sweden)

Dunham Maitreya J

2010-02-01

Full Text Available Abstract Background Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale. New DNA sequencing technologies now allow the genome of parental and evolved strains of microorganisms to be rapidly determined. Results We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast Saccharomyces cerevisiae and its ancestor at >28× depth. Both single nucleotide polymorphisms and copy number amplifications were found, with specific gains over array-based methodologies previously used to analyze these genomes. Applying a segmentation algorithm to quantify structural changes, we determined the approximate genomic boundaries of a 5× gene amplification. These boundaries guided the recovery of breakpoint sequences, which provide insights into the nature of a complex genomic rearrangement. Conclusions This study suggests that whole-genome sequencing can provide a rapid approach to uncover the genetic basis of evolutionary adaptations, with further applications in the study of laboratory selections and mutagenesis screens. In addition, we show how single-end, short read sequencing data can provide detailed information about structural rearrangements, and generate predictions about the genomic features and processes that underlie genome plasticity.

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.

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

Science.gov (United States)

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

2015-07-01

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

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

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Yandell Mark

2010-07-01

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

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

Science.gov (United States)

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

2009-07-10

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

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

International Nuclear Information System (INIS)

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

2002-01-01

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

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.

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

OpenAIRE

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

2012-01-01

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

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

Science.gov (United States)

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

2017-03-31

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

Extruded plastic scintillator for MINERvA

International Nuclear Information System (INIS)

Pla-Dalmau, Anna; Bross, Alan D.; FermilabRykalin, Victor V.; Wood, Brian M.; NICADD, DeKalb

2005-01-01

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. 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. The D0 and MINOS experiments are already using extruded scintillator strips in their detectors. A new experiment at Fermilab is pursuing the use of extruded plastic scintillator. A new plastic scintillator strip is being tested and its properties characterized. The initial results are presented here

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

Science.gov (United States)

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

2015-06-01

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

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

Collapse Scenarios of High-Rise Buildings Using Plastic Limit Analysis

Directory of Open Access Journals (Sweden)

G. Liu

2009-01-01

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

Mechanical Properties of High Performance Concrete Containing Waste Plastic as Aggregate

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Abdulkader Ismail Al-Hadithi

2015-08-01

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

Seabirds, gyres and global trends in plastic pollution

NARCIS (Netherlands)

Franeker, van J.A.; Law, K.L.

2015-01-01

Fulmars are effective biological indicators of the abundance of floating plastic marine debris. Long-term data reveal high plastic abundance in the southern North Sea, gradually decreasing to the north at increasing distance from population centres, with lowest levels in high-arctic waters. Since

Amphibious fishes: evolution and phenotypic plasticity.

Science.gov (United States)

Wright, Patricia A; Turko, Andy J

2016-08-01

Amphibious fishes spend part of their life in terrestrial habitats. The ability to tolerate life on land has evolved independently many times, with more than 200 extant species of amphibious fishes spanning 17 orders now reported. Many adaptations for life out of water have been described in the literature, and adaptive phenotypic plasticity may play an equally important role in promoting favourable matches between the terrestrial habitat and behavioural, physiological, biochemical and morphological characteristics. Amphibious fishes living at the interface of two very different environments must respond to issues relating to buoyancy/gravity, hydration/desiccation, low/high O2 availability, low/high CO2 accumulation and high/low NH3 solubility each time they traverse the air-water interface. Here, we review the literature for examples of plastic traits associated with the response to each of these challenges. Because there is evidence that phenotypic plasticity can facilitate the evolution of fixed traits in general, we summarize the types of investigations needed to more fully determine whether plasticity in extant amphibious fishes can provide indications of the strategies used during the evolution of terrestriality in tetrapods. © 2016. Published by The Company of Biologists Ltd.

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

Science.gov (United States)

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

2018-01-01

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

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

OpenAIRE

Aljanabi, S M; Martinez, I

1997-01-01

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

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

Science.gov (United States)

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

2013-09-01

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

A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

Directory of Open Access Journals (Sweden)

Myburg Alexander A

2010-06-01

Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

Science.gov (United States)

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

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

Directory of Open Access Journals (Sweden)

Michelle Hawkins

2013-11-01

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

The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

Science.gov (United States)

Sakai, Hiroaki; Naito, Ken; Takahashi, Yu; Sato, Toshiyuki; Yamamoto, Toshiya; Muto, Isamu; Itoh, Takeshi; Tomooka, Norihiko

2016-01-01

The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Phyllosphere yeasts rapidly break down biodegradable plastics

OpenAIRE

Kitamoto, Hiroko K; Shinozaki, Yukiko; Cao, Xiao-hong; Morita, Tomotake; Konishi, Masaaki; Tago, Kanako; Kajiwara, Hideyuki; Koitabashi, Motoo; Yoshida, Shigenobu; Watanabe, Takashi; Sameshima-Yamashita, Yuka; Nakajima-Kambe, Toshiaki; Tsushima, Seiya

2011-01-01

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily ...

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

International Nuclear Information System (INIS)

Anantha Ramu, S.

1981-01-01

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

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.

Directory of Open Access Journals (Sweden)

Kamila Maliszewska-Olejniczak

2015-07-01

Full Text Available Because of their nuclear dimorphism, ciliates provide a unique opportunity to study the role of non-coding RNAs (ncRNAs in the communication between germline and somatic lineages. In these unicellular eukaryotes, a new somatic nucleus develops at each sexual cycle from a copy of the zygotic (germline nucleus, while the old somatic nucleus degenerates. In the ciliate Paramecium tetraurelia, the genome is massively rearranged during this process through the reproducible elimination of repeated sequences and the precise excision of over 45,000 short, single-copy Internal Eliminated Sequences (IESs. Different types of ncRNAs resulting from genome-wide transcription were shown to be involved in the epigenetic regulation of genome rearrangements. To understand how ncRNAs are produced from the entire genome, we have focused on a homolog of the TFIIS elongation factor, which regulates RNA polymerase II transcriptional pausing. Six TFIIS-paralogs, representing four distinct families, can be found in P. tetraurelia genome. Using RNA interference, we showed that TFIIS4, which encodes a development-specific TFIIS protein, is essential for the formation of a functional somatic genome. Molecular analyses and high-throughput DNA sequencing upon TFIIS4 RNAi demonstrated that TFIIS4 is involved in all kinds of genome rearrangements, including excision of ~48% of IESs. Localization of a GFP-TFIIS4 fusion revealed that TFIIS4 appears specifically in the new somatic nucleus at an early developmental stage, before IES excision. RT-PCR experiments showed that TFIIS4 is necessary for the synthesis of IES-containing non-coding transcripts. We propose that these IES+ transcripts originate from the developing somatic nucleus and serve as pairing substrates for germline-specific short RNAs that target elimination of their homologous sequences. Our study, therefore, connects the onset of zygotic non coding transcription to the control of genome plasticity in Paramecium

Stress Wave Propagation in Viscoelastic-Plastic Rock-Like Materials

Directory of Open Access Journals (Sweden)

Liu Lang

2016-05-01

Full Text Available Rock-like materials are composites that can be regarded as a mixture composed of elastic, plastic, and viscous components. They exhibit viscoelastic-plastic behavior under a high-strain-rate loading according to element model theory. This paper presents an analytical solution for stress wave propagation in viscoelastic-plastic rock-like materials under a high-strain-rate loading and verifies the solution through an experimental test. A constitutive equation of viscoelastic-plastic rock-like materials was first established, and then kinematic and kinetic equations were then solved to derive the analytic solution for stress wave propagation in viscoelastic-plastic rock-like materials. An experimental test using the SHPB (Split Hopkinson Pressure Bar for a concrete specimen was conducted to obtain a stress-strain curve under a high-strain-rate loading. Inverse analysis based on differential evolution was conducted to estimate undetermined variables for constitutive equations. Finally, the relationship between the attenuation factor and the strain rate in viscoelastic-plastic rock-like materials was investigated. According to the results, the frequency of the stress wave, viscosity coefficient, modulus of elasticity, and density play dominant roles in the attenuation of the stress wave. The attenuation decreases with increasing strain rate, demonstrating strongly strain-dependent attenuation in viscoelastic-plastic rock-like materials.

Replacing fossil based plastic performance products by bio-based plastic products-Technical feasibility.

Science.gov (United States)

van den Oever, Martien; Molenveld, Karin

2017-07-25

Larger scale market introduction of new bio-based products requires a clear advantage regarding sustainability, as well as an adequate techno-economic positioning relative to fossil based products. In a previous paper [Broeren et al., 2016], LCA results per kg and per functionality equivalent of bio-based plastics were presented, together with economic considerations. The present paper discusses the mechanical and thermal properties of a range of commercially available bio-based plastics based on polylactic acid (PLA), cellulose esters, starch and polyamides, and the feasibility of replacing fossil-based counterparts based on performance. The evaluation is approached from an end user perspective. First, potentially suitable bio-based plastics are selected based on manufacturers' specifications in technical data sheets, then a first experimental evaluation is performed on injection moulded ISO specimens, and finally a further selection of plastics is tested on large 50×70cm panels. This technical feasibility study indicates that so far bio-based plastics do not completely match the properties of high performance materials like flame retardant V-0 PC/ABS blends used in electronic devices. The performance gap is being decreased by the development of stereocomplex PLA and hybrid PLA blends with polycarbonate, which offer clearly improved properties with respect to maximum usage temperature and toughness. In addition, several materials meet the V-0 flammability requirements needed in specific durable applications. On the other hand, improving these properties so far has negative consequences for the bio-based content. This study also shows that replacement of bulk polymers like PS is feasible using PLA compounds with a bio-based content as high as 85%. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Directory of Open Access Journals (Sweden)

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

2014-12-01

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

The plastic-associated microorganisms of the North Pacific Gyre

International Nuclear Information System (INIS)

Carson, Henry S.; Nerheim, Magnus S.; Carroll, Katherine A.; Eriksen, Marcus

2013-01-01

Highlights: • Microorganisms mediate processes affecting the fate and impacts of marine plastic. • North Pacific Gyre (NPG) plastics were examined with scanning-electron microscopy. • Bacillus bacteria and pennate diatoms dominated the NPG plastic fouling community. • Bacterial abundance was patchily distributed but increased on foamed polystyrene. • Diatom abundance increased on rough surfaces and at sites with high plastic density. -- Abstract: Microorganisms likely mediate processes affecting the fate and impacts of marine plastic pollution, including degradation, chemical adsorption, and colonization or ingestion by macroorganisms. We investigated the relationship between plastic-associated microorganism communities and factors such as location, temperature, salinity, plankton abundance, plastic concentration, item size, surface roughness, and polymer type. Small plastic items from the surface of the North Pacific Gyre in 2011 were examined using scanning electron microscopy. Bacillus bacteria (mean 1664 ± 247 individuals mm −2 ) and pennate diatoms (1097 ± 154 mm −2 ) were most abundant, with coccoid bacteria, centric diatoms, dinoflagellates, coccolithophores, and radiolarians present. Bacterial abundance was patchy, but increased on foamed polystyrene. Diatom abundance increased on items with rough surfaces and at sites with high plastic concentrations. Morphotype richness increased slightly on larger fragments, and a biogeographic transition occurred between pennate diatom groups. Better characterizing this community will aid in understanding how it interacts with plastic pollution

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

Science.gov (United States)

2013-01-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Preparation of plastic-cellulose compounds by high energy gamma radiation

International Nuclear Information System (INIS)

Rosa, M.C.F.

1978-01-01

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

Plastic surgery and global health: how plastic surgery impacts the global burden of surgical disease.

Science.gov (United States)

Semer, Nadine B; Sullivan, Stephen R; Meara, John G

2010-08-01

The global burden of surgical disease is estimated as being 11% of the total global burden of disease. In this article we discuss the portion of this burden which could be ameliorated with plastic surgical expertise. Although not necessarily seen as a major player in issues related to global health, plastic surgeons are uniquely qualified to decrease the burden of surgical disease afflicting people in the developing world. Burns, traumatic injuries, and congenital anomalies are some of the areas where the presence of plastic surgical expertise can make a significant difference in patient outcomes and thereby decrease the years of life lost due to disability due to these highly treatable conditions. In light of the severe shortage of plastic surgeons throughout the developing world, it falls to those concentrated in the developed world to harness their skills and address the vast unmet needs of the developing world so as to enhance global health. Copyright 2009 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

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

Science.gov (United States)

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

2013-03-01

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

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 " ...

Particle fracture and plastic deformation in vanadium pentoxide

Indian Academy of Sciences (India)

Particle fracture and plastic deformation in vanadium pentoxide powders induced by high energy vibrational ball-mill ... Keywords. X-ray diffraction; ball-milling; plastic deformation; microstrain. ... Bulletin of Materials Science | News.

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.)

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

International Nuclear Information System (INIS)

Chong Chon Sing

1995-01-01

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

Doped polymer electrodes for high performance ferroelectric capacitors on plastic substrates

KAUST Repository

Khan, M. A.

2012-10-03

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

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

NARCIS (Netherlands)

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

2015-01-01

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

Roles of the plasticity regions of Helicobacter pylori in gastroduodenal pathogenesis.

Science.gov (United States)

Yamaoka, Yoshio

2008-05-01

Putative virulence genes of Helicobacter pylori are generally classified into three categories: strain-specific genes, phase-variable genes and genes with variable structures/genotypes. Among these, there has recently been considerable interest in strain-specific genes found outside of the cag pathogenicity island, especially genes in the plasticity regions. Nearly half of the strain-specific genes of H. pylori are located in the plasticity regions in strains 26695 and J99. Strain HPAG1, however, seems to lack a typical plasticity region; instead it has 43 HPAG1-specific genes which are either undetectable or incompletely represented in the genomes of strains 26695 and J99. Recent studies showed that certain genes or combination of genes in this region may play important roles in the pathogenesis of H. pylori-associated gastroduodenal diseases. Most previous studies have focused on the plasticity region in strain J99 (jhp0914-jhp0961) and the jhp0947 gene and the duodenal ulcer promoting (dupA) gene are good candidate markers for gastroduodenal diseases although there are some paradoxical findings. The jhp0947 gene is reported to be associated with an increased risk of both duodenal ulcers and gastric cancers, whereas the dupA gene, which encompasses jhp0917 and jhp0918, is reported to be associated with an increased risk of duodenal ulcers and protection against gastric cancers. In addition, recent studies showed that approximately 10-30 % of clinical isolates possess a 16.3 kb type IV secretion apparatus (tfs3) in the plasticity region. Studies on the plasticity region have only just begun, and further investigation is necessary to elucidate the roles of genes in this region in gastroduodenal pathogenesis.

Comparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence.

Science.gov (United States)

Lu, Wei; Wise, Michael J; Tay, Chin Yen; Windsor, Helen M; Marshall, Barry J; Peacock, Christopher; Perkins, Tim

2014-03-01

Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (∼170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-07-01

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

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

International Nuclear Information System (INIS)

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

2011-01-01

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

A complete life cycle assessment of high density polyethylene plastic bottle

Science.gov (United States)

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

2017-07-01

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

Tracking plastics in the Mediterranean: 2D Lagrangian model.

Science.gov (United States)

Liubartseva, S; Coppini, G; Lecci, R; Clementi, E

2018-04-01

Drift of floating debris is studied with a 2D Lagrangian model with stochastic beaching and sedimentation of plastics. An ensemble of >10 10 virtual particles is tracked from anthropogenic sources (coastal human populations, rivers, shipping lanes) to environmental destinations (sea surface, coastlines, seabed). Daily analyses of ocean currents and waves provided by CMEMS at a horizontal resolution of 1/16° are used to force the plastics. High spatio-temporal variability in sea-surface plastic concentrations without any stable long-term accumulations is found. Substantial accumulation of plastics is detected on coastlines and the sea bottom. The most contaminated areas are in the Cilician subbasin, Catalan Sea, and near the Po River Delta. Also, highly polluted local patches in the vicinity of sources with limited circulation are identified. An inverse problem solution, used to quantify the origins of plastics, shows that plastic pollution of every Mediterranean country is caused primarily by its own terrestrial sources. Copyright © 2018 Elsevier Ltd. All rights reserved.

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.

2018-05-24

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.; Neelamegam, Sivakumar; Arslan, Muhammad; Saleem, Hamna; Alqarawi, Sami

2018-01-01

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Effect of HDPE plastic waste towards batako properties

Science.gov (United States)

Nursyamsi, N.; Indrawan, I.; Theresa, V.

2018-02-01

Indonesia is the world’s second largest producer of plastic waste to the sea, after China. Most of the plastic waste is polyethylene. Polyethylene is a polymer consisting of long chains of ethylene monomers. Moreover, polyethylene is plastic that has characteristics such as; thermoplastic, elastic, non-translucent, odorless, slightly opaque and transparent, resistant to impact and has a resistance of up to 135 degrees Celsius. The type of HDPE plastic (high-density polyethylene), which has been cleaned and chopped as a substitute of fine aggregate, is used in the brick’s making process. HDPE has a stronger, harder, smoother and more resistant to high-temperature properties. In this study, a weight variation of 0%, 10%, and 20% of HDPE plastic wastes was used from the total weight of sand as a substitution. Furthermore, the tensile and compressive strength were tested on day 7. Based on the research, the quality of the specimen achieved was categorized in quality III according to SNI 03-0349-1989.

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

Science.gov (United States)

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

2009-07-01

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

Karyotype Variability and Inter-Population Genomic Differences in Freshwater Ostracods (Crustacea Showing Geographical Parthenogenesis

Directory of Open Access Journals (Sweden)

Radka Symonová

2018-03-01

Full Text Available Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820, where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed. Hence, we employed comparative genomic hybridization (CGH within and among sexual and asexual populations to get insights into E. virens genome arrangements. CGH disclosed substantial genomic imbalances among the populations analyzed, and three patterns of genome arrangement between these populations: 1. Only putative ribosomal DNA (rDNA-bearing regions were conserved in the two populations compared indicating a high sequence divergence between these populations. This pattern is comparable with our findings at the interspecies level of comparison; 2. Chromosomal regions were shared by both populations to a varying extent with a distinct copy number variation in pericentromeric and presumable rDNA-bearing regions. This indicates a different rate of evolution in repetitive sequences; 3. A mosaic pattern of distribution of genomic material that can be explained as non-reciprocal genetic introgression and evidence of a hybrid origin of these individuals. We show an overall increased chromosomal dynamics in E. virens that is complementary with available phylogenetic and population genetic data reporting highly differentiated diploid sexual and asexual lineages with a wide variety of genetic backgrounds.

Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment

Directory of Open Access Journals (Sweden)

Manuela Silva

2012-07-01

Full Text Available The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization.

All-natural bio-plastics using starch-betaglucan composites.

Science.gov (United States)

Sagnelli, Domenico; Kirkensgaard, Jacob J K; Giosafatto, Concetta Valeria L; Ogrodowicz, Natalia; Kruczała, Krzysztof; Mikkelsen, Mette S; Maigret, Jean-Eudes; Lourdin, Denis; Mortensen, Kell; Blennow, Andreas

2017-09-15

Grain polysaccharides represent potential valuable raw materials for next-generation advanced and environmentally friendly plastics. Thermoplastic starch (TPS) is processed using conventional plastic technology, such as casting, extrusion, and molding. However, to adapt the starch to specific functionalities chemical modifications or blending with synthetic polymers, such as polycaprolactone are required (e.g. Mater-Bi). As an alternative, all-natural and compostable bio-plastics can be produced by blending starch with other polysaccharides. In this study, we used a maize starch (ST) and an oat β-glucan (BG) composite system to produce bio-plastic prototype films. To optimize performing conditions, we investigated the full range of ST:BG ratios for the casting (100:0, 75:25, 50:50, 25:75 and 0:100 BG). The plasticizer used was glycerol. Electron Paramagnetic Resonance (EPR), using TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) as a spin probe, showed that the composite films with high BG content had a flexible chemical environment. They showed decreased brittleness and improved cohesiveness with high stress and strain values at the break. Wide-angle X-ray diffraction displayed a decrease in crystallinity at high BG content. Our data show that the blending of starch with other natural polysaccharides is a noteworthy path to improve the functionality of all-natural polysaccharide bio-plastics systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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) ...

High-resolution characterization of a hepatocellular carcinoma genome.

Science.gov (United States)

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

2011-05-01

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

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

Science.gov (United States)

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

2017-07-01

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

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

Science.gov (United States)

Domagała-Świątkiewicz, Iwona; Siwek, Piotr

2018-01-01

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

Physico-chemical modifications of plastics by ionization

International Nuclear Information System (INIS)

Rouif, S.

2002-01-01

The industrial use of ionizing radiations (beta and gamma), initially for the sterilization of medico-surgical instruments and for the preservation of food products, has led to the development of the chemistry of polymers under radiations. Ionizing radiations can initiate chemical reactions (chain cutting, poly-additions, polymerization etc..) thanks to the formation of free radicals. The main applications concerns the degradation of plastics, the reticulation of plastics and of woods impregnated with resin, and the grafting of polymers. The processing of plastic materials was initially performed with low energy electron accelerators (0.1 to 3 MeV), allowing only surface treatments, while recent high energy accelerators (10 MeV) and gamma facilities allow the treatment in depth of materials (from few cm to 1 m). This article describes the industrial treatments performed with such high energy facilities: 1 - action of ionizing radiations on plastic materials: different types of ionizing radiations, action of beta and gamma radiations, chemical changes induced by beta and gamma radiations; 2 - reticulation of plastic materials submitted to beta and gamma radiations: radio-'reticulable' polymers and reticulation co-agents, modification of the properties of reticulated plastic materials under beta and gamma radiations; 3 - industrial aspects of reticulation under beta and gamma radiation: industrial irradiation facilities, dosimetry and radio-reticulation control, applications; 4 - conclusion. (J.S.)

Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth.

Directory of Open Access Journals (Sweden)

Anupama Yadav

Full Text Available The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it's evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with the environment specific regulators is not well understood. Saccharomyces cerevisiae is highly sensitive to the environment, which acts as not just external stimulus but also as signalling cue for this unicellular, sessile organism. We used a previously published dataset of a biparental yeast population grown in 34 diverse environments and mapped genetic loci regulating variation in phenotypic plasticity, plasticity QTL, and compared them with environment-specific QTL. Plasticity QTL is one whose one allele exhibits high plasticity whereas the other shows a relatively canalised behaviour. We mapped phenotypic plasticity using two parameters-environmental variance, an environmental order-independent parameter and reaction norm (slope, an environmental order-dependent parameter. Our results show a partial overlap between pleiotropic QTL and plasticity QTL such that while some plasticity QTL are also pleiotropic, others have a significant effect on phenotypic plasticity without being significant in any environment independently. Furthermore, while some plasticity QTL are revealed only in specific environmental orders, we identify large effect plasticity QTL, which are order-independent such that whatever the order of the environments, one allele is always plastic and the other is canalised. Finally, we show that the environments can be divided into two categories based on the phenotypic diversity of the population within them and the two categories have

Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.

Science.gov (United States)

Lin, Yu; Hu, Fei; Tang, Jijun; Moret, Bernard M E

2013-01-01

The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.

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

Directory of Open Access Journals (Sweden)

Kui Lin

2014-01-01

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

Plastic reactor suitable for high pressure and supercritical fluid electrochemistry

DEFF Research Database (Denmark)

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

2017-01-01

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

Plastic ingestion by Flesh-footed Shearwaters (Puffinus carneipes): Implications for fledgling body condition and the accumulation of plastic-derived chemicals

International Nuclear Information System (INIS)

Lavers, Jennifer L.; Bond, Alexander L.; Hutton, Ian

2014-01-01

To provide much needed quantitative data on the lethal and sublethal effects of plastic pollution on marine wildlife, we sampled breast feathers and stomach contents from Flesh-footed Shearwater (Puffinus carneipes) fledglings in eastern Australia. Birds with high levels of ingested plastic exhibited reduced body condition and increased contaminant load (p < 0.05). More than 60% of fledglings exceed international targets for plastic ingestion by seabirds, with 16% of fledglings failing these targets after a single feeding (range: 0.13–3.21 g of plastic/feeding). As top predators, seabirds are considered sentinels of the marine environment. The amount of plastic ingested and corresponding damage to Flesh-footed Shearwater fledglings is the highest reported for any marine vertebrate, suggesting the condition of the Australian marine environment is poor. These findings help explain the ongoing decline of this species and are worrying in light of increasing levels of plastic pollution in our oceans. - Highlights: • Proportion of the shearwater population ingesting plastic increased over four years. • Shearwater body condition is negatively influenced by the amount of ingested plastic. • Shearwater contaminant load is positively related to the amount of ingested plastic. • Many chicks exceed international targets for ingested plastic after a single feeding. • Plastic ingestion in this study is the highest reported for any marine vertebrate. - Flesh-footed Shearwaters ingest large quantities of marine plastic, which is correlated with poor body condition and increased concentrations of trace metals such as chromium

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

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

Science.gov (United States)

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

2012-01-01

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

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

DEFF Research Database (Denmark)

Liu, Yilan; Yang, Maohua; Yan, Daojiang

2016-01-01

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

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...

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....

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

DEFF Research Database (Denmark)

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

2012-01-01

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

Benthic plastic debris in marine and fresh water environments.

Science.gov (United States)

Corcoran, Patricia L

2015-08-01

This review provides a discussion of the published literature concerning benthic plastic debris in ocean, sea, lake, estuary and river bottoms throughout the world. Although numerous investigations of shoreline, surface and near-surface plastic debris provide important information on plastic types, distribution, accumulation, and degradation, studies of submerged plastic debris have been sporadic in the past and have become more prominent only recently. The distribution of benthic debris is controlled mainly by combinations of urban proximity and its association with fishing-related activities, geomorphology, hydrological conditions, and river input. High density plastics, biofouled products, polymers with mineral fillers or adsorbed minerals, and plastic-metal composites all have the potential to sink. Once deposited on the bottoms of water basins and channels, plastics are shielded from UV light, thus slowing the degradation process significantly. Investigations of the interactions between benthic plastic debris and bottom-dwelling organisms will help shed light on the potential dangers of submerged plastic litter.

Long-term sorption of metals is similar among plastic types: implications for plastic debris in aquatic environments.

Directory of Open Access Journals (Sweden)

Chelsea M Rochman

Full Text Available Concerns regarding plastic debris and its ability to accumulate large concentrations of priority pollutants in the aquatic environment led us to quantify relationships between different types of mass-produced plastic and metals in seawater. At three locations in San Diego Bay, we measured the accumulation of nine targeted metals (aluminum, chromium, manganese, iron, cobalt, nickel, zinc, cadmium and lead sampling at 1, 3, 6, 9 and 12 months, to five plastic types: polyethylene terephthalate (PET, high-density polyethylene (HDPE, polyvinyl chloride (PVC, low-density polyethylene (LDPE, and polypropylene (PP. Accumulation patterns were not consistent over space and time, and in general all types of plastic tended to accumulate similar concentrations of metals. When we did observe significant differences among concentrations of metals at a single sampling period or location in San Diego Bay, we found that HDPE typically accumulated lesser concentrations of metals than the other four polymers. Furthermore, over the 12-month study period, concentrations of all metals increased over time, and chromium, manganese, cobalt, nickel, zinc and lead did not reach saturation on at least one plastic type during the entire 12-month exposure. This suggests that plastic debris may accumulate greater concentrations of metals the longer it remains at sea. Overall, our work shows that a complex mixture of metals, including those listed as priority pollutants by the US EPA (Cd, Ni, Zn and Pb, can be found on plastic debris composed of various plastic types.

Long-term sorption of metals is similar among plastic types: implications for plastic debris in aquatic environments.

Science.gov (United States)

Rochman, Chelsea M; Hentschel, Brian T; Teh, Swee J

2014-01-01

Concerns regarding plastic debris and its ability to accumulate large concentrations of priority pollutants in the aquatic environment led us to quantify relationships between different types of mass-produced plastic and metals in seawater. At three locations in San Diego Bay, we measured the accumulation of nine targeted metals (aluminum, chromium, manganese, iron, cobalt, nickel, zinc, cadmium and lead) sampling at 1, 3, 6, 9 and 12 months, to five plastic types: polyethylene terephthalate (PET), high-density polyethylene (HDPE), polyvinyl chloride (PVC), low-density polyethylene (LDPE), and polypropylene (PP). Accumulation patterns were not consistent over space and time, and in general all types of plastic tended to accumulate similar concentrations of metals. When we did observe significant differences among concentrations of metals at a single sampling period or location in San Diego Bay, we found that HDPE typically accumulated lesser concentrations of metals than the other four polymers. Furthermore, over the 12-month study period, concentrations of all metals increased over time, and chromium, manganese, cobalt, nickel, zinc and lead did not reach saturation on at least one plastic type during the entire 12-month exposure. This suggests that plastic debris may accumulate greater concentrations of metals the longer it remains at sea. Overall, our work shows that a complex mixture of metals, including those listed as priority pollutants by the US EPA (Cd, Ni, Zn and Pb), can be found on plastic debris composed of various plastic types.

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

Science.gov (United States)

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

2015-11-17

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

Plastic ingestion by Flesh-footed Shearwaters (Puffinus carneipes): Implications for fledgling body condition and the accumulation of plastic-derived chemicals.

Science.gov (United States)

Lavers, Jennifer L; Bond, Alexander L; Hutton, Ian

2014-04-01

To provide much needed quantitative data on the lethal and sublethal effects of plastic pollution on marine wildlife, we sampled breast feathers and stomach contents from Flesh-footed Shearwater (Puffinus carneipes) fledglings in eastern Australia. Birds with high levels of ingested plastic exhibited reduced body condition and increased contaminant load (p plastic ingestion by seabirds, with 16% of fledglings failing these targets after a single feeding (range: 0.13-3.21 g of plastic/feeding). As top predators, seabirds are considered sentinels of the marine environment. The amount of plastic ingested and corresponding damage to Flesh-footed Shearwater fledglings is the highest reported for any marine vertebrate, suggesting the condition of the Australian marine environment is poor. These findings help explain the ongoing decline of this species and are worrying in light of increasing levels of plastic pollution in our oceans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetical Genomics for Evolutionary Studies

NARCIS (Netherlands)

Prins, J.C.P.; Smant, G.; Jansen, R.C.

2012-01-01

Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

Ocean acidification challenges copepod phenotypic plasticity

Science.gov (United States)

Vehmaa, Anu; Almén, Anna-Karin; Brutemark, Andreas; Paul, Allanah; Riebesell, Ulf; Furuhagen, Sara; Engström-Öst, Jonna

2016-11-01

Ocean acidification is challenging phenotypic plasticity of individuals and populations. Calanoid copepods (zooplankton) are shown to be fairly plastic against altered pH conditions, and laboratory studies indicate that transgenerational effects are one mechanism behind this plasticity. We studied phenotypic plasticity of the copepod Acartia sp. in the course of a pelagic, large-volume mesocosm study that was conducted to investigate ecosystem and biogeochemical responses to ocean acidification. We measured copepod egg production rate, egg-hatching success, adult female size and adult female antioxidant capacity (ORAC) as a function of acidification (fCO2 ˜ 365-1231 µatm) and as a function of quantity and quality of their diet. We used an egg transplant experiment to reveal whether transgenerational effects can alleviate the possible negative effects of ocean acidification on offspring development. We found significant negative effects of ocean acidification on adult female size. In addition, we found signs of a possible threshold at high fCO2, above which adaptive maternal effects cannot alleviate the negative effects of acidification on egg-hatching and nauplii development. We did not find support for the hypothesis that insufficient food quantity (total particulate carbon < 55 µm) or quality (C : N) weakens the transgenerational effects. However, females with high-ORAC-produced eggs with high hatching success. Overall, these results indicate that Acartia sp. could be affected by projected near-future CO2 levels.

From Modeling of Plasticity in Single-Crystal Superalloys to High-Resolution X-rays Three-Crystal Diffractometer Peaks Simulation

Science.gov (United States)

Jacques, Alain

2016-12-01

The dislocation-based modeling of the high-temperature creep of two-phased single-crystal superalloys requires input data beyond strain vs time curves. This may be obtained by use of in situ experiments combining high-temperature creep tests with high-resolution synchrotron three-crystal diffractometry. Such tests give access to changes in phase volume fractions and to the average components of the stress tensor in each phase as well as the plastic strain of each phase. Further progress may be obtained by a new method making intensive use of the Fast Fourier Transform, and first modeling the behavior of a representative volume of material (stress fields, plastic strain, dislocation densities…), then simulating directly the corresponding diffraction peaks, taking into account the displacement field within the material, chemical variations, and beam coherence. Initial tests indicate that the simulated peak shapes are close to the experimental ones and are quite sensitive to the details of the microstructure and to dislocation densities at interfaces and within the soft γ phase.

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

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

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Patil Ashwini

2005-04-01

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

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

International Nuclear Information System (INIS)

Liu, Xun; Lan, Shuhuai; Ni, Jun

2013-01-01

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

Low temperature fabrication of ZnO compact layer for high performance plastic dye-sensitized ZnO solar cells

International Nuclear Information System (INIS)

Hu Fangyi; Xia Yujing; Guan Zisheng; Yin Xiong; He Tao

2012-01-01

Highlights: ► ZnO compact layer is prepared via simple electrochemical method at low temperature. ► Compact layer can effectively block electron transfer from TCO to electrolyte. ► DSC PCE is improved by 17% when ZnO compact layer is introduced. ► Plastic DSCs with ZnO compact layer show a PCE of 3.29% under AM1.5 100 mW cm −2 . ► The above efficiency is comparable to that with high temperature sintering step. - Abstract: ZnO compact layer has been fabricated on transparent conducting oxide glass and plastic polymer substrates at low temperature via electrodeposition. The results of dark current and cyclic voltammetric measurements demonstrate that the compact layer can effectively reduce the short circuit from transparent conducting oxide to electrolyte in dye-sensitized ZnO solar cells, leading to an increase of open-circuit photovoltage and fill factor of the devices and, thereby, the power conversion efficiency. The resultant plastic dye-sensitized ZnO solar cell presents an efficiency of 3.29% under illumination of 100 mW cm −2 , AM 1.5G. This indicates that electrodeposition is a viable method to fabricate ZnO compact layer for high performance flexible devices.

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

Science.gov (United States)

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

2018-01-22

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

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

Directory of Open Access Journals (Sweden)

Davies Jonathan J

2006-12-01

Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Plastic fragments in the environment: Origin, dispersion, consequences

International Nuclear Information System (INIS)

Beone, G.; De Simone, R.

1989-01-01

An overview of data on plastic pollution remarks a lake on its environmental fate, but debris, created by photodegradation, seems to have high hazard. In this paper, distribution and transport of plastic in ecological system and biological significance are discussed. (author)

Phenotypic Plasticity of Cuticular Hydrocarbon Profiles in Insects.

Science.gov (United States)

Otte, Tobias; Hilker, Monika; Geiselhardt, Sven

2018-03-01

The insect integument is covered by cuticular hydrocarbons (CHCs) which provide protection against environmental stresses, but are also used for communication. Here we review current knowledge on environmental and insect-internal factors which shape phenotypic plasticity of solitary living insects, especially herbivorous ones. We address the dynamics of changes which may occur within minutes, but may also last weeks, depending on the species and conditions. Two different modes of changes are suggested, i.e. stepwise and gradual. A switch between two distinct environments (e.g. host plant switch by phytophagous insects) results in stepwise formation of two distinct adaptive phenotypes, while a gradual environmental change (e.g. temperature gradients) induces a gradual change of numerous adaptive CHC phenotypes. We further discuss the ecological and evolutionary consequences of phenotypic plasticity of insect CHC profiles by addressing the question at which conditions is CHC phenotypic plasticity beneficial. The high plasticity of CHC profiles might be a trade-off for insects using CHCs for communication. We discuss how insects cope with the challenge to produce and "understand" a highly plastic, environmentally dependent CHC pattern that conveys reliable and comprehensible information. Finally, we outline how phenotypic plasticity of CHC profiles may promote speciation in insects that rely on CHCs for mate recognition.

Boron effect on stainless steel plasticity under hot deformation

International Nuclear Information System (INIS)

Bulat, S.I.; Kardonov, B.A.; Sorokina, N.A.

1978-01-01

The effect of boron on plasticity of stainless steels at temperatures of hot deformation has been studied at three levels of alloying, i.e. 0-0.01% (micro-alloying or modifying), 0.01-0.02% (low alloying) and 0.02-2.0% (high alloying). Introduction of 0.001-0.005% of boron increases hot plasticity of both low and high carbon stainless steels due to decrease in grain size and strengthening of grain boundaries. Microalloying by boron has a positive effect at temperatures below 1200-1220 deg C. At higher temperatures, particularly when its content exceeds 0.008%, boron deteriorates plasticity by increasing the size of grains and weakening their boundaries. 0.1-2% boron strengthen the stainless steel and dectease its plasticity

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

Science.gov (United States)

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

2015-01-01

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

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

Science.gov (United States)

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

2015-01-01

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

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

International Nuclear Information System (INIS)

Miura, Yasufumi

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

Trout-Yakel Keri M

2010-02-01

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

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

Science.gov (United States)

Liu, Tina T; Behrmann, Marlene

2017-10-01

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

Microarray-based ultra-high resolution discovery of genomic deletion mutations

Science.gov (United States)

2014-01-01

Background Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. Results Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. Conclusions Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. PMID:24655320

Get your high-quality low-cost genome sequence

NARCIS (Netherlands)

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

2014-01-01

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

High-conductance low-voltage organic thin film transistor with locally rearranged poly(3-hexylthiophene) domain by current annealing on plastic substrate

Science.gov (United States)

Pei, Zingway; Tsai, Hsing-Wang; Lai, Hsin-Cheng

2016-02-01

The organic material based thin film transistors (TFTs) are attractive for flexible optoelectronics applications due to the ability of lager area fabrication by solution and low temperature process on plastic substrate. Recently, the research of organic TFT focus on low operation voltage and high output current to achieve a low power organic logic circuit for optoelectronic device,such as e-paper or OLED displayer. To obtain low voltage and high output current, high gate capacitance and high channel mobility are key factors. The well-arranged polymer chain by a high temperature postannealing, leading enhancement conductivity of polymer film was a general method. However, the thermal annealing applying heat for all device on the substrate and may not applicable to plastic substrate. Therefore, in this work, the low operation voltage and high output current of polymer TFTs was demonstrated by locally electrical bias annealing. The poly(styrene-comethyl methacrylate) (PS-r-PMMA) with ultra-thin thickness is used as gate dielectric that the thickness is controlled by thermal treatment after spin coated on organic electrode. In electrical bias-annealing process, the PS-r- PMMA is acted a heating layer. After electrical bias-annealing, the polymer TFTs obtain high channel mobility at low voltage that lead high output current by a locally annealing of P3HT film. In the future, the locally electrical biasannealing method could be applied on plastic substrate for flexible optoelectronic application.

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

Science.gov (United States)

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

2016-11-01

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

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....

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

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Christian M. Tobias

2008-11-01

Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

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

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Bekim Sadikovic

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2007-03-29

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

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.

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

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders.

Science.gov (United States)

Debroas, Didier; Mone, Anne; Ter Halle, Alexandra

2017-12-01

Plastic is a broad name given to different polymers with high molecular weight that impact wildlife. Their fragmentation leads to a continuum of debris sizes (meso to microplastics) entrapped in gyres and colonized by microorganisms. In the present work, the structure of eukaryotes, bacteria and Archaea was studied by a metabarcoding approach, and statistical analysis associated with network building was used to define a core microbiome at the plastic surface. Most of the bacteria significantly associated with the plastic waste originated from non-marine ecosystems, and numerous species can be considered as hitchhikers, whereas others act as keystone species (e.g., Rhodobacterales, Rhizobiales, Streptomycetales and Cyanobacteria) in the biofilm. The chemical analysis provides evidence for a specific colonization of the polymers. Alphaproteobacteria and Gammaproteobacteria significantly dominated mesoplastics consisting of poly(ethylene terephthalate) and polystyrene. Polyethylene was also dominated by these bacterial classes and Actinobacteria. Microplastics were made of polyethylene but differed in their crystallinity, and the majorities were colonized by Betaproteobacteria. Our study indicated that the bacteria inhabiting plastics harboured distinct metabolisms from those present in the surrounding water. For instance, the metabolic pathway involved in xenobiotic degradation was overrepresented on the plastic surface. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Impact of Bio-Based Plastics on Current Recycling of Plastics

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Luc Alaerts

2018-05-01

Full Text Available Bio-based plastics are increasingly appearing in a range of consumption products, and after use they often end up in technical recycling chains. Bio-based plastics are different from fossil-based ones and could disturb the current recycling of plastics and hence inhibit the closure of plastic cycles, which is undesirable given the current focus on a transition towards a circular economy. In this paper, this risk has been assessed via three elaborated case studies using data and information retrieved through an extended literature search. No overall risks were revealed for bio-based plastics as a group; rather, every bio-based plastic is to be considered as a potential separate source of contamination in current recycling practices. For PLA (polylactic acid, a severe incompatibility with PET (polyethylene terephthalate recycling is known; hence, future risks are assessed by measuring amounts of PLA ending up in PET waste streams. For PHA (polyhydroxy alkanoate there is no risk currently, but it will be crucial to monitor future application development. For PEF (polyethylene furanoate, a particular approach for contamination-related issues has been included in the upcoming market introduction. With respect to developing policy, it is important that any introduction of novel plastics is well guided from a system perspective and with a particular eye on incompatibilities with current and upcoming practices in the recycling of plastics.

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

Science.gov (United States)

Suwinarti, W.; Amirta, R.; Yuliansyah

2018-04-01

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

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

Science.gov (United States)

2013-01-01

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

Experimental evaluation of the interaction effect between plastic and creep deformation

International Nuclear Information System (INIS)

Ikegami, K.; Niitsu, Y.

1985-01-01

An experimental study of plasticity-creep interaction effects is reported. The combined stress tests are performed on thin wall tubular specimens of SUS 304 stainless steel at room temperature and high temperature (600 0 C). The plastic behaviors subsequent to creep pre-strain and creep behaviors subsequent to plastic pre-strain are obtained for loading along straight stress paths with a corner. The inelastic behaviors including both plastic and creep deformations are experimentally investigated. The interaction effects between plastic and creep deformations are quantitatively estimated with the equi-plastic strain surface. (author)

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

Directory of Open Access Journals (Sweden)

Zhigang Liu

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

Prospects for microbiological solutions to environmental pollution with plastics.

Science.gov (United States)

Krueger, Martin C; Harms, Hauke; Schlosser, Dietmar

2015-11-01

Synthetic polymers, commonly named plastics, are among the most widespread anthropogenic pollutants of marine, limnic and terrestrial ecosystems. Disruptive effects of plastics are known to threaten wildlife and exert effects on natural food webs, but signs for and knowledge on plastic biodegradation are limited. Microorganisms are the most promising candidates for an eventual bioremediation of environmental plastics. Laboratory studies have reported various effects of microorganisms on many types of polymers, usually by enzymatic hydrolysis or oxidation. However, most common plastics have proved to be highly recalcitrant even under conditions known to favour microbial degradation. Knowledge on environmental degradation is yet scarcer. With this review, we provide a comprehensive overview of the current knowledge on microbiological degradation of several of the most common plastic types. Furthermore, we illustrate the analytical challenges concerning the evaluation of plastic biodegradation as well as constraints likely standing against the evolution of effective biodegradation pathways.

Ocean acidification challenges copepod phenotypic plasticity

Directory of Open Access Journals (Sweden)

A. Vehmaa

2016-11-01

Full Text Available Ocean acidification is challenging phenotypic plasticity of individuals and populations. Calanoid copepods (zooplankton are shown to be fairly plastic against altered pH conditions, and laboratory studies indicate that transgenerational effects are one mechanism behind this plasticity. We studied phenotypic plasticity of the copepod Acartia sp. in the course of a pelagic, large-volume mesocosm study that was conducted to investigate ecosystem and biogeochemical responses to ocean acidification. We measured copepod egg production rate, egg-hatching success, adult female size and adult female antioxidant capacity (ORAC as a function of acidification (fCO2  ∼  365–1231 µatm and as a function of quantity and quality of their diet. We used an egg transplant experiment to reveal whether transgenerational effects can alleviate the possible negative effects of ocean acidification on offspring development. We found significant negative effects of ocean acidification on adult female size. In addition, we found signs of a possible threshold at high fCO2, above which adaptive maternal effects cannot alleviate the negative effects of acidification on egg-hatching and nauplii development. We did not find support for the hypothesis that insufficient food quantity (total particulate carbon < 55 µm or quality (C : N weakens the transgenerational effects. However, females with high-ORAC-produced eggs with high hatching success. Overall, these results indicate that Acartia sp. could be affected by projected near-future CO2 levels.

Phyllosphere yeasts rapidly break down biodegradable plastics.

Science.gov (United States)

Kitamoto, Hiroko K; Shinozaki, Yukiko; Cao, Xiao-Hong; Morita, Tomotake; Konishi, Masaaki; Tago, Kanako; Kajiwara, Hideyuki; Koitabashi, Motoo; Yoshida, Shigenobu; Watanabe, Takashi; Sameshima-Yamashita, Yuka; Nakajima-Kambe, Toshiaki; Tsushima, Seiya

2011-11-29

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands.

Phyllosphere yeasts rapidly break down biodegradable plastics

Science.gov (United States)

2011-01-01

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands. PMID:22126328

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator.

Science.gov (United States)

Lin, Y; Rajan, V; Moret, B M E

2011-09-01

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current approaches are limited to small collections of genomes and low-resolution data (typically a few hundred syntenic blocks). Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis. We describe a fast and accurate algorithm for rearrangement analysis that scales up, in both time and accuracy, to modern high-resolution genomic data. We also describe a novel approach to estimate the robustness of results-an equivalent to the bootstrapping analysis used in sequence-based phylogenetic reconstruction. We present the results of extensive testing on both simulated and real data showing that our algorithm returns very accurate results, while scaling linearly with the size of the genomes and cubically with their number. We also present extensive experimental results showing that our approach to robustness testing provides excellent estimates of confidence, which, moreover, can be tuned to trade off thresholds between false positives and false negatives. Together, these two novel approaches enable us to attack heretofore intractable problems, such as phylogenetic inference for high-resolution vertebrate genomes, as we demonstrate on a set of six vertebrate genomes with 8,380 syntenic blocks. A copy of the software is available on demand.

Developmental Plasticity and Language: A Comparative Perspective.

Science.gov (United States)

Griebel, Ulrike; Pepperberg, Irene M; Oller, D Kimbrough

2016-04-01

The growing field of evo-devo is increasingly demonstrating the complexity of steps involved in genetic, intracellular regulatory, and extracellular environmental control of the development of phenotypes. A key result of such work is an account for the remarkable plasticity of organismal form in many species based on relatively minor changes in regulation of highly conserved genes and genetic processes. Accounting for behavioral plasticity is of similar potential interest but has received far less attention. Of particular interest is plasticity in communication systems, where human language represents an ultimate target for research. The present paper considers plasticity of language capabilities in a comparative framework, focusing attention on examples of a remarkable fact: Whereas there exist design features of mature human language that have never been observed to occur in non-humans in the wild, many of these features can be developed to notable extents when non-humans are enculturated through human training (especially with intensive social interaction). These examples of enculturated developmental plasticity across extremely diverse taxa suggest, consistent with the evo-devo theme of highly conserved processes in evolution, that human language is founded in part on cognitive capabilities that are indeed ancient and that even modern humans show self-organized emergence of many language capabilities in the context of rich enculturation, built on the special social/ecological history of the hominin line. Human culture can thus be seen as a regulatory system encouraging language development in the context of a cognitive background with many highly conserved features. Copyright © 2016 Cognitive Science Society, Inc.

Challenges and Alternatives to Plastics Recycling in the Automotive Sector

Directory of Open Access Journals (Sweden)

Lindsay Miller

2014-08-01

Full Text Available Plastics are increasingly a preferred material choice in designing and developing complex, consumer products, such as automobiles, because they are mouldable, lightweight, and are often perceived to be highly recyclable materials. However, actually recycling the heterogeneous plastics used in such durable items is challenging, and presents very different scenarios to how simple products, such as water bottles, are recovered via curbside or container recycling initiatives. While the technology exists to recycle plastics, their feasibility to do so from high level consumer or industrial applications is bounded by technological and economical restraints. Obstacles include the lack of market for recyclates, and the lack of cost efficient recovery infrastructures or processes. Furthermore, there is a knowledge gap between manufacturers, consumers, and end-of-life facility operators. For these reasons, end-of-life plastics are more likely to end up down-cycled, or as shredder residue and then landfilled. This paper reviews these challenges and several alternatives to recycling plastics in order to broaden the mindset surrounding plastics recycling to improve their sustainability. The paper focuses on the automotive sector for examples, but discussion can be applied to a wide range of plastic components from similarly complex products.

Challenges and Alternatives to Plastics Recycling in the Automotive Sector

Science.gov (United States)

Miller, Lindsay; Soulliere, Katie; Sawyer-Beaulieu, Susan; Tseng, Simon; Tam, Edwin

2014-01-01

Plastics are increasingly a preferred material choice in designing and developing complex, consumer products, such as automobiles, because they are mouldable, lightweight, and are often perceived to be highly recyclable materials. However, actually recycling the heterogeneous plastics used in such durable items is challenging, and presents very different scenarios to how simple products, such as water bottles, are recovered via curbside or container recycling initiatives. While the technology exists to recycle plastics, their feasibility to do so from high level consumer or industrial applications is bounded by technological and economical restraints. Obstacles include the lack of market for recyclates, and the lack of cost efficient recovery infrastructures or processes. Furthermore, there is a knowledge gap between manufacturers, consumers, and end-of-life facility operators. For these reasons, end-of-life plastics are more likely to end up down-cycled, or as shredder residue and then landfilled. This paper reviews these challenges and several alternatives to recycling plastics in order to broaden the mindset surrounding plastics recycling to improve their sustainability. The paper focuses on the automotive sector for examples, but discussion can be applied to a wide range of plastic components from similarly complex products. PMID:28788167

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.

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

Directory of Open Access Journals (Sweden)

Pengpeng Li

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

The Prevalence of Cosmetic Facial Plastic Procedures among Facial Plastic Surgeons.

Science.gov (United States)

Moayer, Roxana; Sand, Jordan P; Han, Albert; Nabili, Vishad; Keller, Gregory S

2018-04-01

This is the first study to report on the prevalence of cosmetic facial plastic surgery use among facial plastic surgeons. The aim of this study is to determine the frequency with which facial plastic surgeons have cosmetic procedures themselves. A secondary aim is to determine whether trends in usage of cosmetic facial procedures among facial plastic surgeons are similar to that of nonsurgeons. The study design was an anonymous, five-question, Internet survey distributed via email set in a single academic institution. Board-certified members of the American Academy of Facial Plastic and Reconstructive Surgery (AAFPRS) were included in this study. Self-reported history of cosmetic facial plastic surgery or minimally invasive procedures were recorded. The survey also queried participants for demographic data. A total of 216 members of the AAFPRS responded to the questionnaire. Ninety percent of respondents were male ( n  = 192) and 10.3% were female ( n  = 22). Thirty-three percent of respondents were aged 31 to 40 years ( n  = 70), 25% were aged 41 to 50 years ( n  = 53), 21.4% were aged 51 to 60 years ( n  = 46), and 20.5% were older than 60 years ( n  = 44). Thirty-six percent of respondents had a surgical cosmetic facial procedure and 75% has at least one minimally invasive cosmetic facial procedure. Facial plastic surgeons are frequent users of cosmetic facial plastic surgery. This finding may be due to access, knowledge base, values, or attitudes. By better understanding surgeon attitudes toward facial plastic surgery, we can improve communication with patients and delivery of care. This study is a first step in understanding use of facial plastic procedures among facial plastic surgeons. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Whole genome DNA copy number changes identified by high density oligonucleotide arrays

Directory of Open Access Journals (Sweden)

Huang Jing

2004-05-01

Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

Process combinations for the manufacturing of metal-plastic hybrid parts

International Nuclear Information System (INIS)

Drossel, W-G; Lies, C; Albert, A; Haase, R; Müller, R; Scholz, P

2016-01-01

The usage of innovative lightweight materials and processing technologies gains importance in manifold industrial scopes. Especially for moving parts and mobility products the weight is decisively. The aerospace and automotive industries use light and high-strength materials to reduce weight and energy consumption and thereby improve the performance of their products. Composites with reinforced plastics are of particular importance. They offer a low density in combination with high specific stiffness and strength. A pure material substitution through reinforced plastics is still not economical. The approach of using hybrid metal-plastic structures with the principle of “using the right material at the right place” is a promising solution for the economical realization of lightweight structures with a high achievement potential. The article shows four innovative manufacturing possibilities for the realization of metal-plastic-hybrid parts. (paper)

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

Science.gov (United States)

Pivnenko, K; Eriksen, M K; Martín-Fernández, J A; Eriksson, E; Astrup, T F

2016-08-01

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 volumes and are commonly used as plasticisers in plastics manufacturing. Potential impacts on human health require restricted use in selected applications and a need for the closer monitoring of potential sources of human exposure. Although the presence of phthalates in a variety of plastics has been 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 had the highest frequency of detection in the samples analysed, with 360μg/g, 460μg/g and 2700μg/g as the maximum measured concentrations, respectively. Among other, statistical analysis of the analytical results suggested that phthalates were potentially added in the later stages of plastic 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 is recommended if recycled plastics are to be used as raw material in production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

KAUST Repository

Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan

2011-01-01

The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

KAUST Repository

Wang, Yong

2011-12-21

The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

Directory of Open Access Journals (Sweden)

Yong Wang

Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

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

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Chen eYang

2015-05-01

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

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...

Leaching behavior of solidified plastics radioactive wastes

International Nuclear Information System (INIS)

Yook, Chong Chul; Lee, Byung Hun; Jae, Won Mok; Kim, Kyung Eung

1986-01-01

It is highly needed to develope the solidification process to dispose safely the radioactive wastes increasing with the growth of the nuclear industry. The leaching mechanisms of the solidified plastic wastes were investigated and the leaching rates of the plastic wastes were also measured among the many solidification processes. In addition, the transport equation based on the diffusion or the diffusion-dissolution was compared with the empirical equation derived from the experimental data by graphical method. Consequently, leaching process of the solidified plastic wastes is quite well agreed with the mass transport theory, but it may be difficult to simulate leaching process by diffusion dissolution mechanism. But the theoretical equation could be applicable to the cumulative amount of radionuclides leached form the plastic wastes disposed into the environment. (Author)

Response function measurement of plastic scintillator for high energy neutrons

International Nuclear Information System (INIS)

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

2003-01-01

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

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

Science.gov (United States)

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

2017-07-31

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

Plasticity of cortical excitatory-inhibitory balance.

Science.gov (United States)

Froemke, Robert C

2015-07-08

Synapses are highly plastic and are modified by changes in patterns of neural activity or sensory experience. Plasticity of cortical excitatory synapses is thought to be important for learning and memory, leading to alterations in sensory representations and cognitive maps. However, these changes must be coordinated across other synapses within local circuits to preserve neural coding schemes and the organization of excitatory and inhibitory inputs, i.e., excitatory-inhibitory balance. Recent studies indicate that inhibitory synapses are also plastic and are controlled directly by a large number of neuromodulators, particularly during episodes of learning. Many modulators transiently alter excitatory-inhibitory balance by decreasing inhibition, and thus disinhibition has emerged as a major mechanism by which neuromodulation might enable long-term synaptic modifications naturally. This review examines the relationships between neuromodulation and synaptic plasticity, focusing on the induction of long-term changes that collectively enhance cortical excitatory-inhibitory balance for improving perception and behavior.

Structural Plasticity Denoises Responses and Improves Learning Speed

Directory of Open Access Journals (Sweden)

Robin Spiess

2016-09-01

Full Text Available Despite an abundance of computational models for learning of synaptic weights, there has been relatively little research on structural plasticity, i.e. the creation and elimination of synapses. Especially, it is not clear how structural plasticity works in concert with spike-timing-dependent plasticity (STDP and what advantages their combination offers.Here we present a fairly large-scale functional model that uses leaky integrate-and-fire neurons, STDP, homeostasis, recurrent connections, and structural plasticity to learn the input encoding, the relation between inputs, and to infer missing inputs. Using this model, we compare the error and the amount of noise in the network's responses with and without structural plasticity and the influence of structural plasticity on the learning speed of the network.Using structural plasticity during learning shows good results for learning the representation of input values, i.e. structural plasticity strongly reduces the noise of the response by preventing spikes with a high error.For inferring missing inputs we see similar results, with responses having less noise if the network was trained using structural plasticity.Additionally, using structural plasticity with pruning significantly decreased the time to learn weights suitable for inference.Presumably, this is due to the clearer signal containing less spikes that misrepresent the desired value. Therefore, this work shows that structural plasticity is not only able to improve upon the performance using STDP without structural plasticity but also speeds up learning.Additionally, it addresses the practical problem of limited resources for connectivity that is not only apparent in the mammalian neocortex but also in computer hardware or neuromorphic (brain-inspired hardware by efficiently pruning synapses without losing performance.

Knowledge and perception of plastic surgery among tertiary ...

African Journals Online (AJOL)

Conclusion: The level of awareness is high in the sampled population with associated increase in acceptance of its practice and willing utilization. All public hospitals should be encouraged to employ the services of plastic surgeons. Appropriate branding of specialized hospitals where plastic surgery service is available will ...

GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

Directory of Open Access Journals (Sweden)

Pablo H C G de Sá

Full Text Available The advent of NGS (Next Generation Sequencing technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

Triboelectrostatic separation for granular plastic waste recycling: a review.

Science.gov (United States)

Wu, Guiqing; Li, Jia; Xu, Zhenming

2013-03-01

The world's plastic consumption has increased incredibly in recent decades, generating more and more plastic waste, which makes it a great public concern. Recycling is the best treatment for plastic waste since it cannot only reduce the waste but also reduce the consumption of oil for producing new virgin plastic. Mechanical recycling is recommended for plastic waste to avoid the loss of its virgin value. As a mechanical separation technology, triboelectrostatic separation utilizes the difference between surface properties of different materials to get them oppositely charged, deflected in the electric field and separately collected. It has advantages such as high efficiency, low cost, no concern of water disposal or secondary pollution and a relatively wide processing range of particle size especially suitable for the granular plastic waste. The process of triboelectrostatic separation for plastic waste is reviewed in this paper. Different devices have been developed and proven to be effective for separation of plastic waste. The influence factors are also discussed. It can be concluded that the triboelectrostatic separation of plastic waste is a promising technology. However, more research is required before it can be widely applied in industry. Copyright © 2012 Elsevier Ltd. All rights reserved.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

OpenAIRE

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gen...

Mechanically equivalent elastic-plastic deformations and the problem of plastic spin

Directory of Open Access Journals (Sweden)

Steigmann David J.

2011-01-01

Full Text Available The problem of plastic spin is phrased in terms of a notion of mechanical equivalence among local intermediate configurations of an elastic/ plastic crystalline solid. This idea is used to show that, without further qualification, the plastic spin may be suppressed at the constitutive level. However, the spin is closely tied to an underlying undistorted crystal lattice which, once specified, eliminates the freedom afforded by mechanical equivalence. As a practical matter a constitutive specification of plastic spin is therefore required. Suppression of plastic spin thus emerges as merely one such specification among many. Restrictions on these are derived in the case of rate-independent response.

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

Directory of Open Access Journals (Sweden)

Walid Mottawea

2018-05-01

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

Waste Plastic Converting into Hydrocarbon Fuel Materials

Energy Technology Data Exchange (ETDEWEB)

Sarker, Moinuddin; Mamunor Rashid, Mohammad; Molla, Mohammad

2010-09-15

The increased demand and high prices for energy sources are driving efforts to convert organic compounds into useful hydrocarbon fuels. Although much of this work has focused on biomass, there are strong benefits to deriving fuels from waste plastic material. Natural State Research Inc. (NSR) has invented a simple and economically viable process to decompose the hydrocarbon polymers of waste plastic into the shorter chain hydrocarbon of liquid fuel (patent pending). The method and principle of the production / process will be discussed. Initial tests with several widely used polymers indicate a high potential for commercialization.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

Andrew Paul Hutchins

2014-01-01

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

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

Science.gov (United States)

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

2014-01-01

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

Plastics disassembly versus bulk recycling: engineering design for end-of-life electronics resource recovery.

Science.gov (United States)

Rios, Pedro; Stuart, Julie Ann; Grant, Ed

2003-12-01

Annual plastic flows through the business and consumer electronics manufacturing supply chain include nearly 3 billion lb of high-value engineering plastics derived from petroleum. The recovery of resource value from this stream presents critical challenges in areas of materials identification and recycling process design that demand new green engineering technologies applied together with life cycle assessment and ecological supply chain analysis to create viable plastics-to-plastics supply cycles. The sustainable recovery of potentially high-value engineering plastics streams requires that recyclers either avoid mixing plastic parts or purify later by separating smaller plastic pieces created in volume reduction (shredding) steps. Identification and separation constitute significant barriers in the plastics-to-plastics recycling value proposition. In the present work, we develop a model that accepts randomly arriving electronic products to study scenarios by which a recycler might identify and separate high-value engineering plastics as well as metals. Using discrete eventsimulation,we compare current mixed plastics recovery with spectrochemical plastic resin identification and subsequent sorting. Our results show that limited disassembly with whole-part identification can produce substantial yields in separated streams of recovered engineering thermoplastics. We find that disassembly with identification does not constitute a bottleneck, but rather, with relatively few workers, can be configured to pull the process and thus decrease maximum staging space requirements.

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.

Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5' Untranslated Region.

Science.gov (United States)

Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

2015-01-01

Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species' C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5' untranslated region (5' UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5' UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5' UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5' UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5' UTR. By contrast to the recombination of the cVDPV with the 5' UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5' UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages.

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

International Nuclear Information System (INIS)

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

1987-01-01

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

Living with genome instability: the adaptation of phytoplasmas todiverse environments of their insect and plant hosts

Energy Technology Data Exchange (ETDEWEB)

Bai, Xiaodong; Zhang, Jianhua; Ewing, Adam; Miller, Sally A.; Radek, Agnes; Shevchenko, Dimitriy; Tsukerman, Kiryl; Walunas, Theresa; Lapidus, Alla; Campbell, John W.; Hogenhout Saskia A.

2006-02-17

Phytoplasmas (Candidatus Phytoplasma, Class Mollicutes) cause disease in hundreds of economically important plants, and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. The repeated DNAs are organized into large clusters, potential mobile units (PMUs), which contain tra5 insertion sequences (ISs), and specialized sigma factors and membrane proteins. So far, PMUs are unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore phytoplasmas probably use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of {approx}250 kb, located between genes lplA and glnQ are syntenic between the two phytoplasmas, contain the majority of the metabolic genes and no ISs. AY-WB is further along in the reductive evolution process than OY-M. The AY-WB genome is {approx}154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Further, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M. This is the first comparative phytoplasma genome analysis and report of the existence of PMUs in phytoplasma genomes.

BC-454 boron-loaded plastic scintillator

International Nuclear Information System (INIS)

Bellian, J.G.

1984-01-01

Prototype samples of plastic scintillators containing up to 10% by weight of natural boron have been produced. The maximum size scintillators made to date are 28 mm dia. x 100 mm long. Rods containing up to 2% boron are now made routinely and work is progressing on higher concentrations. The plastics are clear and emit the same blue fluorescence as other common plastic scintillators. It is expected that rods up to 3'' dia. containing 5% boron will be produced during the next few months. BC-454 is particularly useful in neutron research, materials studies, some types of neutron dosimetry, and monitoring of medium to high energy neutrons in the presence of other types radiation. It combines attractive features that enhance its usefulness to the physics community

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...

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...

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.

Science.gov (United States)

Chain, Patrick S G; Denef, Vincent J; Konstantinidis, Konstantinos T; Vergez, Lisa M; Agulló, Loreine; Reyes, Valeria Latorre; Hauser, Loren; Córdova, Macarena; Gómez, Luis; González, Myriam; Land, Miriam; Lao, Victoria; Larimer, Frank; LiPuma, John J; Mahenthiralingam, Eshwar; Malfatti, Stephanie A; Marx, Christopher J; Parnell, J Jacob; Ramette, Alban; Richardson, Paul; Seeger, Michael; Smith, Daryl; Spilker, Theodore; Sul, Woo Jun; Tsoi, Tamara V; Ulrich, Luke E; Zhulin, Igor B; Tiedje, James M

2006-10-17

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.

Burkholderia xernovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

Energy Technology Data Exchange (ETDEWEB)

Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Denef, Vincent [University of California, Berkeley; Konstantinidis, Konstantinos T [Michigan State University, East Lansing; Vergez, Lisa [Lawrence Livermore National Laboratory (LLNL); Agullo, Loreine [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Reyes, Valeria Latorre [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Hauser, Loren John [ORNL; Cordova, Macarena [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Gomez, Luis [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Gonzalez, Myriam [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Land, Miriam L [ORNL; Lao, Victoria [Lawrence Livermore National Laboratory (LLNL); Larimer, Frank W [ORNL; LiPuma, John J [University of Michigan; Mahenthiralingam, Eshwar [Cardiff University, Wales; Malfatti, Stephanie [Lawrence Livermore National Laboratory (LLNL); Marx, Christopher J [Harvard University; Parnell, J Jacob [Michigan State University, East Lansing; Ramette, Alban [Michigan State University, East Lansing; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Seeger, Michael [Universidad Tecnica Federico Santa Maria, Casilla 110-V; Smith, Daryl [University of British Columbia, Vancouver; Spilker, Theodore [University of Michigan; Sul, Woo Jun [Michigan State University, East Lansing; Tsoi, Tamara V [Michigan State University, East Lansing; Zhulin, Igor B [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Tiedje, James M. [Michigan State University, East Lansing

2006-01-01

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven 'central aromatic' and twenty 'peripheral aromatic' pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.

Core Characteristics Deterioration due to Plastic Deformation

Science.gov (United States)

Kaido, Chikara; Arai, Satoshi

This paper discusses the effect of plastic deformation at core manufacturing on the characteristics of cores where non-oriented electrical steel sheets are used as core material. Exciting field and iron loss increase proportionally to plastic deformation in the case of rPeddy currents increase because plastic deformations of crystalline grains are distributed and then the flux distribution is induced. In the case of rP>20, the deterioration tend to saturate, and the increases in magnetic field and iron loss are 1000 to 1500A/m and 2 to 4W/kg. They are related to grain size, and high grade with larger grain may have lager field increase and smaller iron loss increase. Anomalous eddy current losses scarcely increase in this region. In actual motors, the plastic deformation affects iron loss increase although exciting current increases a little.

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

Science.gov (United States)

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

2017-11-01

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

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

Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity

KAUST Repository

Orlando, Marta

2017-10-17

Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABAA Receptors (GABAARs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABAAR clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABAAR clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity

KAUST Repository

Orlando, Marta; Ravasenga, Tiziana; Petrini, Enrica Maria; Falqui, Andrea; Marotta, Roberto; Barberis, Andrea

2017-01-01

Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABAA Receptors (GABAARs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABAAR clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABAAR clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

Correlating Fluorescence and High-Resolution Scanning Electron Microscopy (HRSEM) for the study of GABAA receptor clustering induced by inhibitory synaptic plasticity.

Science.gov (United States)

Orlando, Marta; Ravasenga, Tiziana; Petrini, Enrica Maria; Falqui, Andrea; Marotta, Roberto; Barberis, Andrea

2017-10-23

Both excitatory and inhibitory synaptic contacts display activity dependent dynamic changes in their efficacy that are globally termed synaptic plasticity. Although the molecular mechanisms underlying glutamatergic synaptic plasticity have been extensively investigated and described, those responsible for inhibitory synaptic plasticity are only beginning to be unveiled. In this framework, the ultrastructural changes of the inhibitory synapses during plasticity have been poorly investigated. Here we combined confocal fluorescence microscopy (CFM) with high resolution scanning electron microscopy (HRSEM) to characterize the fine structural rearrangements of post-synaptic GABA A Receptors (GABA A Rs) at the nanometric scale during the induction of inhibitory long-term potentiation (iLTP). Additional electron tomography (ET) experiments on immunolabelled hippocampal neurons allowed the visualization of synaptic contacts and confirmed the reorganization of post-synaptic GABA A R clusters in response to chemical iLTP inducing protocol. Altogether, these approaches revealed that, following the induction of inhibitory synaptic potentiation, GABA A R clusters increase in size and number at the post-synaptic membrane with no other major structural changes of the pre- and post-synaptic elements.

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.