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  1. Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family.

    Science.gov (United States)

    Dassa, Bareket; London, Nir; Stoddard, Barry L; Schueler-Furman, Ora; Pietrokovski, Shmuel

    2009-05-01

    Inteins are genetic elements, inserted in-frame into protein-coding genes, whose products catalyze their removal from the protein precursor via a protein-splicing reaction. Intein domains can be split into two fragments and still ligate their flanks by a trans-protein-splicing reaction. A bioinformatic analysis of environmental metagenomic data revealed 26 different loci with a novel genomic arrangement. In each locus, a conserved enzyme coding region is broken in two by a split intein, with a free-standing endonuclease gene inserted in between. Eight types of DNA synthesis and repair enzymes have this 'fractured' organization. The new types of naturally split-inteins were analyzed in comparison to known split-inteins. Some loci include apparent gene control elements brought in with the endonuclease gene. A newly predicted homing endonuclease family, related to very-short patch repair (Vsr) endonucleases, was found in half of the loci. These putative homing endonucleases also appear in group-I introns, and as stand-alone inserts in the absence of surrounding intervening sequences. The new fractured genes organization appears to be present mainly in phage, shows how endonucleases can integrate into inteins, and may represent a missing link in the evolution of gene breaking in general, and in the creation of split-inteins in particular.

  2. Evolution of gastropod mitochondrial genome arrangements

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    Zardoya Rafael

    2008-02-01

    Full Text Available Abstract Background Gastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis, and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods. Results Comparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group. Conclusion Four main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia. The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P

  3. Parental Educational Involvement Conceived as the Arrangement of Contingency Operations

    Science.gov (United States)

    Mellon, Robert C.; Moutavelis, Adrianos G.

    2009-01-01

    This study explored the utility of a conception of parental educational involvement as the arrangement of contingency operations that normatively change: the frequency of children's school-related behaviour, the reinforcing potency of stimuli produced by studying, and children's tendencies to request parental intervention. A child-report measure…

  4. The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region.

    Science.gov (United States)

    Hauth, Amy M; Maier, Uwe G; Lang, B Franz; Burger, Gertraud

    2005-01-01

    To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs approximately 40-700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, approximately 3 kb, inverted repeat and several potentially stable approximately 40-80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.

  5. Genomic Aspects of Research Involving Polyploid Plants

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    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  6. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome.

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    Shearer, Lindsay A; Anderson, Lorinda K; de Jong, Hans; Smit, Sandra; Goicoechea, José Luis; Roe, Bruce A; Hua, Axin; Giovannoni, James J; Stack, Stephen M

    2014-05-30

    The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps.

  7. 26 CFR 1.7701(l)-3 - Recharacterizing financing arrangements involving fast-pay stock.

    Science.gov (United States)

    2010-04-01

    ... involving fast-pay stock. 1.7701(l)-3 Section 1.7701(l)-3 Internal Revenue INTERNAL REVENUE SERVICE....7701(l)-3 Recharacterizing financing arrangements involving fast-pay stock. (a) Purpose and scope. This... corporation has fast-pay stock outstanding for any part of its taxable year. (2) Fast-pay stock—(i)...

  8. The Chloroplast Genome of Euglena mutabilis-Cluster Arrangement, Intron Analysis, and Intrageneric Trends.

    Science.gov (United States)

    Dabbagh, Nadja; Preisfeld, Angelika

    2017-01-01

    A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon-intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1.

  9. The mitochondrial genome sequence of a deep-sea, hydrothermal vent limpet, Lepetodrilus nux, presents a novel vetigastropod gene arrangement.

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    Nakajima, Yuichi; Shinzato, Chuya; Khalturina, Mariia; Nakamura, Masako; Watanabe, Hiromi; Satoh, Noriyuki; Mitarai, Satoshi

    2016-08-01

    While mitochondrial (mt) genomes are used extensively for comparative and evolutionary genomics, few mt genomes of deep-sea species, including hydrothermal vent species, have been determined. The Genus Lepetodrilus is a major deep-sea gastropod taxon that occurs in various deep-sea ecosystems. Using next-generation sequencing, we determined nearly the complete mitochondrial genome sequence of Lepetodrilus nux, which inhabits hydrothermal vents in the Okinawa Trough. The total length of the mitochondrial genome is 16,353bp, excluding the repeat region. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, typical of most metazoan genomes. Compared with other vetigastropod mt genome sequences, L. nux employs a novel mt gene arrangement. Other novel arrangements have been identified in the vetigastropod, Fissurella volcano, and in Chrysomallon squamiferum, a neomphaline gastropod; however, all three gene arrangements are different, and Bayesian inference suggests that each lineage diverged independently. Our findings suggest that vetigastropod mt gene arrangements are more diverse than previously realized.

  10. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta).

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    Fučíková, Karolina; Lewis, Paul O; González-Halphen, Diego; Lewis, Louise A

    2014-08-08

    The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available-that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mitochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25-53 kb and variation in intron content (0-11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis. In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Complete mitochondrial genome of Camponotus atrox (Hymenoptera: Formicidae): a new tRNA arrangement in Hymenoptera.

    Science.gov (United States)

    Kim, Min Jee; Hong, Eui Jeong; Kim, Iksoo

    2016-01-01

    We sequenced the complete mitochondrial (mt) genome of Camponotus atrox (Hymenoptera: Formicidae), which is only distributed in Korea. The genome was 16 540 bp in size and contained typical sets of genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs). The C. atrox A+T-rich region, at 1402 bp, was the longest of all sequenced ant genomes and was composed of an identical tandem repeat consisting of six 100-bp copies and one 96-bp copy. A total of 315 bp of intergenic spacer sequence was spread over 23 regions. An alignment of the spacer sequences in ants was largely feasible among congeneric species, and there was substantial sequence divergence, indicating their potential use as molecular markers for congeneric species. The A/T contents at the first and second codon positions of protein-coding genes (PCGs) were similar for ant species, including C. atrox (73.9% vs. 72.3%, on average). With increased taxon sampling among hymenopteran superfamilies, differences in the divergence rates (i.e., the non-synonymous substitution rates) between the suborders Symphyta and Apocrita were detected, consistent with previous results. The C. atrox mt genome had a unique gene arrangement, trnI-trnM-trnQ, at the A+T-rich region and ND2 junction (underline indicates inverted gene). This may have originated from a tandem duplication of trnM-trnI, resulting in trnM-trnI-trnM-trnI-trnQ, and the subsequent loss of the first trnM and second trnI, resulting in trnI-trnM-trnQ.

  12. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

    Science.gov (United States)

    Modern biological analyses are often assisted by recent technologies making the sequencing of complex genomes both technically possible and feasible. We recently sequenced the tomato genome that, like many eukaryotic genomes, is large and complex. Current sequencing technologies allow the developmen...

  13. The complete mitochondrial genome of the mountainous duskywing, Erynnis montanus (Lepidoptera: Hesperiidae): a new gene arrangement in Lepidoptera.

    Science.gov (United States)

    Wang, Ah Rha; Jeong, Heon Cheon; Han, Yeon Soo; Kim, Iksoo

    2014-04-01

    The mountainous duskywing, Erynnis montanus, belongs to a lepidopteran family Hesperiidae. The 15,530-bp long complete mitochondrial genome (mitogenome) of the species has the typical gene content of animals (13 protein-coding genes, two rRNA genes, 22 tRNA genes and one major non-coding A+T-rich region). As typical in lepidopteran mitogenome E. montanus mitogenome also contained a high A/T content in the whole genome (81.7%) and the CGA (arginine) as the start codon for the COI gene. Unlike other lepidopteran species, including two sequenced skippers, the E. montanus mitogenome has a unique arrangement tRNA(Ser)-tRNA(Asn), instead of the tRNA(Asn)-tRNA(Ser) found unanimously in other lepidopteran species, providing a new gene arrangement in Lepidoptera. Such rearrangement probably was likely caused by duplication of gene block tRNA(Ser)-tRNA(Asn) and subsequent random loss of tRNA(Asn) in the first copy and tRNA(Ser) in the second copy, resulting in the arrangement tRNA(Ser)-tRNA(Asn).

  14. Mitochondrial rRNA secondary structures and genome arrangements distinguish chelicerates: comparisons with a harvestman (Arachnida: Opiliones: Phalangium opilio).

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    Masta, Susan E

    2010-01-01

    Arachnids are a highly diverse group of arthropods, and many of the mitochondrial genomes that have been sequenced from arachnids possess unusual features in their inferred gene structures and genome organization. The first complete sequence of a mitochondrial genome from the arachnid order Opiliones (harvestmen) is presented here. Secondary structures of the two mitochondrial ribosomal subunits of Phalangium opilio are inferred and compared to mitochondrial rRNA structures of a hexapod and a chelicerate. The large subunit rRNA of P. opilio is found to have more helices conserved than in other arthropods, while the small subunit rRNA shows a complexity similar to that of other arthropods. These comparisons suggest that a reduction in rRNA complexity occurred in Pancrustacea after the divergence of Pancrustacea and Chelicerata from a common ancestor. The gene arrangement of the mitochondrial genome of P. opilio is compared with the gene order of taxa from all seven other orders of arachnids for which representative mitochondrial genomes have been sequenced. Taxa from five of these seven orders possess gene arrangements identical to that of Limulus polyphemus, and P. opilio is found to have a similar arrangement. However, in P. opilio, some genes near the putative control region are rearranged, with the suite of genes encoding tRNA(Gln), the control region, and tRNA(Ile) located downstream of the two ribosomal RNA genes, and upstream of where they are typically located in chelicerates. The genome encodes only 21 of the typical 22 mitochondrial tRNA genes and lacks the gene for tRNA(Leu(CUN)). The protein-coding genes in the mitochondrial genome of P. opilio show a significantly decreased use of codons recognized by tRNA(Leu(CUN)), likely due to selection to utilize the more specific tRNA(Leu(UUR)) anticodon. The gene arrangement and lack of a tRNA(Leu(CUN)) gene in P. opilio is most parsimoniously explained by the occurrence of at least two translocation events, one

  15. The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae.

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    Chen, Shi-Chun; Wang, Xiao-Qing; Li, Pin-Wu; Hu, Xiang; Wang, Jin-Jun; Peng, Ping

    2016-11-07

    There are numerous gene rearrangements and transfer RNA gene absences existing in mitochondrial (mt) genomes of Aleyrodidae species. To understand how mt genomes evolved in the family Aleyrodidae, we have sequenced the complete mt genome of Aleurocanthus camelliae and comparatively analyzed all reported whitefly mt genomes. The mt genome of A. camelliae is 15,188 bp long, and consists of 13 protein-coding genes, two rRNA genes, 21 tRNA genes and a putative control region (GenBank: KU761949). The tRNA gene, trnI, has not been observed in this genome. The mt genome has a unique gene order and shares most gene boundaries with Tetraleurodes acaciae. Nineteen of 21 tRNA genes have the conventional cloverleaf shaped secondary structure and two (trnS₁ and trnS₂) lack the dihydrouridine (DHU) arm. Using ARWEN and homologous sequence alignment, we have identified five tRNA genes and revised the annotation for three whitefly mt genomes. This result suggests that most absent genes exist in the genomes and have not been identified, due to be lack of technology and inference sequence. The phylogenetic relationships among 11 whiteflies and Drosophila melanogaster were inferred by maximum likelihood and Bayesian inference methods. Aleurocanthus camelliae and T. acaciae form a sister group, and all three Bemisia tabaci and two Bemisia afer strains gather together. These results are identical to the relationships inferred from gene order. We inferred that gene rearrangement plays an important role in the mt genome evolved from whiteflies.

  16. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements.

    Science.gov (United States)

    Liu, Pengfei; Erez, Ayelet; Nagamani, Sandesh C Sreenath; Dhar, Shweta U; Kołodziejska, Katarzyna E; Dharmadhikari, Avinash V; Cooper, M Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A; Bacino, Carlos A; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R; McLean, Scott D; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L; Patel, Ankita; Cheung, Sau Wai; Hastings, P J; Stankiewicz, Paweł; Lupski, James R; Bi, Weimin

    2011-09-16

    Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.

  17. Chloroplast Genome Sequence of the Moss Tortula ruralis: Gene Content and Structural Arrangement Relative to Other Green Plant Chloroplast Genomes

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    Tortula ruralis, a widely distributed moss species in the family Pottiaceae, is increasingly being used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of Tortula ruralis, only the second publishe...

  18. Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98.

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    Surendra Vikram

    Full Text Available Biodegradation of para-Nitrophenol (PNP proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT and hydroquinone (HQ as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM and p-benzoquinone reductase (BqR. Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ, while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ. Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.

  19. Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements

    OpenAIRE

    2015-01-01

    The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma arthritidis MAV-1. Comparative analysis with the genome of M. hominis PG21T reveals distinctive arrangements of repeat-containing surface proteins.

  20. Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements.

    Science.gov (United States)

    Calcutt, Michael J; Foecking, Mark F

    2015-02-26

    The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma arthritidis MAV-1. Comparative analysis with the genome of M. hominis PG21(T) reveals distinctive arrangements of repeat-containing surface proteins.

  1. The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species.

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    Zhang, Juan; Wu, Xiangyun; Li, Yanwei; Zhao, Mengwei; Xie, Mingquan; Li, Anxing

    2014-10-01

    The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

  2. The complete mitochondrial genome of the tapeworm Cladotaenia vulturi (Cestoda: Paruterinidae): gene arrangement and phylogenetic relationships with other cestodes.

    Science.gov (United States)

    Guo, Aijiang

    2016-08-31

    Tapeworms Cladotaenia spp. are among the most important wildlife pathogens in birds of prey. The genus Cladotaenia is placed in the family Paruterinidae based on morphological characteristics and hosts. However, limited molecular information is available for studying the phylogenetic position of this genus in relation to other cestodes. In this study, the complete mitochondrial (mt) genome of Cladotaenia vulturi was amplified using "Long-PCR" and then sequenced by primer walking. Sequence annotation and gene identification were performed by comparison with published flatworm mt genomes. The phylogenetic relationships of C. vulturi with other cestode species were established using the concatenated amino acid sequences of 12 protein-coding genes with Bayesian Inference and Maximum Likelihood methods. The complete mitochondrial genome of the Cladotaenia vulturi is 13,411 kb in size and contains 36 genes. The gene arrangement of C. vulturi is identical to those in Anoplocephala spp. (Anoplocephalidae), Hymenolepis spp. (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but different from that in taeniids owing to the order shift between the tRNA (L1) and tRNA (S2) genes. Phylogenetic analyses based on the amino acid sequences of the concatenated 12 protein-coding genes showed that the species in the Taeniidae form a group and C. vulturi is a sister taxon to the species of the family Taeniidae. To our knowledge, the present study provides the first molecular data to support the early proposal from morphological evidence that the Taeniidae is a sister group to the family Paruterinidae. This novel mt genome sequence will be useful for further investigations into the population genetics, phylogenetics and systematics of the family Paruterinidae and inferring phylogenetic relationships among several lineages within the order Cyclophyllidea.

  3. An arranged marriage for precision medicine: hypoxia and genomic assays in localized prostate cancer radiotherapy.

    Science.gov (United States)

    Bristow, R G; Berlin, A; Dal Pra, A

    2014-03-01

    Prostate cancer (CaP) is the most commonly diagnosed malignancy in males in the Western world with one in six males diagnosed in their lifetime. Current clinical prognostication groupings use pathologic Gleason score, pre-treatment prostatic-specific antigen and Union for International Cancer Control-TNM staging to place patients with localized CaP into low-, intermediate- and high-risk categories. These categories represent an increasing risk of biochemical failure and CaP-specific mortality rates, they also reflect the need for increasing treatment intensity and justification for increased side effects. In this article, we point out that 30-50% of patients will still fail image-guided radiotherapy or surgery despite the judicious use of clinical risk categories owing to interpatient heterogeneity in treatment response. To improve treatment individualization, better predictors of prognosis and radiotherapy treatment response are needed to triage patients to bespoke and intensified CaP treatment protocols. These should include the use of pre-treatment genomic tests based on DNA or RNA indices and/or assays that reflect cancer metabolism, such as hypoxia assays, to define patient-specific CaP progression and aggression. More importantly, it is argued that these novel prognostic assays could be even more useful if combined together to drive forward precision cancer medicine for localized CaP.

  4. The complete mitochondrial genomes of two weevils, Eucryptorrhynchus chinensis and E. brandti: conserved genome arrangement in Curculionidae and deficiency of tRNA-Ile gene

    Directory of Open Access Journals (Sweden)

    Liu Zhen-Kai

    2016-01-01

    Full Text Available The weevils Eucryptorrhynchus chinensis and Eucryptorrhynchus brandti (Coleoptera: Curculionidae, are two of the most important pests of the tree-of-heaven, Ailanthus altissima, which is found throughout China. In this study, the complete mitogenomes of the two weevils have been sequenced using Illumina HiSeqTM 2000. The mitogenomes of E. chinensis and E. brandti are 15,628bp and 15,597bp long with A+T contents of 77.7% and 76.6%, respectively. Both species have typical circular mitochondrial genomes that encode 36 genes. Except the deficiency of tRNA-Ile, the gene composition and order of E. chinensis and E. brandti are identical to the inferred ancestral gene arrangement of insects. In both mitochondrial genomes, the start codons for COI and ND1 are AAT and TTG, respectively. A5bp motif (TACTA is detected in intergenic region between the tRNA-Ser (UCN and ND1 genes. The ATP8/ATP6 and ND4L/ND4 gene pairs appear to overlap four or seven nucleotides (ATAA/ATGATAA in different reading frames. The complete sequences of AT-rich region have two regions including tandem repeats. The study identifies useful genetic markers for studying the population genetics, molecular identification and phylogeographics of Eucryptorrhynchus weevils. The features of the mitochondrial genomes are expected to be valuable in

  5. Mitochondrial genomes of Japanese Babina frogs (Ranidae, Anura): unique gene arrangements and the phylogenetic position of genus Babina.

    Science.gov (United States)

    Kakehashi, Ryosuke; Kurabayashi, Atsushi; Oumi, Shohei; Katsuren, Seiki; Hoso, Masaki; Sumida, Masayuki

    2013-01-01

    Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina frogs, B. holsti, B. okinavana, and B. subaspera and 1 ranid frog Lithobates catesbeianus. The genes of NADH dehydrogenase subunit 5 (nad5) and the control region (CR) were found to have high sequence divergences and to be usable for population genetics studies. At present, no consensus on the phylogenetic position of genus Babina has been reached. To resolve this problem, we performed molecular phylogenetic analyses with the largest dataset used to date (11,345 bp from 2 ribosomal RNA- and 13 protein-encoding genes) in studies dealing with Babina phylogeny. These analyses revealed monophyly of Babina and Odorrana. It is well known that mt gene rearrangements of animals can provide usable phylogenetic information. Thus, we also compared the mt gene arrangements among Babina species and other related genera. Of the surveyed species, only L. catesbeianus manifested typical neobatrachian-type mt gene organization. In the B. okinavana, an additional pseudogene of tRNA-His (trnH) was observed in the CR downstream region. Furthermore, in the B. holsti and B. subaspera, the trnH/nad5 block was translocated from its typical position to the CR downstream region, and the translocated trnH became a pseudogene. The position of the trnH pseudogene is consistent with the translocated trnH position reported in Odorrana. Consequently, the trnH rearrangement seems to be a common ancestry characteristic (synapomorphy) of Babina and Odorrana. Based on the "duplication and deletion" gene rearrangement model, a single genomic duplication event can explain the order of derived mt genes found in Babina and Odorrana.

  6. Identification and characterization of adult alpha-and beta-globin genes and their genomic arrangement in Pseudosciaena crocea

    Institute of Scientific and Technical Information of China (English)

    CHU Wuying; QIAN Ronghua; WANG Lianshen; YU Xiameng; YOU Zhenqiang; YU Lian

    2006-01-01

    The α- and β-globin genes from Pseudosciaena crocea were cloned by rapid amplification of cDNA 3'-end (3'-RACE). The cDNA of the α-globin is 595 bp with the ATG start codon located at Position 37, the TAA stop codon at Position 469 and the AATAAA polyadenylation signal at Position 560, which codifies 145 amino acids. The entire open reading frame of the β-globin gene is 447 bp long, which encodes 148 amino acids. Amino acid identity of the α- globin or β-globin gene compared with those reported in other fish species, ranged from 31.9% to 76.4%. When comparing with human α- and β-globins, three important alterations in the structural regions can be noted: α39 Thr→Gln, α113 His→Tyr and β117 His→Lys. The α-globin has a unique inserted amino acid residue in the 47th position. To understand the process of globin gene duplication and identify the regulatory elements present in the intergenic and intragenic regions of globin genes, the genomic arrangement of α- and β-globin genes was investigated. The results showed that the orientation of the two genes was head-to-head relative to each other. The intergenic region between the translation initiation codons of the linked α- and β-globin genes contains classical promoter elements and the length of it is much shorter than that reported in other fish.

  7. Complete Sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: Gene arrangements indicate that platyhelminths are eutrochozoans

    Energy Technology Data Exchange (ETDEWEB)

    von Nickisch-Rosenegk, Markus; Brown, Wesley M.; Boore, Jeffrey L.

    2001-01-01

    Using ''long-PCR'' we have amplified in overlapping fragments the complete mitochondrial genome of the tapeworm Hymenolepis diminuta (Platyhelminthes: Cestoda) and determined its 13,900 nucleotide sequence. The gene content is the same as that typically found for animal mitochondrial DNA (mtDNA) except that atp8 appears to be lacking, a condition found previously for several other animals. Despite the small size of this mtDNA, there are two large non-coding regions, one of which contains 13 repeats of a 31 nucleotide sequence and a potential stem-loop structure of 25 base pairs with an 11-member loop. Large potential secondary structures are identified also for the non-coding regions of two other cestode mtDNAs. Comparison of the mitochondrial gene arrangement of H. diminuta with those previously published supports a phylogenetic position of flatworms as members of the Eutrochozoa, rather than being basal to either a clade of protostomes or a clade of coelomates.

  8. Genome-wide characterization of vibrio phage ϕpp2 with unique arrangements of the mob-like genes

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    Lin Ying-Rong

    2012-06-01

    Full Text Available Abstract Background Vibrio parahaemolyticus is associated with gastroenteritis, wound infections, and septicemia in human and animals. Phages can control the population of the pathogen. So far, the only one reported genome among giant vibriophages is KVP40: 244,835 bp with 26% coding regions that have T4 homologs. Putative homing endonucleases (HE were found in Vibrio phage KVP40 bearing one segD and Vibrio cholerae phage ICP1 carrying one mobC/E and one segG. Results A newly isolated Vibrio phage ϕpp2, which was specific to the hosts of V. parahaemolyticus and V. alginolyticus, featured a long nonenveloped head of ~90 × 150 nm and tail of ~110 nm. The phage can survive at 50°C for more than one hour. The genome of the phage ϕpp2 was sequenced to be 246,421 bp, which is 1587 bp larger than KVP40. 383 protein-encoding genes (PEGs and 30 tRNAs were found in the phage ϕpp2. Between the genomes of ϕpp2 and KVP40, 254 genes including 29 PEGs for viral structure were of high similarity, whereas 17 PEGs of KVP40 and 21 PEGs of ϕpp2 were unmatched. In both genomes, the capsid and tail genes have been identified, as well as the extensive representation of the DNA replication, recombination, and repair enzymes. In addition to the three giant indels of 1098, 1143 and 3330 nt, ϕpp2 possessed unique proteins involved in potassium channel, gp2 (DNA end protector, tRNA nucleotidyltransferase, and mob-type HEs, which were not reported in KVP40. The ϕpp2 PEG274, with strong promoters and translational initiation, was identified to be a mobE type, flanked by NrdA and NrdB/C homologs. Coincidently, several pairs of HE-flanking homologs with empty center were found in the phages of Vibrio phages ϕpp2 and KVP40, as well as in Aeromonas phages (Aeh1 and Ae65, and cyanophage P-SSM2. Conclusions Vibrio phage ϕpp2 was characterized by morphology, growth, and genomics with three giant indels and different types of HEs. The gene analysis on the required

  9. Comparative genomics of proteins involved in RNA nucleocytoplasmic export

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    Goldenberg Samuel

    2011-01-01

    Full Text Available Abstract Background The establishment of the nuclear membrane resulted in the physical separation of transcription and translation, and presented early eukaryotes with a formidable challenge: how to shuttle RNA from the nucleus to the locus of protein synthesis. In prokaryotes, mRNA is translated as it is being synthesized, whereas in eukaryotes mRNA is synthesized and processed in the nucleus, and it is then exported to the cytoplasm. In metazoa and fungi, the different RNA species are exported from the nucleus by specialized pathways. For example, tRNA is exported by exportin-t in a RanGTP-dependent fashion. By contrast, mRNAs are associated to ribonucleoproteins (RNPs and exported by an essential shuttling complex (TAP-p15 in human, Mex67-mtr2 in yeast that transports them through the nuclear pore. The different RNA export pathways appear to be well conserved among members of Opisthokonta, the eukaryotic supergroup that includes Fungi and Metazoa. However, it is not known whether RNA export in the other eukaryotic supergroups follows the same export routes as in opisthokonts. Methods Our objective was to reconstruct the evolutionary history of the different RNA export pathways across eukaryotes. To do so, we screened an array of eukaryotic genomes for the presence of homologs of the proteins involved in RNA export in Metazoa and Fungi, using human and yeast proteins as queries. Results Our genomic comparisons indicate that the basic components of the RanGTP-dependent RNA pathways are conserved across eukaryotes, and thus we infer that these are traceable to the last eukaryotic common ancestor (LECA. On the other hand, several of the proteins involved in RanGTP-independent mRNA export pathways are less conserved, which would suggest that they represent innovations that appeared later in the evolution of eukaryotes. Conclusions Our analyses suggest that the LECA possessed the basic components of the different RNA export mechanisms found today

  10. Reproductive medicine involving genome editing: clinical uncertainties and embryological needs.

    Science.gov (United States)

    Ishii, Tetsuya

    2017-01-01

    Genome editing based on site-directed nucleases facilitated efficient and versatile genetic modifications in human cells. However, recent reports, demonstrating CRISPR/Cas9-mediated genome editing in human embryos have raised profound concerns worldwide. This commentary explores the clinical justification and feasibility of reproductive medicine using germline genome editing. Despite the perceived utility of reproductive medicine for treating intractable infertility, it is difficult to justify germline genome editing from the perspective of the prospective child. As suggested by the UK legalization regarding mitochondrial donation, the prevention of genetic disease in offspring by genome editing might be acceptable in limited cases of serious or life-threatening conditions, where no alternative medicine is available. Nonetheless, the mosaicism underlying human embryos as well as the off-target effect by artificial nucleases will likely hamper preimplantation genetic diagnosis prior to embryo transfer. Such considerations suggest that this type of reproductive medicine should not be developed toward a clinical application. However, the clinical uncertainties underscore the need for embryology that can address fundamental questions regarding germline aneuploidy and mosaicism using genome editing. Copyright © 2016 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  11. The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart: a novel gene arrangement among arthropods

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    Vanholme Bartel

    2009-03-01

    Full Text Available Abstract Background The apparent scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks. This subclass encompasses over 48,000 species and forms the largest group within the Arachnida. Although mitochondrial genomes are widely utilised for phylogenetic and population genetic studies, only 20 mitochondrial genomes of Acari have been determined, of which only one belongs to the diverse order of the Sarcoptiformes. In this study, we describe the mitochondrial genome of the European house dust mite Dermatophagoides pteronyssinus, the most important member of this largely neglected group. Results The mitochondrial genome of D. pteronyssinus is a circular DNA molecule of 14,203 bp. It contains the complete set of 37 genes (13 protein coding genes, 2 rRNA genes and 22 tRNA genes, usually present in metazoan mitochondrial genomes. The mitochondrial gene order differs considerably from that of other Acari mitochondrial genomes. Compared to the mitochondrial genome of Limulus polyphemus, considered as the ancestral arthropod pattern, only 11 of the 38 gene boundaries are conserved. The majority strand has a 72.6% AT-content but a GC-skew of 0.194. This skew is the reverse of that normally observed for typical animal mitochondrial genomes. A microsatellite was detected in a large non-coding region (286 bp, which probably functions as the control region. Almost all tRNA genes lack a T-arm, provoking the formation of canonical cloverleaf tRNA-structures, and both rRNA genes are considerably reduced in size. Finally, the genomic sequence was used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analysis clustered D. pteronyssinus with Steganacarus magnus, forming a sistergroup of the Trombidiformes. Conclusion Although the mitochondrial genome of D. pteronyssinus shares different features with previously characterised Acari mitochondrial genomes, it is unique in many ways. Gene

  12. The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae.

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    Hu Li

    Full Text Available Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5% of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.

  13. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

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    Wolf Paul G

    2010-02-01

    Full Text Available Abstract Background Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant. Results The Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered. Conclusions Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.

  14. Next-Generation Sequencing of Two Mitochondrial Genomes from Family Pompilidae (Hymenoptera: Vespoidea Reveal Novel Patterns of Gene Arrangement

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    Peng-Yan Chen

    2016-10-01

    Full Text Available Animal mitochondrial genomes have provided large and diverse datasets for evolutionary studies. Here, the first two representative mitochondrial genomes from the family Pompilidae (Hymenoptera: Vespoidea were determined using next-generation sequencing. The sequenced region of these two mitochondrial genomes from the species Auplopus sp. and Agenioideus sp. was 16,746 bp long with an A + T content of 83.12% and 16,596 bp long with an A + T content of 78.64%, respectively. In both species, all of the 37 typical mitochondrial genes were determined. The secondary structure of tRNA genes and rRNA genes were predicted and compared with those of other insects. Atypical trnS1 using abnormal anticodons TCT and lacking D-stem pairings was identified. There were 49 helices belonging to six domains in rrnL and 30 helices belonging to three domains in rrns present. Compared with the ancestral organization, four and two tRNA genes were rearranged in mitochondrial genomes of Auplopus and Agenioideus, respectively. In both species, trnM was shuffled upstream of the trnI-trnQ-trnM cluster, and trnA was translocated from the cluster trnA-trnR-trnN-trnS1-trnE-trnF to the region between nad1 and trnL1, which is novel to the Vespoidea. In Auplopus, the tRNA cluster trnW-trnC-trnY was shuffled to trnW-trnY-trnC. Phylogenetic analysis within Vespoidea revealed that Pompilidae and Mutillidae formed a sister lineage, and then sistered Formicidae. The genomes presented in this study have enriched the knowledge base of molecular markers, which is valuable in respect to studies about the gene rearrangement mechanism, genomic evolutionary processes and phylogeny of Hymenoptera.

  15. Unique genomic arrangements in an invasive serotype M23 strain of Streptococcus pyogenes identify genes that induce hypervirulence.

    Science.gov (United States)

    Bao, Yunjuan; Liang, Zhong; Booyjzsen, Claire; Mayfield, Jeffrey A; Li, Yang; Lee, Shaun W; Ploplis, Victoria A; Song, Hui; Castellino, Francis J

    2014-12-01

    The first genome sequence of a group A Streptococcus pyogenes serotype M23 (emm23) strain (M23ND), isolated from an invasive human infection, has been completed. The genome of this opacity factor-negative (SOF(-)) strain is composed of a circular chromosome of 1,846,477 bp. Gene profiling showed that this strain contained six phage-encoded and 24 chromosomally inherited well-known virulence factors, as well as 11 pseudogenes. The bacterium has acquired four large prophage elements, ΦM23ND.1 to ΦM23ND.4, harboring genes encoding streptococcal superantigen (ssa), streptococcal pyrogenic exotoxins (speC, speH, and speI), and DNases (spd1 and spd3), with phage integrase genes being present at one flank of each phage insertion, suggesting that the phages were integrated by horizontal gene transfer. Comparative analyses revealed unique large-scale genomic rearrangements that result in genomic rearrangements that differ from those of previously sequenced GAS strains. These rearrangements resulted in an imbalanced genomic architecture and translocations of chromosomal virulence genes. The covS sensor in M23ND was identified as a pseudogene, resulting in the attenuation of speB function and increased expression of the genes for the chromosomal virulence factors multiple-gene activator (mga), M protein (emm23), C5a peptidase (scpA), fibronectin-binding proteins (sfbI and fbp54), streptolysin O (slo), hyaluronic acid capsule (hasA), streptokinase (ska), and DNases (spd and spd3), which were verified by PCR. These genes are responsible for facilitating host epithelial cell binding and and/or immune evasion, thus further contributing to the virulence of M23ND. In conclusion, strain M23ND has become highly pathogenic as the result of a combination of multiple genetic factors, particularly gene composition and mutations, prophage integrations, unique genomic rearrangements, and regulated expression of critical virulence factors.

  16. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

    OpenAIRE

    Wolf Paul G; Everett Karin DE; Mandoli Dina F; Boore Jeffrey L; Kuehl Jennifer V; Mishler Brent D; Murdock Andrew G; Oliver Melvin J; Duffy Aaron M; Karol Kenneth G

    2010-01-01

    Abstract Background Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-t...

  17. Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium.

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    Miroslav Arambasic

    Full Text Available The epigenetic influence of maternal cells on the development of their progeny has long been studied in various eukaryotes. Multicellular organisms usually provide their zygotes not only with nutrients but also with functional elements required for proper development, such as coding and non-coding RNAs. These maternally deposited RNAs exhibit a variety of functions, from regulating gene expression to assuring genome integrity. In ciliates, such as Paramecium these RNAs participate in the programming of large-scale genome reorganization during development, distinguishing germline-limited DNA, which is excised, from somatic-destined DNA. Only a handful of proteins playing roles in this process have been identified so far, including typical RNAi-derived factors such as Dicer-like and Piwi proteins. Here we report and characterize two novel proteins, Pdsg1 and Pdsg2 (Paramecium protein involved in Development of the Somatic Genome 1 and 2, involved in Paramecium genome reorganization. We show that these proteins are necessary for the excision of germline-limited DNA during development and the survival of sexual progeny. Knockdown of PDSG1 and PDSG2 genes affects the populations of small RNAs known to be involved in the programming of DNA elimination (scanRNAs and iesRNAs and chromatin modification patterns during development. Our results suggest an association between RNA-mediated trans-generational epigenetic signal and chromatin modifications in the process of Paramecium genome reorganization.

  18. Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

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    Maria Virginia Sanchez-Puerta

    2014-12-01

    Full Text Available This review focuses on plant-to-plant horizontal gene transfer (HGT involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

  19. A Pilot Genome-Wide Association Study Identifies Potential Metabolic Pathways Involved in Tinnitus

    Science.gov (United States)

    Gilles, Annick; Van Camp, Guy; Van de Heyning, Paul; Fransen, Erik

    2017-01-01

    Tinnitus, the perception of an auditory phantom sound in the form of ringing, buzzing, roaring, or hissing in the absence of an external sound source, is perceived by ~15% of the population and 2.5% experiences a severely bothersome tinnitus. The contribution of genes on the development of tinnitus is still under debate. The current manuscript reports a pilot Genome Wide Association Study (GWAS) into tinnitus, in a small cohort of 167 independent tinnitus subjects, and 749 non-tinnitus controls, who were collected as part of a cross-sectional study. After genotyping, imputation, and quality checking, the association between the tinnitus phenotype and 4,000,000 single-nucleotide polymorphisms (SNPs) was tested followed by gene set enrichment analysis. None of the SNPs reached the threshold for genome-wide significance (p tinnitus phenotype. Despite the lack of genome-wide significant SNPs, which is, at least in part, due to the limited sample size of the current study, evidence was found for a genetic involvement in tinnitus. Gene set enrichment analysis showed several metabolic pathways to be significantly enriched with SNPs having a low p-value in the GWAS. These pathways are involved in oxidative stress, endoplasmatic reticulum (ER) stress, and serotonin reception mediated signaling. These results are a promising basis for further research into the genetic basis of tinnitus, including GWAS with larger sample sizes and considering tinnitus subtypes for which a greater genetic contribution is more likely. PMID:28303087

  20. Comparative genomics of plant-asssociated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions

    NARCIS (Netherlands)

    Loper, J.E.; Hassan, K.A.; Mavrodi, D.V.; Davis II, E.W.; Lim, C.K.; Shaffer, B.T.; Elbourne, L.D.H.; Stockwell, V.O.; Hartney, S.L.; Breakwell, K.; Henkels, M.D.; Tetu, S.G.; Rangel, L.I.; Kidarsa, T.A.; Wilson, N.L.; Mortel, van de J.E.; Song, C.; Blumhagen, R.; Radune, D.; Hostetler, J.B.; Brinkac, L.M.; Durkin, A.C.; Kluepfel, D.A.; Wechter, W.P.; Anderson, A.J.; Kim, Y.C.; Pierson III, L.S.; Pierson, E.A.; Lindow, S.E.; Kobayashi, D.Y.; Raaijmakers, J.; Weller, D.M.; Thomashow, L.S.; Allen, A.E.; Paulsen, I.T.

    2012-01-01

    We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multi

  1. Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

    Science.gov (United States)

    Martinez, Diego A.; Oliver, Brian G.; Gräser, Yvonne; Goldberg, Jonathan M.; Li, Wenjun; Martinez-Rossi, Nilce M.; Monod, Michel; Shelest, Ekaterina; Barton, Richard C.; Birch, Elizabeth; Brakhage, Axel A.; Chen, Zehua; Gurr, Sarah J.; Heiman, David; Heitman, Joseph; Kosti, Idit; Rossi, Antonio; Saif, Sakina; Samalova, Marketa; Saunders, Charles W.; Shea, Terrance; Summerbell, Richard C.; Xu, Jun; Young, Sarah; Zeng, Qiandong; Birren, Bruce W.; Cuomo, Christina A.; White, Theodore C.

    2012-01-01

    ABSTRACT The major cause of athlete’s foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response. PMID:22951933

  2. A genomic region involved in the formation of adhesin fibers in Bacillus cereus biofilms

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    Joaquín eCaro-Astorga

    2015-01-01

    Full Text Available Bacillus cereus is a bacterial pathogen that is responsible for many recurrent disease outbreaks due to food contamination. Spores and biofilms are considered the most important reservoirs of B. cereus in contaminated fresh vegetables and fruits. Biofilms are bacterial communities that are difficult to eradicate from biotic and abiotic surfaces because of their stable and extremely strong extracellular matrix. These extracellular matrixes contain exopolysaccharides, proteins, extracellular DNA, and other minor components. Although B. cereus can form biofilms, the bacterial features governing assembly of the protective extracellular matrix are not known. Using the well-studied bacterium B. subtilis as a model, we identified two genomic loci in B. cereus, which encodes two orthologs of the amyloid-like protein TasA of B. subtilis and a SipW signal peptidase. Deletion of this genomic region in B. cereus inhibited biofilm assembly; notably, mutation of the putative signal peptidase SipW caused the same phenotype. However, mutations in tasA or calY did not completely prevent biofilm formation; strains that were mutated for either of these genes formed phenotypically different surface attached biofilms. Electron microscopy studies revealed that TasA polymerizes to form long and abundant fibers on cell surfaces, whereas CalY does not aggregate similarly. Heterologous expression of this amyloid-like cassette in a B. subtilis strain lacking the factors required for the assembly of TasA amyloid-like fibers revealed i the involvement of this B. cereus genomic region in formation of the air-liquid interphase pellicles and ii the intrinsic ability of TasA to form fibers similar to the amyloid-like fibers produced by its B. subtilis ortholog.

  3. Candidate driver genes involved in genome maintenance and DNA repair in Sézary syndrome.

    Science.gov (United States)

    Woollard, Wesley J; Pullabhatla, Venu; Lorenc, Anna; Patel, Varsha M; Butler, Rosie M; Bayega, Anthony; Begum, Nelema; Bakr, Farrah; Dedhia, Kiran; Fisher, Joshua; Aguilar-Duran, Silvia; Flanagan, Charlotte; Ghasemi, Aria A; Hoffmann, Ricarda M; Castillo-Mosquera, Nubia; Nuttall, Elisabeth A; Paul, Arisa; Roberts, Ceri A; Solomonidis, Emmanouil G; Tarrant, Rebecca; Yoxall, Antoinette; Beyers, Carl Z; Ferreira, Silvia; Tosi, Isabella; Simpson, Michael A; de Rinaldis, Emanuele; Mitchell, Tracey J; Whittaker, Sean J

    2016-06-30

    Sézary syndrome (SS) is a leukemic variant of cutaneous T-cell lymphoma (CTCL) and represents an ideal model for study of T-cell transformation. We describe whole-exome and single-nucleotide polymorphism array-based copy number analyses of CD4(+) tumor cells from untreated patients at diagnosis and targeted resequencing of 101 SS cases. A total of 824 somatic nonsynonymous gene variants were identified including indels, stop-gain/loss, splice variants, and recurrent gene variants indicative of considerable molecular heterogeneity. Driver genes identified using MutSigCV include POT1, which has not been previously reported in CTCL; and TP53 and DNMT3A, which were also identified consistent with previous reports. Mutations in PLCG1 were detected in 11% of tumors including novel variants not previously described in SS. This study is also the first to show BRCA2 defects in a significant proportion (14%) of SS tumors. Aberrations in PRKCQ were found to occur in 20% of tumors highlighting selection for activation of T-cell receptor/NF-κB signaling. A complex but consistent pattern of copy number variants (CNVs) was detected and many CNVs involved genes identified as putative drivers. Frequent defects involving the POT1 and ATM genes responsible for telomere maintenance were detected and may contribute to genomic instability in SS. Genomic aberrations identified were enriched for genes implicated in cell survival and fate, specifically PDGFR, ERK, JAK STAT, MAPK, and TCR/NF-κB signaling; epigenetic regulation (DNMT3A, ASLX3, TET1-3); and homologous recombination (RAD51C, BRCA2, POLD1). This study now provides the basis for a detailed functional analysis of malignant transformation of mature T cells and improved patient stratification and treatment.

  4. Voluntary Environmental Governance Arrangements

    NARCIS (Netherlands)

    van der Heijden, J.

    2012-01-01

    Voluntary environmental governance arrangements have focal attention in studies on environmental policy, regulation and governance. The four major debates in the contemporary literature on voluntary environmental governance arrangements are studied. The literature falls short of sufficiently

  5. Voluntary Environmental Governance Arrangements

    NARCIS (Netherlands)

    van der Heijden, J.

    2012-01-01

    Voluntary environmental governance arrangements have focal attention in studies on environmental policy, regulation and governance. The four major debates in the contemporary literature on voluntary environmental governance arrangements are studied. The literature falls short of sufficiently specify

  6. Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker

    Directory of Open Access Journals (Sweden)

    Berline eFopa Fomeju

    2015-09-01

    Full Text Available All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the

  7. A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus).

    Science.gov (United States)

    Vilas, Román; Vandamme, Sara G; Vera, Manuel; Bouza, Carmen; Maes, Gregory E; Volckaert, Filip A M; Martínez, Paulino

    2015-10-01

    Partitioning phenotypic variance in genotypic and environmental variance may benefit from the population genomic assignment of genes putatively involved in adaptation. We analyzed a total of 256 markers (120 microsatellites and 136 Single Nucleotide Polymorphisms - SNPs), several of them associated to Quantitative Trait Loci (QTL) for growth and resistance to pathologies, with the aim to identify potential adaptive variation in turbot Scophthalmus maximus L. The study area in the Northeastern Atlantic Ocean, from Iberian Peninsula to the Baltic Sea, involves a gradual change in temperature and an abrupt change in salinity conditions. We detected 27 candidate loci putatively under selection. At least four of the five SNPs identified as outliers are located within genes coding for ribosomal proteins or directly related with the production of cellular proteins. One of the detected outliers, previously identified as part of a QTL for growth, is a microsatellite linked to a gene coding for a growth factor receptor. A similar set of outliers was detected when natural populations were compared with a sample subjected to strong artificial selection for growth along four generations. The observed association between FST outliers and growth-related QTL supports the hypothesis of changes in growth as an adaptation to differences in temperature and salinity conditions. However, further work is needed to confirm this hypothesis.

  8. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

    Science.gov (United States)

    Loper, Joyce E; Hassan, Karl A; Mavrodi, Dmitri V; Davis, Edward W; Lim, Chee Kent; Shaffer, Brenda T; Elbourne, Liam D H; Stockwell, Virginia O; Hartney, Sierra L; Breakwell, Katy; Henkels, Marcella D; Tetu, Sasha G; Rangel, Lorena I; Kidarsa, Teresa A; Wilson, Neil L; van de Mortel, Judith E; Song, Chunxu; Blumhagen, Rachel; Radune, Diana; Hostetler, Jessica B; Brinkac, Lauren M; Durkin, A Scott; Kluepfel, Daniel A; Wechter, W Patrick; Anderson, Anne J; Kim, Young Cheol; Pierson, Leland S; Pierson, Elizabeth A; Lindow, Steven E; Kobayashi, Donald Y; Raaijmakers, Jos M; Weller, David M; Thomashow, Linda S; Allen, Andrew E; Paulsen, Ian T

    2012-07-01

    We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to

  9. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

    Directory of Open Access Journals (Sweden)

    Joyce E Loper

    2012-07-01

    Full Text Available We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring

  10. Genomic imbalances in esophageal carcinoma cell lines involve Wnt pathway genes

    Institute of Scientific and Technical Information of China (English)

    Jacqueline Brown; Hannelie Bothma; Robin Veale; Pascale Willem

    2011-01-01

    AIM: To identify molecular markers shared across South African esophageal squamous cell carcinoma (ESCC) cell lines using cytogenetics, fluorescence in situ hybridization (FISH) and single nucleotide polymorphism (SNP) array copy number analysis. METHODS: We used conventional cytogenetics, FISH, and multicolor FISH to characterize the chromosomal rearrangements of five ESCC cell lines established in South Africa. The whole genome copy number profile was established from 250K SNP arrays, and data was analyzed with the CNAT 4.0 and GISTIC software. RESULTS: We detected common translocation breakpoints involving chromosomes 1p11-12 and 3p11.2, the latter correlated with the deletion, or interruption of the EPHA3 gene. The most significant amplifications involved the following chromosomal regions and genes: 11q13.3 ( CCND1, FGF3, FGF4, FGF19, MYEOV), 8q24.21( C-MYC, FAM84B), 11q22.1-q22.3 ( BIRC2, BIRC3), 5p15.2 ( CTNND2), 3q11.2-q12.2 ( MINA) and 18p11.32 ( TYMS, YES1). The significant deletions included 1p31.2-p31.1 ( CTH, GADD45α, DIRAS3), 2q22.1 ( LRP1B), 3p12.1-p14.2 ( FHIT), 4q22.1-q32.1 ( CASP6, SMAD1), 8p23.2-q11.1 ( BNIP3L) and 18q21.1-q21.2 ( SMAD4, DCC). The 3p11.2 translocation breakpoint was shared across four cell lines, supporting a role for genes involved at this site, in particular, the EPHA3 gene which has previously been reported to be deleted in ESCC. CONCLUSION: The finding that a significant number of genes that were amplified (FGF3 , FGF4 , FGF19 , CCND1 and C-MYC ) or deleted (SFRP2 gene) are involved in the Wnt and fibroblast growth factor signaling pathways, suggests that these pathways may be activated in these cell lines.

  11. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Kohane Isaac

    2005-11-01

    Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

  12. Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar.

    Science.gov (United States)

    Tollenaere, C; Jacquet, S; Ivanova, S; Loiseau, A; Duplantier, J-M; Streiff, R; Brouat, C

    2013-01-01

    Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection. © 2012 Blackwell Publishing Ltd.

  13. On arrangements of pseudohyperplanes

    Indian Academy of Sciences (India)

    PRIYAVRAT DESHPANDE

    2016-08-01

    To every realizable oriented matroid there corresponds an arrangement of real hyperplanes. The homeomorphism type of the complexified complement of such an arrangement is completely determined by the oriented matroid. In this paper we study arrangements of pseudohyperplanes; they correspond to non-realizable oriented matroids. These arrangements arise as a consequence of the Folkman--Lawrence topological representation theorem. We propose a generalization of the complexification process in this context. In particular we construct a space naturally associated with these pseudo-arrangements which is homeomorphic to the complexified complement in the realizable case. Further, we generalize the classical theorem of Salvetti and show that this space has the homotopy type of a cell complex defined in terms of the oriented matroid.

  14. Optical Arrangement and Method

    DEFF Research Database (Denmark)

    2010-01-01

    Processing of electromagnetic radiation is described, said incoming electromagnetic radiation comprising radiation in a first wavelength interval and a plurality of spatial frequencies. An arrangement comprises a focusing arrangement for focusing the incoming electromagnetic radiation, a first...... cavity configured to comprise an intra cavity laser beam, a nonlinear crystal arranged in the first cavity such that it is capable of receiving the focused electromagnetic radiation and, in dependence on the spatial overlap between the focused electromagnetic radiation and the intra-cavity laser beam......, by interaction with the intra-cavity laser beam provide processed electromagnetic radiation, said processed electromagnetic radiation comprising radiation in a second wavelength interval and at least a subset of said plurality of spatial frequencies. In other words, such an arrangement is capable of enabling...

  15. Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio genus.

    Directory of Open Access Journals (Sweden)

    Stefano eRomano

    2016-03-01

    Full Text Available Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage.Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus.Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche

  16. Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus.

    Science.gov (United States)

    Romano, Stefano; Fernàndez-Guerra, Antonio; Reen, F Jerry; Glöckner, Frank O; Crowley, Susan P; O'Sullivan, Orla; Cotter, Paul D; Adams, Claire; Dobson, Alan D W; O'Gara, Fergal

    2016-01-01

    Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its

  17. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

    Science.gov (United States)

    Ravcheev, Dmitry A.; Thiele, Ines

    2016-01-01

    Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM. PMID:26904004

  18. The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism.

    Directory of Open Access Journals (Sweden)

    Erik Lysøe

    Full Text Available Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

  19. The Genome of the Generalist Plant Pathogen Fusarium avenaceum Is Enriched with Genes Involved in Redox, Signaling and Secondary Metabolism

    Science.gov (United States)

    Lysøe, Erik; Harris, Linda J.; Walkowiak, Sean; Subramaniam, Rajagopal; Divon, Hege H.; Riiser, Even S.; Llorens, Carlos; Gabaldón, Toni; Kistler, H. Corby; Jonkers, Wilfried; Kolseth, Anna-Karin; Nielsen, Kristian F.; Thrane, Ulf; Frandsen, Rasmus J. N.

    2014-01-01

    Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts. PMID:25409087

  20. Genome-wide identification and functional analysis of long noncoding RNAs involved in the response to graphene oxide.

    Science.gov (United States)

    Wu, Qiuli; Zhou, Xuefeng; Han, Xiaoxiao; Zhuo, Yizhou; Zhu, Siting; Zhao, Yunli; Wang, Dayong

    2016-09-01

    Long noncoding RNAs (lncRNAs), which are defined as noncoding RNAs having at least 200 nucleotides, can potentially regulate various biological processes. However, the roles of lncRNAs in regulating cellular response to engineered nanomaterials (ENMs) are still unclear. Using Hiseq 2000 sequencing technique, we performed a genome-wide screen to identify lncRNAs involved in the control of toxicity of graphene oxide (GO) using in vivo Caenorhabditis elegans assay system. HiSeq 2000 sequencing, followed by quantitative analysis, identified only 34 dysregulated lncRNAs in GO exposed nematodes. Bioinformatics analysis implies the biological processes and signaling pathways mediated by candidate lncRNAs involved in the control of GO toxicity. A lncRNAs-miRNAs network possibly involved in the control of GO toxicity was further raised. Moreover, we identified the shared lncRNAs based on the molecular regulation basis for chemical surface modifications and/or genetic mutations in reducing GO toxicity. We further provide direct evidence that these shared lncRNAs, linc-37 and linc-14, were involved in the control of chemical surface modifications and genetic mutations in reducing GO toxicity. linc-37 binding to transcriptional factor FOXO/DAF-16 might be important for the control of GO toxicity. Our whole-genome identification and functional analysis of lncRNAs highlights the important roles of lncRNAs based molecular mechanisms for cellular responses to ENMs in organisms.

  1. A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Richard J Poole

    2011-06-01

    Full Text Available One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome, we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1 the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2 the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single

  2. Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency

    Science.gov (United States)

    Frankowiack, Marcel; Kierczak, Marcin; Bergvall, Kerstin; Axelsson, Erik; Tintle, Linda; Marti, Eliane; Roosje, Petra; Leeb, Tosso; Hedhammar, Åke; Hammarström, Lennart; Lindblad-Toh, Kerstin

    2015-01-01

    Immunoglobulin A deficiency (IgAD) is the most common primary immune deficiency disorder in both humans and dogs, characterized by recurrent mucosal tract infections and a predisposition for allergic and other immune mediated diseases. In several dog breeds, low IgA levels have been observed at a high frequency and with a clinical resemblance to human IgAD. In this study, we used genome-wide association studies (GWAS) to identify genomic regions associated with low IgA levels in dogs as a comparative model for human IgAD. We used a novel percentile groups-approach to establish breed-specific cut-offs and to perform analyses in a close to continuous manner. GWAS performed in four breeds prone to low IgA levels (German shepherd, Golden retriever, Labrador retriever and Shar-Pei) identified 35 genomic loci suggestively associated (p IgA levels. In German shepherd, three genomic regions (candidate genes include KIRREL3 and SERPINA9) were genome-wide significantly associated (p IgA levels. A ~20kb long haplotype on CFA28, significantly associated (p = 0.0005) to IgA levels in Shar-Pei, was positioned within the first intron of the gene SLIT1. Both KIRREL3 and SLIT1 are highly expressed in the central nervous system and in bone marrow and are potentially important during B-cell development. SERPINA9 expression is restricted to B-cells and peaks at the time-point when B-cells proliferate into antibody-producing plasma cells. The suggestively associated regions were enriched for genes in Gene Ontology gene sets involving inflammation and early immune cell development. PMID:26225558

  3. Best connected rectangular arrangements

    Directory of Open Access Journals (Sweden)

    Krishnendra Shekhawat

    2016-03-01

    Full Text Available It can be found quite often in the literature that many well-known architects have employed either the golden rectangle or the Fibonacci rectangle in their works. On contrary, it is rare to find any specific reason for using them so often. Recently, Shekhawat (2015 proved that the golden rectangle and the Fibonacci rectangle are one of the best connected rectangular arrangements and this may be one of the reasons for their high presence in architectural designs. In this work we present an algorithm that generates n-4 best connected rectangular arrangements so that the proposed solutions can be further used by architects for their designs.

  4. Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation.

    Science.gov (United States)

    Filatov, Victor; Dowdle, John; Smirnoff, Nicholas; Ford-Lloyd, Brian; Newbury, H John; Macnair, Mark R

    2006-09-01

    One of the challenges of comparative genomics is to identify specific genetic changes associated with the evolution of a novel adaptation or trait. We need to be able to disassociate the genes involved with a particular character from all the other genetic changes that take place as lineages diverge. Here we show that by comparing the transcriptional profile of segregating families with that of parent species differing in a novel trait, it is possible to narrow down substantially the list of potential target genes. In addition, by assuming synteny with a related model organism for which the complete genome sequence is available, it is possible to use the cosegregation of markers differing in transcription level to identify regions of the genome which probably contain quantitative trait loci (QTLs) for the character. This novel combination of genomics and classical genetics provides a very powerful tool to identify candidate genes. We use this methodology to investigate zinc hyperaccumulation in Arabidopsis halleri, the sister species to the model plant, Arabidopsis thaliana. We compare the transcriptional profile of A. halleri with that of its sister nonaccumulator species, Arabidopsis petraea, and between accumulator and nonaccumulator F(3)s derived from the cross between the two species. We identify eight genes which consistently show greater expression in accumulator phenotypes in both roots and shoots, including two metal transporter genes (NRAMP3 and ZIP6), and cytoplasmic aconitase, a gene involved in iron homeostasis in mammals. We also show that there appear to be two QTLs for zinc accumulation, on chromosomes 3 and 7.

  5. Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production.

    Directory of Open Access Journals (Sweden)

    Nupoor Chowdhary

    Full Text Available Caldicellulosiruptor saccharolyticus has proven itself to be an excellent candidate for biological hydrogen (H2 production, but still it has major drawbacks like sensitivity to high osmotic pressure and low volumetric H2 productivity, which should be considered before it can be used industrially. A whole genome re-annotation work has been carried out as an attempt to update the incomplete genome information that causes gap in the knowledge especially in the area of metabolic engineering, to improve the H2 producing capabilities of C. saccharolyticus. Whole genome re-annotation was performed through manual means for 2,682 Coding Sequences (CDSs. Bioinformatics tools based on sequence similarity, motif search, phylogenetic analysis and fold recognition were employed for re-annotation. Our methodology could successfully add functions for 409 hypothetical proteins (HPs, 46 proteins previously annotated as putative and assigned more accurate functions for the known protein sequences. Homology based gene annotation has been used as a standard method for assigning function to novel proteins, but over the past few years many non-homology based methods such as genomic context approaches for protein function prediction have been developed. Using non-homology based functional prediction methods, we were able to assign cellular processes or physical complexes for 249 hypothetical sequences. Our re-annotation pipeline highlights the addition of 231 new CDSs generated from MicroScope Platform, to the original genome with functional prediction for 49 of them. The re-annotation of HPs and new CDSs is stored in the relational database that is available on the MicroScope web-based platform. In parallel, a comparative genome analyses were performed among the members of genus Caldicellulosiruptor to understand the function and evolutionary processes. Further, with results from integrated re-annotation studies (homology and genomic context approach, we strongly

  6. Power distribution arrangement

    DEFF Research Database (Denmark)

    2010-01-01

    An arrangement and a method for distributing power supplied by a power source to two or more of loads (e.g., electrical vehicular systems) is disclosed, where a representation of the power taken by a particular one of the loads from the source is measured. The measured representation of the amount...

  7. A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken.

    Science.gov (United States)

    Dorshorst, Ben; Molin, Anna-Maja; Rubin, Carl-Johan; Johansson, Anna M; Strömstedt, Lina; Pham, Manh-Hung; Chen, Chih-Feng; Hallböök, Finn; Ashwell, Chris; Andersson, Leif

    2011-12-01

    Dermal hyperpigmentation or Fibromelanosis (FM) is one of the few examples of skin pigmentation phenotypes in the chicken, where most other pigmentation variants influence feather color and patterning. The Silkie chicken is the most widespread and well-studied breed displaying this phenotype. The presence of the dominant FM allele results in extensive pigmentation of the dermal layer of skin and the majority of internal connective tissue. Here we identify the causal mutation of FM as an inverted duplication and junction of two genomic regions separated by more than 400 kb in wild-type individuals. One of these duplicated regions contains endothelin 3 (EDN3), a gene with a known role in promoting melanoblast proliferation. We show that EDN3 expression is increased in the developing Silkie embryo during the time in which melanoblasts are migrating, and elevated levels of expression are maintained in the adult skin tissue. We have examined four different chicken breeds from both Asia and Europe displaying dermal hyperpigmentation and conclude that the same structural variant underlies this phenotype in all chicken breeds. This complex genomic rearrangement causing a specific monogenic trait in the chicken illustrates how novel mutations with major phenotypic effects have been reused during breed formation in domestic animals.

  8. Genomic analysis of clonal eosinophils by CGH arrays reveals new genetic regions involved in chronic eosinophilia.

    Science.gov (United States)

    Arefi, Maryam; Robledo, Cristina; Peñarrubia, María J; García de Coca, Alfonso; Cordero, Miguel; Hernández-Rivas, Jesús M; García, Juan Luis

    2014-11-01

    To assess the presence of genetic imbalances in patients with myeloproliferative neoplasms (MPNs), 38 patients with chronic eosinophilia were studied by array comparative genomic hybridization (aCGH): seven had chronic myelogenous leukaemia (CML), BCR-ABL1 positive, nine patients had myeloproliferative neoplasia Ph- (MPN-Ph-), three had a myeloid neoplasm associated with a PDGFRA rearrangement, and the remaining two cases were Lymphoproliferative T neoplasms associated with eosinophilia. In addition, 17 patients had a secondary eosinophilia and were used as controls. Eosinophilic enrichment was carried out in all cases. Genomic imbalances were found in 76% of all MPN patients. Losses on 20q were the most frequent genetic abnormality in MPNs (32%), affected the three types of MPN studied. This study also found losses at 11q13.3 in 26% of patients with MPN-Ph- and in 19p13.11 in two of the three patients with an MPN associated with a PDGFRA rearrangement. In addition, 29% of patients with CML had losses on 8q24. In summary, aCGH revealed clonality in eosinophils in most MPNs, suggesting that it could be a useful technique for defining clonality in these diseases. The presence of genetic losses in new regions could provide new insights into the knowledge of these MPN associated with eosinophilia. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Genome sequence comparison reveals a candidate gene involved in male-hermaphrodite differentiation in papaya (Carica papaya) trees.

    Science.gov (United States)

    Ueno, Hiroki; Urasaki, Naoya; Natsume, Satoshi; Yoshida, Kentaro; Tarora, Kazuhiko; Shudo, Ayano; Terauchi, Ryohei; Matsumura, Hideo

    2015-04-01

    The sex type of papaya (Carica papaya) is determined by the pair of sex chromosomes (XX, female; XY, male; and XY(h), hermaphrodite), in which there is a non-recombining genomic region in the Y and Y(h) chromosomes. This region is presumed to be involved in determination of males and hermaphrodites; it is designated as the male-specific region in the Y chromosome (MSY) and the hermaphrodite-specific region in the Y(h) chromosome (HSY). Here, we identified the genes determining male and hermaphrodite sex types by comparing MSY and HSY genomic sequences. In the MSY and HSY genomic regions, we identified 14,528 nucleotide substitutions and 965 short indels with a large gap and two highly diverged regions. In the predicted genes expressed in flower buds, we found no nucleotide differences leading to amino acid changes between the MSY and HSY. However, we found an HSY-specific transposon insertion in a gene (SVP like) showing a similarity to the Short Vegetative Phase (SVP) gene. Study of SVP-like transcripts revealed that the MSY allele encoded an intact protein, while the HSY allele encoded a truncated protein. Our findings demonstrated that the SVP-like gene is a candidate gene for male-hermaphrodite determination in papaya.

  10. Comparative genomic analysis of a neurotoxigenic Clostridium species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism.

    Science.gov (United States)

    Alam, Syed Imteyaz; Dixit, Aparna; Tomar, Arvind; Singh, Lokendra

    2010-04-01

    Clostridial organisms produce neurotoxins, which are generally regarded as the most potent toxic substances of biological origin and potential biological warfare agents. Clostridium tetani produces tetanus neurotoxin and is responsible for the fatal tetanus disease. In spite of the extensive immunization regimen, the disease is an important cause of death especially among neonates. Strains of C. tetani have not been genetically characterized except the complete genome sequencing of strain E88. The present study reports the genetic makeup and phylogenetic affiliations of an environmental strain of this bacterium with respect to C. tetani E88 and other clostridia. A shot gun library was constructed from the genomic DNA of C. tetani drde, isolated from decaying fish sample. Unique clones were sequenced and sequences compared with its closest relative C. tetani E88. A total of 275 clones were obtained and 32,457 bases of non-redundant sequence were generated. A total of 150 base changes were observed over the entire length of sequence obtained, including, additions, deletions and base substitutions. Of the total 120 ORFs detected, 48 exhibited closest similarity to E88 proteins of which three are hypothetical proteins. Eight of the ORFs exhibited similarity with hypothetical proteins from other organisms and 10 aligned with other proteins from unrelated organisms. There is an overall conservation of protein sequences among the two strains of C. tetani and. Selected ORFs involved in cellular processes and metabolism were subjected to phylogenetic analysis.

  11. Genomic hallmarks of genes involved in chromosomal translocations in hematological cancer.

    Directory of Open Access Journals (Sweden)

    Mikhail Shugay

    Full Text Available Reciprocal chromosomal translocations (RCTs leading to the formation of fusion genes are important drivers of hematological cancers. Although the general requirements for breakage and fusion are fairly well understood, quantitative support for a general mechanism of RCT formation is still lacking. The aim of this paper is to analyze available high-throughput datasets with computational and robust statistical methods, in order to identify genomic hallmarks of translocation partner genes (TPGs. Our results show that fusion genes are generally overexpressed due to increased promoter activity of 5' TPGs and to more stable 3'-UTR regions of 3' TPGs. Furthermore, expression profiling of 5' TPGs and of interaction partners of 3' TPGs indicates that these features can help to explain tissue specificity of hematological translocations. Analysis of protein domains retained in fusion proteins shows that the co-occurrence of specific domain combinations is non-random and that distinct functional classes of fusion proteins tend to be associated with different components of the gene fusion network. This indicates that the configuration of fusion proteins plays an important role in determining which 5' and 3' TPGs will combine in specific fusion genes. It is generally accepted that chromosomal proximity in the nucleus can explain the specific pairing of 5' and 3' TPGS and the recurrence of hematological translocations. Using recently available data for chromosomal contact probabilities (Hi-C we show that TPGs are preferentially located in early replicated regions and occupy distinct clusters in the nucleus. However, our data suggest that, in general, nuclear position of TPGs in hematological cancers explains neither TPG pairing nor clinical frequency. Taken together, our results support a model in which genomic features related to regulation of expression and replication timing determine the set of candidate genes more likely to be translocated in

  12. Intermediate links of line arrangements

    CERN Document Server

    Bodin, Arnaud

    2012-01-01

    We investigate several topological properties of line arrangements. The first result is that two generic complex line arrangements are equivalent. In fact for a line arrangement A we associate its defining polynomial f= prod_i (a_ix+b_iy+c_i), so that A = (f=0). We even prove that the defining polynomials of two generic line arrangements are topologically equivalent. In higher dimension the related result is that within a family of equivalent hyperplane arrangements the defining polynomials are topologically equivalent. A second type of objects associated to a line arrangement are links A cap S^3_r(0) obtained by intersecting the arrangement with some spheres. Several topics are discussed: (a) some link configurations can be realized by complex line arrangements but not by real line arrangements; (b) if we intersect the arrangements with a vertical band instead of a sphere, what link configurations can be obtained? (c) relations between link configurations obtained by bands and spheres.

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

    Directory of Open Access Journals (Sweden)

    Chong Kang

    2009-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

  14. Imaging arrangement and microscope

    Science.gov (United States)

    Pertsinidis, Alexandros; Chu, Steven

    2015-12-15

    An embodiment of the present invention is an imaging arrangement that includes imaging optics, a fiducial light source, and a control system. In operation, the imaging optics separate light into first and second tight by wavelength and project the first and second light onto first and second areas within first and second detector regions, respectively. The imaging optics separate fiducial light from the fiducial light source into first and second fiducial light and project the first and second fiducial light onto third and fourth areas within the first and second detector regions, respectively. The control system adjusts alignment of the imaging optics so that the first and second fiducial light projected onto the first and second detector regions maintain relatively constant positions within the first and second detector regions, respectively. Another embodiment of the present invention is a microscope that includes the imaging arrangement.

  15. Steerable catoptric arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Rambauske, W.R.

    1976-04-13

    Catoptric arrangements for steering a laser beam by moving one, or more, mirrors relative to two substantially orthogonal axis of rotation are shown. In the various embodiments illustrated, one of such axes of rotation, around which all of the mirrors in each embodiment are rotatable, is coincident with the longitudinal axis of the laser beam to be steered so as to direct such longitudinal axis toward different points on a first focal circle. Means are provided to rotate all of the mirrors in each embodiment, except the mirror irradiated by the laser beam to be steered, around the second axis of rotation to direct the longitudinal axis of such beam toward different points on a second focal circle substantially orthogonal to the first focal circle. Also shown are exemplary modifications to position the mirrors within each arrangement to aim the steered beam to points adjacent to the first and second focal circles.

  16. Hyperplane arrangements an introduction

    CERN Document Server

    Dimca, Alexandru

    2017-01-01

    This textbook provides an accessible introduction to the rich and beautiful area of hyperplane arrangement theory, where discrete mathematics, in the form of combinatorics and arithmetic, meets continuous mathematics, in the form of the topology and Hodge theory of complex algebraic varieties. The topics discussed in this book range from elementary combinatorics and discrete geometry to more advanced material on mixed Hodge structures, logarithmic connections and Milnor fibrations. The author covers a lot of ground in a relatively short amount of space, with a focus on defining concepts carefully and giving proofs of theorems in detail where needed. Including a number of surprising results and tantalizing open problems, this timely book also serves to acquaint the reader with the rapidly expanding literature on the subject. Hyperplane Arrangements will be particularly useful to graduate students and researchers who are interested in algebraic geometry or algebraic topology. The book contains numerous exercise...

  17. Coloring and Guarding Arrangements

    CERN Document Server

    Bose, Prosenjit; Collette, Sébastien; Hurtado, Ferran; Korman, Matias; Langerman, Stefan; Taslakian, Perouz

    2012-01-01

    Given an arrangement of lines in the plane, what is the minimum number $c$ of colors required to color the lines so that no cell of the arrangement is monochromatic? In this paper we give bounds on the number c both for the above question, as well as some of its variations. We redefine these problems as geometric hypergraph coloring problems. If we define $\\Hlinecell$ as the hypergraph where vertices are lines and edges represent cells of the arrangement, the answer to the above question is equal to the chromatic number of this hypergraph. We prove that this chromatic number is between $\\Omega (\\log n / \\log\\log n)$. and $O(\\sqrt{n})$. Similarly, we give bounds on the minimum size of a subset $S$ of the intersections of the lines in $\\mathcal{A}$ such that every cell is bounded by at least one of the vertices in $S$. This may be seen as a problem on guarding cells with vertices when the lines act as obstacles. The problem can also be defined as the minimum vertex cover problem in the hypergraph $\\Hvertexcell$...

  18. Genome scan for locus involved in mandibular prognathism in pedigrees from China.

    Directory of Open Access Journals (Sweden)

    Qin Li

    Full Text Available BACKGROUND: It is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped. METHODOLOGY: In order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM. Multipoint parametric and non-parametric (model-free linkage analyses were used for the pedigrees. PRINCIPAL FINDING: The most statistically significant linkage results were with markers on chromosome 4 (LOD=3.166 and NPL=3.65 with rs 875864, 4p16.1, 8.38 cM. Candidate genes within the 4p16.1 include EVC, EVC2. CONCLUSION: We detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism.

  19. Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence

    OpenAIRE

    Barret, Matthieu; Morrissey, John P.; O’Gara, Fergal

    2011-01-01

    In soil, some specific bacterial populations, called plant growth-promoting rhizobacteria are able to promote plant growth and/or reduce the incidence of soil-borne diseases. Rhizosphere competence is an important prerequisite for the efficacy of these biocontrol strains. Therefore, over decades, multiple approaches have been combined to understand the molecular basis of bacterial traits involved in rhizosphere competence. This review addresses the bacterial genes expressed during bacterial–p...

  20. Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.

    Science.gov (United States)

    Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

    2016-02-24

    Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.

  1. Whole-genome resequencing and transcriptomic analysis to identify genes involved in leaf-color diversity in ornamental rice plants.

    Directory of Open Access Journals (Sweden)

    Chang-Kug Kim

    Full Text Available Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.

  2. Whole-Genome Resequencing and Transcriptomic Analysis to Identify Genes Involved in Leaf-Color Diversity in Ornamental Rice Plants

    Science.gov (United States)

    Shin, Younhee; Lim, Hye-Min; Lee, Gang-Seob; Kim, A-Ram; Lee, Tae-Ho; Lee, Jae-Hee; Park, Dong-Suk; Yoo, Seungil; Kim, Yong-Hwan; Kim, Yong-Kab

    2015-01-01

    Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways. PMID:25897514

  3. A 5'-proximal region of the Citrus tristeza virus genome encoding two leader proteases is involved in virus superinfection exclusion.

    Science.gov (United States)

    Atallah, Osama O; Kang, Sung-Hwan; El-Mohtar, Choaa A; Shilts, Turksen; Bergua, María; Folimonova, Svetlana Y

    2016-02-01

    Superinfection exclusion (SIE), a phenomenon in which a primary virus infection prevents a secondary infection with the same or closely related virus, has been observed with various viruses. Earlier we demonstrated that SIE by Citrus tristeza virus (CTV) requires viral p33 protein. In this work we show that p33 alone is not sufficient for virus exclusion. To define the additional viral components that are involved in this phenomenon, we engineered a hybrid virus in which a 5'-proximal region in the genome of the T36 isolate containing coding sequences for the two leader proteases L1 and L2 has been substituted with a corresponding region from the genome of a heterologous T68-1 isolate. Sequential inoculation of plants pre-infected with the CTV L1L2T68 hybrid with T36 CTV resulted in superinfection with the challenge virus, which indicated that the substitution of the L1-L2 coding region affected SIE ability of the virus. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Genome-wide retroviral insertional tagging of genes involved in cancer in Cdkn2a-deficient mice.

    Science.gov (United States)

    Lund, Anders H; Turner, Geoffrey; Trubetskoy, Alla; Verhoeven, Els; Wientjens, Ellen; Hulsman, Danielle; Russell, Robert; DePinho, Ronald A; Lenz, Jack; van Lohuizen, Maarten

    2002-09-01

    We have used large-scale insertional mutagenesis to identify functional landmarks relevant to cancer in the recently completed mouse genome sequence. We infected Cdkn2a(-/-) mice with Moloney murine leukemia virus (MoMuLV) to screen for loci that can participate in tumorigenesis in collaboration with loss of the Cdkn2a-encoded tumor suppressors p16INK4a and p19ARF. Insertional mutagenesis by the latent retrovirus was synergistic with loss of Cdkn2a expression, as indicated by a marked acceleration in the development of both myeloid and lymphoid tumors. We isolated 747 unique sequences flanking retroviral integration sites and mapped them against the mouse genome sequence databases from Celera and Ensembl. In addition to 17 insertions targeting gene loci known to be cancer-related, we identified a total of 37 new common insertion sites (CISs), of which 8 encode components of signaling pathways that are involved in cancer. The effectiveness of large-scale insertional mutagenesis in a sensitized genetic background is demonstrated by the preference for activation of MAP kinase signaling, collaborating with Cdkn2a loss in generating the lymphoid and myeloid tumors. Collectively, our results show that large-scale retroviral insertional mutagenesis in genetically predisposed mice is useful both as a system for identifying genes underlying cancer and as a genetic framework for the assignment of such genes to specific oncogenic pathways.

  5. Genomic approaches towards identification of components involved in peptide based cell growth of Arabidopsis thailana

    DEFF Research Database (Denmark)

    Mahmood, Khalid

    Secreted peptides are considered now as important signaling molecules involved in plant growth and development. Plant peptide containing sulfated tyrosine 1 (PSY1) is a small peptide that promotes cell elongation and expansion at nanomolar concentration. This is achieved through binding...... elongation. FAB1C is highly down regulated in psy1r mutant plants and is assumed to play role in acidification and formation of vacuole that may contribute in cell elongation. In short, our work provides insights how growth coordinated through cellular communication using PSY1 as a signal molecule....... to extracellular domain of the leucine-rich repeat (LRR) receptor kinase called PSY1R. Upon binding of the peptide, PSY1R transduces the signal by phosphorylating the plasma membrane H+-ATPase (AHA2) leading to proton extrusion results in cell elongation. To understand the molecular basis of PSY1 response...

  6. An evolutionary genomic approach to identify genes involved in human birth timing.

    Directory of Open Access Journals (Sweden)

    Jevon Plunkett

    2011-04-01

    Full Text Available Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition.

  7. Genomic Expression Program Involving the Haa1p-Regulon in Saccharomyces cerevisiae Response to Acetic Acid

    Science.gov (United States)

    Becker, Jorg D.; Sá-Correia, Isabel

    2010-01-01

    Abstract The alterations occurring in yeast genomic expression during early response to acetic acid and the involvement of the transcription factor Haa1p in this transcriptional reprogramming are described in this study. Haa1p was found to regulate, directly or indirectly, the transcription of approximately 80% of the acetic acid-activated genes, suggesting that Haa1p is the main player in the control of yeast response to this weak acid. The genes identified in this work as being activated in response to acetic acid in a Haa1p-dependent manner include protein kinases, multidrug resistance transporters, proteins involved in lipid metabolism, in nucleic acid processing, and proteins of unknown function. Among these genes, the expression of SAP30 and HRK1 provided the strongest protective effect toward acetic acid. SAP30 encode a subunit of a histone deacetylase complex and HRK1 encode a protein kinase belonging to a family of protein kinases dedicated to the regulation of plasma membrane transporters activity. The deletion of the HRK1 gene was found to lead to the increase of the accumulation of labeled acetic acid into acid-stressed yeast cells, suggesting that the role of both HAA1 and HRK1 in providing protection against acetic acid is, at least partially, related with their involvement in the reduction of intracellular acetate concentration. PMID:20955010

  8. Phenotypic, Proteomic, and Genomic Characterization of a Putative ABC-Transporter Permease Involved in Listeria monocytogenes Biofilm Formation

    DEFF Research Database (Denmark)

    Zhu, Xinna; Liu, Weibing; Lametsch, René

    2011-01-01

    enhanced ability for biofilm formation as the LM-49 strain using a crystal violet staining assay. DNA microarrays and two-dimensional gel electrophoresis revealed 49 and 11 differentially expressed (twofold or more) genes or proteins in Δ1771, respectively. The transcriptomics study indicated that lm......The foodborne pathogen Listeria monocytogenes is able to form biofilms in food processing environments. Previously, we have reported that an lm.G_1771 gene (encoding a putative ABC-transporter permease) was involved in negative regulation of L. monocytogenes biofilm formation using LM-49, a biofilm......-enhanced mutant isolated on Tn917 mutagenesis (AEM 2008 p.7675–7683). Here, the possible action of this ABC-transporter permease in L. monocytogenes biofilm formation was characterized by phenotypic, proteomic, and genomic analyses using an lm.G_1771 gene deletant (Δ1771). The Δ1771 mutant exhibited the same...

  9. Peak load arrangements : Assessment of Nordel guidelines

    Energy Technology Data Exchange (ETDEWEB)

    2009-07-01

    taken after consultation with parties in other Nordic countries, and involving also regulators and TSOs. In NordREG's view there are basically three principles that should be guiding any decision to introduce peak load arrangements in the Nordic countries: i), the peak load arrangements should be introduced only in situations when security of supply cannot be met without these arrangements. Since the decision to introduce peak load arrangements might be of a political/legal nature, the length of such arrangement cannot be fixed. However, there should be a regular evaluation by the competent authority of any need or prolonged need for peak load arrangements and its effects of price formation in the Nordic market. ii), when peak load arrangements are introduced they should be designed to minimize the adverse effects on price formation in the Nordic market. Furthermore, if there are to be peak load arrangements, there might be a need for how to distinguish these peak load reserves from other reserves at the disposal of the TSOs. However, this issue needs further discussions and development. iii), Nordic consultation should be carried out where the views of all relevant authorities and stake holders in the market affected are invited. It is recommended that the governments consult with their Nordic counter parties before submitting legal proposals on peak load arrangements affecting Nordic price formation. These consultations should also be with regulators and TSOs who are involved in the design of the actual peak load arrangements. (Author)

  10. MUSICAL ARRANGEMENT OF MEDIA ADS

    Directory of Open Access Journals (Sweden)

    Chernyshov Alexander V.

    2015-01-01

    Full Text Available The music-compositional principles of commercial and political advertising and also the self-promotion of electronic media (radio, television, Internet are considered in this mediatext: from the elementary beeps, symbolic functions, emblems/logos and musical brands to the sound engineering technology to underscore the product's name and the complex synthesis between music and intra movements and color-light design of frames. Simultaneously examines, how the musical arrangement of ethereal advertising is involved in creation the emotional drama or bravado which reach the level of explicit or associative counterpoint 'music with the advertised object or subject' and which extend to expression of cultural image of all the broadcast channel. The article explores the works of the next genres like infomercial, teleshopping, film-ad, and autonomous commercials that have been produced in European countries or USA.

  11. Auspicious tatami mat arrangements

    CERN Document Server

    Erickson, Alejandro; Schurch, Mark; Woodcock, Jennifer

    2011-01-01

    An \\emph{auspicious tatami mat arrangement} is a tiling of a rectilinear region with two types of tiles, $1 \\times 2$ tiles (dimers) and $1 \\times 1$ tiles (monomers). The tiles must cover the region and satisfy the constraint that no four corners of the tiles meet; such tilings are called \\emph{tatami tilings}. The main focus of this paper is when the rectilinear region is a rectangle. We provide a structural characterization of rectangular tatami tilings and use it to prove that the tiling is completely determined by the tiles that are on its border. We prove that the number of tatami tilings of an $n \\times n$ square with $n$ monomers is $n2^{n-1}$. We also show that, for fixed-height, the generating function for the number of tatami tilings of a rectangle is a rational function, and outline an algorithm that produces the generating function.

  12. Candida's arranged marriage.

    Science.gov (United States)

    Gow, N A; Brown, A J; Odds, F C

    2000-07-14

    Biologists who study the fungus Candida albicans have always assumed that this organism reproduces asexually because they have not found evidence of mating, meiosis, or a haploid stage of the life cycle. However, as Gow et al. explain in a Perspective, sequencing of the C. albicans genome has revealed the existence of a possible mating type locus. This finding has now been extended to demonstrate actual mating in the fungus (Hull et al., Magee and Magee).

  13. Critical illness research involving collection of genomic data: the conundrum posed by low levels of genomic literacy among surrogate decision makers for critically ill patients.

    Science.gov (United States)

    Iverson, Ellen; Celious, Aaron; Shehane, Erica; Oerke, Mandy; Warren, Victoria; Eastman, Alexander; Kennedy, Carie R; Freeman, Bradley D

    2013-07-01

    Critical illness clinical trials that entail genomic data collection pose unique challenges. In this qualitative study, we found that surrogate decision makers (SDMs) for critically ill individuals, such as those who would be approached for study participation, appeared to have a limited grasp of genomic principles. We argue that low levels of genomic literacy should neither preclude nor be in conflict with the conduct of ethically rigorous clinical trials.

  14. Genome wide expression profiling of the mesodiencephalic region identifies novel factors involved in early and late dopaminergic development

    Directory of Open Access Journals (Sweden)

    Koushik Chakrabarty

    2012-05-01

    Meso-diencephalic dopaminergic (mdDA neurons are critical for motor control and cognitive functioning and their loss or dysfunction is associated with disorders such as Parkinson's disease (PD, schizophrenia and addiction. However, relatively little is known about the molecular mechanisms underlying mdDA neuron development and maintenance. Here, we determined the spatiotemporal map of genes involved in the development of mdDA neurons to gain further insight into their molecular programming. Genome-wide gene expression profiles of the developing ventral mesencephalon (VM were compared at different developmental stages leading to the identification of novel regulatory roles of neuronal signaling through nicotinic acthylcholine receptors (Chrna6 and Chrnb3 subunits and the identification of novel transcription factors (Oc2 and 3 involved in the generation of the mdDA neuronal field. We show here that Pitx3, in cooperation with Nurr1, is the critical component in the activation of the Chrna6 and Chrnb3 subunits in mdDA neurons. Furthermore, we provide evidence of two divergent regulatory pathways resulting in the expression of Chrna6 and Chrnb3 respectively.

  15. Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation.

    Science.gov (United States)

    Ma, Xiaodong; Ma, Jianchao; Fan, Di; Li, Chaofeng; Jiang, Yuanzhong; Luo, Keming

    2016-09-08

    Higher plants have been shown to experience a juvenile vegetative phase, an adult vegetative phase, and a reproductive phase during its postembryonic development and distinct lateral organ morphologies have been observed at the different development stages. Populus euphratica, commonly known as a desert poplar, has developed heteromorphic leaves during its development. The TCP family genes encode a group of plant-specific transcription factors involved in several aspects of plant development. In particular, TCPs have been shown to influence leaf size and shape in many herbaceous plants. However, whether these functions are conserved in woody plants remains unknown. In the present study, we carried out genome-wide identification of TCP genes in P. euphratica and P. trichocarpa, and 33 and 36 genes encoding putative TCP proteins were found, respectively. Phylogenetic analysis of the poplar TCPs together with Arabidopsis TCPs indicated a biased expansion of the TCP gene family via segmental duplications. In addition, our results have also shown a correlation between different expression patterns of several P. euphratica TCP genes and leaf shape variations, indicating their involvement in the regulation of leaf shape development.

  16. In silico identification and comparative genomics of candidate genes involved in biosynthesis and accumulation of seed oil in plants.

    Science.gov (United States)

    Sharma, Arti; Chauhan, Rajinder Singh

    2012-01-01

    Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs) which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants.

  17. In Silico Identification and Comparative Genomics of Candidate Genes Involved in Biosynthesis and Accumulation of Seed Oil in Plants

    Directory of Open Access Journals (Sweden)

    Arti Sharma

    2012-01-01

    Full Text Available Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants.

  18. The making of local hospital discharge arrangements

    DEFF Research Database (Denmark)

    Burau, Viola; Bro, Flemming

    2015-01-01

    Background Timely discharge is a key component of contemporary hospital governance and raises questions about how to move to more explicit discharge arrangements. Although associated organisational changes closely intersect with professional interests, there are relatively few studies...... and involvement in the process of organisational change: whereas in the ‘add on’ model the professional groups remain at a distance, in the ‘embedded model’ they are closely engaged. Conclusions In terms of understanding the making of hospital discharge arrangements, the study contributes two sets of insights...... in the literature on hospital discharge that explicitly examine the role of professional groups. Recent contributions to the literature on organisational studies of the professions help to specify how professional groups in hospitals contribute to the introduction and routinisation of discharge arrangements...

  19. Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis.

    Directory of Open Access Journals (Sweden)

    Chi-Yi Yu

    Full Text Available Glucocorticoids play important roles in the regulation of distinct aspects of adipocyte biology. Excess glucocorticoids in adipocytes are associated with metabolic disorders, including central obesity, insulin resistance and dyslipidemia. To understand the mechanisms underlying the glucocorticoid action in adipocytes, we used chromatin immunoprecipitation sequencing to isolate genome-wide glucocorticoid receptor (GR binding regions (GBRs in 3T3-L1 adipocytes. Furthermore, gene expression analyses were used to identify genes that were regulated by glucocorticoids. Overall, 274 glucocorticoid-regulated genes contain or locate nearby GBR. We found that many GBRs were located in or nearby genes involved in triglyceride (TG synthesis (Scd-1, 2, 3, GPAT3, GPAT4, Agpat2, Lpin1, lipolysis (Lipe, Mgll, lipid transport (Cd36, Lrp-1, Vldlr, Slc27a2 and storage (S3-12. Gene expression analysis showed that except for Scd-3, the other 13 genes were induced in mouse inguinal fat upon 4-day glucocorticoid treatment. Reporter gene assays showed that except Agpat2, the other 12 glucocorticoid-regulated genes contain at least one GBR that can mediate hormone response. In agreement with the fact that glucocorticoids activated genes in both TG biosynthetic and lipolytic pathways, we confirmed that 4-day glucocorticoid treatment increased TG synthesis and lipolysis concomitantly in inguinal fat. Notably, we found that 9 of these 12 genes were induced in transgenic mice that have constant elevated plasma glucocorticoid levels. These results suggested that a similar mechanism was used to regulate TG homeostasis during chronic glucocorticoid treatment. In summary, our studies have identified molecular components in a glucocorticoid-controlled gene network involved in the regulation of TG homeostasis in adipocytes. Understanding the regulation of this gene network should provide important insight for future therapeutic developments for metabolic diseases.

  20. Identification of novel candidate genes involved in mineralization of dental enamel by genome-wide transcript profiling.

    Science.gov (United States)

    Lacruz, Rodrigo S; Smith, Charles E; Bringas, Pablo; Chen, Yi-Bu; Smith, Susan M; Snead, Malcolm L; Kurtz, Ira; Hacia, Joseph G; Hubbard, Michael J; Paine, Michael L

    2012-05-01

    The gene repertoire regulating vertebrate biomineralization is poorly understood. Dental enamel, the most highly mineralized tissue in mammals, differs from other calcifying systems in that the formative cells (ameloblasts) lack remodeling activity and largely degrade and resorb the initial extracellular matrix. Enamel mineralization requires that ameloblasts undergo a profound functional switch from matrix-secreting to maturational (calcium transport, protein resorption) roles as mineralization progresses. During the maturation stage, extracellular pH decreases markedly, placing high demands on ameloblasts to regulate acidic environments present around the growing hydroxyapatite crystals. To identify the genetic events driving enamel mineralization, we conducted genome-wide transcript profiling of the developing enamel organ from rat incisors and highlight over 300 genes differentially expressed during maturation. Using multiple bioinformatics analyses, we identified groups of maturation-associated genes whose functions are linked to key mineralization processes including pH regulation, calcium handling, and matrix turnover. Subsequent qPCR and Western blot analyses revealed that a number of solute carrier (SLC) gene family members were up-regulated during maturation, including the novel protein Slc24a4 involved in calcium handling as well as other proteins of similar function (Stim1). By providing the first global overview of the cellular machinery required for enamel maturation, this study provide a strong foundation for improving basic understanding of biomineralization and its practical applications in healthcare. Copyright © 2011 Wiley Periodicals, Inc.

  1. Collaborative Service Arrangements

    DEFF Research Database (Denmark)

    Winter, Søren; J. May, Peter

    2007-01-01

    in particular differs among collaborators. Our modeling of the influence of collaboration on perceived employment outcomes suggests that these impacts are relatively minor. They are greater when there is active involvement of municipal employment managers in fostering cooperative relationships...... with collaborators. In short, collaboration requires a healthy and active relationship to foster improved outcomes. These findings have implications for future research about collaborative service delivery concerning the measurement of collaboration, different bases for it, and potential impacts....

  2. Collaborative Service Arrangements

    DEFF Research Database (Denmark)

    J. May, Peter; Winter, Søren

    in particular differs among collaborators. Our modeling of the influence of collaboration on perceived employment outcomes suggests that these impacts are relatively minor. They are greater when there is active involvement of municipal employment managers in fostering cooperative relationships...... with collaborators. In short, collaboration requires a healthy and active relationship to foster improved outcomes. These findings have implications for future research about collaborative service delivery concerning the measurement of collaboration, different bases for it, and potential impacts....

  3. High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.

    Science.gov (United States)

    Ntougias, Spyridon; Lapidus, Alla; Han, James; Mavromatis, Konstantinos; Pati, Amrita; Chen, Amy; Klenk, Hans-Peter; Woyke, Tanja; Fasseas, Constantinos; Kyrpides, Nikos C; Zervakis, Georgios I

    2014-06-15

    Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6(T), together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.

  4. High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway

    Science.gov (United States)

    Ntougias, Spyridon; Lapidus, Alla; Han, James; Mavromatis, Konstantinos; Pati, Amrita; Chen, Amy; Klenk, Hans-Peter; Woyke, Tanja; Fasseas, Constantinos; Kyrpides, Nikos C.; Zervakis, Georgios I.

    2014-01-01

    Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6T, together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis. PMID:25197463

  5. Genome-Wide Identification and Functional Characterization of UDP-Glucosyltransferase Genes Involved in Flavonoid Biosynthesis in Glycine max.

    Science.gov (United States)

    Yin, Qinggang; Shen, Guoan; Di, Shaokang; Fan, Cunying; Chang, Zhenzhan; Pang, Yongzhen

    2017-09-01

    Flavonoids, natural products abundant in the model legume Glycine max, confer benefits to plants and to animal health. Flavonoids are present in soybean mainly as glycoconjugates. However, the mechanisms of biosynthesis of flavonoid glycosides are largely unknown in G. max. In the present study, 212 putative UDP-glycosyltransferase (UGT) genes were identified in G. max by genome-wide searching. The GmUGT genes were distributed differentially among the 20 chromosomes, and they were expressed in various tissues with distinct expression profiles. We further analyzed the enzymatic activities of 11 GmUGTs that are potentially involved in flavonoid glycosylation, and found that six of them (UGT72X4, UGT72Z3, UGT73C20, UGT88A13, UGT88E19 and UGT92G4) exhibited activity toward flavonol, isoflavone, flavone and flavanol aglycones with different kinetic properties. Among them, UGT72X4, UGT72Z3 and UGT92G4 are flavonol-specific UGTs, and UGT73C20 and UGT88E19 exhibited activity toward both flavonol and isoflavone aglycones. In particular, UGT88A13 exhibited activity toward epicatechin, but not for the flavonol aglycones kaempferol and quercetin. Overexpression of these six GmUGT genes significantly increased the contents of isoflavone and flavonol glucosides in soybean hairy roots. In addition, overexpression of these six GmUGT genes also affected flavonol glycoside contents differently in seedlings and seeds of transgenic Arabidopsis thaliana. We provide valuable information on the identification of all UGT genes in soybean, and candidate GmUGT genes for potential metabolic engineering of flavonoid compounds in both Escherichia coli and plants. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development

    Science.gov (United States)

    Chen, Meng; Rothman, Nathaniel; Ye, Yuanqing; Gu, Jian; Scheet, Paul A.; Huang, Maosheng; Chang, David W.; Dinney, Colin P.; Silverman, Debra T.; Figueroa, Jonine D.; Chanock, Stephen J.; Wu, Xifeng

    2016-01-01

    Genome-wide association studies (GWAS) are designed to identify individual regions associated with cancer risk, but only explain a small fraction of the inherited variability. Alternative approach analyzing genetic variants within biological pathways has been proposed to discover networks of susceptibility genes with additional effects. The gene set enrichment analysis (GSEA) may complement and expand traditional GWAS analysis to identify novel genes and pathways associated with bladder cancer risk. We selected three GSEA methods: Gen-Gen, Aligator, and the SNP Ratio Test to evaluate cellular signaling pathways involved in bladder cancer susceptibility in a Texas GWAS population. The candidate genetic polymorphisms from the significant pathway selected by GSEA were validated in an independent NCI GWAS. We identified 18 novel pathways (P < 0.05) significantly associated with bladder cancer risk. Five of the most promising pathways (P ≤ 0.001 in any of the three GSEA methods) among the 18 pathways included two cell cycle pathways and neural cell adhesion molecule (NCAM), platelet-derived growth factor (PDGF), and unfolded protein response pathways. We validated the candidate polymorphisms in the NCI GWAS and found variants of RAPGEF1, SKP1, HERPUD1, CACNB2, CACNA1C, CACNA1S, COL4A2, SRC, and CACNA1C were associated with bladder cancer risk. Two CCNE1 variants, rs8102137 and rs997669, from cell cycle pathways showed the strongest associations; the CCNE1 signal at 19q12 has already been reported in previous GWAS. These findings offer additional etiologic insights highlighting the specific genes and pathways associated with bladder cancer development. GSEA may be a complementary tool to GWAS to identify additional loci of cancer susceptibility.

  7. Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study.

    Directory of Open Access Journals (Sweden)

    Yolande F M Ramos

    Full Text Available Identify gene expression profiles associated with OA processes in articular cartilage and determine pathways changing during the disease process.Genome wide gene expression was determined in paired samples of OA affected and preserved cartilage of the same joint using microarray analysis for 33 patients of the RAAK study. Results were replicated in independent samples by RT-qPCR and immunohistochemistry. Profiles were analyzed with the online analysis tools DAVID and STRING to identify enrichment for specific pathways and protein-protein interactions.Among the 1717 genes that were significantly differently expressed between OA affected and preserved cartilage we found significant enrichment for genes involved in skeletal development (e.g. TNFRSF11B and FRZB. Also several inflammatory genes such as CD55, PTGES and TNFAIP6, previously identified in within-joint analyses as well as in analyses comparing preserved cartilage from OA affected joints versus healthy cartilage were among the top genes. Of note was the high up-regulation of NGF in OA cartilage. RT-qPCR confirmed differential expression for 18 out of 19 genes with expression changes of 2-fold or higher, and immunohistochemistry of selected genes showed a concordant change in protein expression. Most of these changes associated with OA severity (Mankin score but were independent of joint-site or sex.We provide further insights into the ongoing OA pathophysiological processes in cartilage, in particular into differences in macroscopically intact cartilage compared to OA affected cartilage, which seem relatively consistent and independent of sex or joint. We advocate that development of treatment could benefit by focusing on these similarities in gene expression changes and/or pathways.

  8. Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity

    Directory of Open Access Journals (Sweden)

    Fuchs Thilo M

    2008-01-01

    Full Text Available Abstract Background Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but not to humans. In contrast, Y. enterocolitica is widely found in the environment and mainly known to cause gastroenteritis in men, but has only recently been shown to be also toxic for insects. It is expected that both pathogens share an overlap of genetic determinants that play a role within the insect host. Results A selective genome comparison was applied. Proteins belonging to the class of two-component regulatory systems, quorum sensing, universal stress proteins, and c-di-GMP signalling have been analysed. The interorganismic synopsis of selected regulatory systems uncovered common and distinct signalling mechanisms of both pathogens used for perception of signals within the insect host. Particularly, a new class of LuxR-like regulators was identified, which might be involved in detecting insect-specific molecules. In addition, the genetic overlap unravelled a two-component system that is unique for the genera Photorhabdus and Yersinia and is therefore suggested to play a major role in the pathogen-insect relationship. Our analysis also highlights factors of both pathogens that are expressed at low temperatures as encountered in insects in contrast to higher (body temperature, providing evidence that temperature is a yet under-investigated environmental signal for bacterial adaptation to various hosts. Common degradative metabolic pathways are described that might be used to explore nutrients within the insect gut or hemolymph, thus enabling the proliferation of P. luminescens and Y. enterocolitica in their invertebrate hosts. A strikingly higher number of genes encoding insecticidal toxins and other virulence factors in P. luminescens compared to Y. enterocolitica correlates with the higher virulence of P

  9. Floral arrangements and hummingbird feeding.

    Science.gov (United States)

    Hainsworth, F Reed; Mercier, Theresa; Wolf, Larry L

    1983-05-01

    The influence of simulated inflorescence design on feeding behavior of 3 male Eugenes fulgens (Rivoli's hummingbird) and one female Lampornis clemenciae (Bluethroated hummingbird) was studied in the laboratory using artificial flowers. Five two-dimensional and three three-dimensional arrangements provided constant rewards per artificial flower. Visits to two-dimensional arrangements had more flower visits per feeding bout, proportionally more flower revisits, and shorter time between flowers than visits to three-dimensional arrangements. This suggests inflorescence design may influence pollen movement by hummingbirds.

  10. "Fraud alert": joint venture arrangements.

    Science.gov (United States)

    Vipperman, R M

    1989-01-01

    The Office of Inspector General of the Department of Health and Human Services recently issued a special "Fraud Alert" identifying those characteristics of joint venture arrangements that it views as indicators of potentially unlawful activity. As discussed in this article, participants in joint ventures should examine their arrangements to see if one or more of the questionable features are present, and, if so, should take steps to eliminate them, to the extent possible.

  11. The chromosomal arrangement of six soybean leghemoglobin genes

    DEFF Research Database (Denmark)

    Bojsen, Kirsten; Abildsten, Dorte; Jensen, Erik Ø

    1983-01-01

    Clones containing six leghemoglobin (Lb) genes have been isolated from two genomic libraries of soybean. They encompass two independent DNA regions: a 40-kb region containing four genes in the order 5' Lba-Lbc(1)-[unk]Lb-Lbc(3) 3' with the same transcriptional polarity, and another 40-kb region...... containing two genes in the order 5' Lbc(4)-Lbc(2) 3' with the same polarity. The order in which the Lb genes are arranged in the soybean genome imply that they are activated in the opposite order to which they are arranged on the chromosome. There is a close similarity between corresponding DNA regions...... differs from that of the Lb genes. The existence of two very similar Lb gene clusters in soybean suggest that soybean may have evolved from an ancestral form by genome duplication. Udgivelsesdato: 1983-null...

  12. Genome-wide analysis and functional characterization of candidate effector proteins potentially involved in Fusarium graminearum-wheat interactions

    Science.gov (United States)

    Fungal pathogens often produce certain small secreted cysteine-rich proteins (SSCPs) during pathogenesis that may function in triggering resistance or susceptibility in specific host plants. We have identified a total of 190 SSCPs encoded in the genome of the wheat scab fungus Fusarium graminearum a...

  13. Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder

    NARCIS (Netherlands)

    Williams, H.J.; Norton, N.; Dwyer, S.; Moskvina, V.; Nikolov, I.; Carroll, L.; Georgieva, L.; Williams, N.M.; Morris, D.W.; Quinn, E.M.; Giegling, I.; Ikeda, M.; Wood, J.; Lencz, T.; Hultman, C.; Lichtenstein, P.; Thiselton, D.; Maher, B.S.; Malhotra, A.K.; Riley, B.; Kendler, K.S.; Gill, M.; Sullivan, P.; Sklar, P.; Purcell, S.; Nimgaonkar, V.L.; Kirov, G.; Holmans, P.; Corvin, A.; Rujescu, D.; Craddock, N.; Owen, M.J.; O'Donovan, M.C.; GROUP investigators, [No Value

    2011-01-01

    A recent genome-wide association study (GWAS) reported evidence for association between rs1344706 within ZNF804A (encoding zinc-finger protein 804A) and schizophrenia (P = 1.61 x 10(-7)), and stronger evidence when the phenotype was broadened to include bipolar disorder (P = 9.96 x 10(-9)). In this

  14. Arranged marriages annulled by law.

    Science.gov (United States)

    Zhu, H

    1996-06-01

    The arranged marriages of 210 young people in Yongle Town in Zunyi County of Guizhou Province were dissolved in 1995. The proportion of child betrothals, which generally happens among close relatives, is as high as 85% in the town. Some engagements, known as fetus betrothals or belt betrothals, are arranged before the children are born or while they are still infants strapped (belted) to their mothers. Dissemination of information from the Constitution, the Marriage Law, and the Regulations on the Registration of Marriage concerning marriage, healthier births, and good upbringing of children, and other information on reproductive health, has shown young people that they have the freedom to love and marry of their own free will, that their marriage is protected by law, and that consanguineous marriage is harmful to the health of future generations. Some convinced their parents that their arranged marriages should be annulled.

  15. Low-level laser irradiation alters mRNA expression from genes involved in DNA repair and genomic stabilization in myoblasts

    Science.gov (United States)

    Trajano, L. A. S. N.; Sergio, L. P. S.; Silva, C. L.; Carvalho, L.; Mencalha, A. L.; Stumbo, A. C.; Fonseca, A. S.

    2016-07-01

    Low-level lasers are used for the treatment of diseases in soft and bone tissues, but few data are available regarding their effects on genomic stability. In this study, we investigated mRNA expression from genes involved in DNA repair and genomic stabilization in myoblasts exposed to low-level infrared laser. C2C12 myoblast cultures in different fetal bovine serum concentrations were exposed to low-level infrared laser (10, 35 and 70 J cm-2), and collected for the evaluation of DNA repair gene expression. Laser exposure increased gene expression related to base excision repair (8-oxoguanine DNA glycosylase and apurinic/apyrimidinic endonuclease 1), nucleotide excision repair (excision repair cross-complementation group 1 and xeroderma pigmentosum C protein) and genomic stabilization (ATM serine/threonine kinase and tumor protein p53) in normal and low fetal bovine serum concentrations. Results suggest that genomic stability could be part of a biostimulation effect of low-level laser therapy in injured muscles.

  16. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans.

    Science.gov (United States)

    Lavrov, D V; Brown, W M

    2001-01-01

    The complete mitochondrial DNA (mtDNA) of the nematode Trichinella spiralis has been amplified in four overlapping fragments and 16,656 bp of its sequence has been determined. This sequence contains the 37 genes typical of metazoan mtDNAs, including a putative atp8, which is absent from all other nematode mtDNAs examined. The genes are transcribed from both mtDNA strands and have an arrangement relatable to those of coelomate metazoans, but not to those of secernentean nematodes. All protein genes appear to initiate with ATN codons, typical for metazoans. Neither TTG nor GTT start codons, inferred for several genes of other nematodes, were found. The 22 T. spiralis tRNA genes fall into three categories: (i) those with the potential to form conventional "cloverleaf" secondary structures, (ii) those with TPsiC arm + variable arm replacement loops, and (iii) those with DHU-arm replacement loops. Mt-tRNA(R) has a 5'-UCG-3' anticodon, as in most other metazoans, instead of the very unusual 5'-ACG-3' present in the secernentean nematodes. The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level. PMID:11156984

  17. Genomic rearrangements at the FRA2H common fragile site frequently involve non-homologous recombination events across LTR and L1(LINE) repeats.

    Science.gov (United States)

    Brueckner, Lena M; Sagulenko, Evgeny; Hess, Elisa M; Zheglo, Diana; Blumrich, Anne; Schwab, Manfred; Savelyeva, Larissa

    2012-08-01

    Common fragile sites (cFSs) are non-random chromosomal regions that are prone to breakage under conditions of replication stress. DNA damage and chromosomal alterations at cFSs appear to be critical events in the development of various human diseases, especially carcinogenesis. Despite the growing interest in understanding the nature of cFS instability, only a few cFSs have been molecularly characterised. In this study, we fine-mapped the location of FRA2H using six-colour fluorescence in situ hybridisation and showed that it is one of the most active cFSs in the human genome. FRA2H encompasses approximately 530 kb of a gene-poor region containing a novel large intergenic non-coding RNA gene (AC097500.2). Using custom-designed array comparative genomic hybridisation, we detected gross and submicroscopic chromosomal rearrangements involving FRA2H in a panel of 54 neuroblastoma, colon and breast cancer cell lines. The genomic alterations frequently involved different classes of long terminal repeats and long interspersed nuclear elements. An analysis of breakpoint junction sequence motifs predominantly revealed signatures of microhomology-mediated non-homologous recombination events. Our data provide insight into the molecular structure of cFSs and sequence motifs affected by their activation in cancer. Identifying cFS sequences will accelerate the search for DNA biomarkers and targets for individualised therapies.

  18. Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder

    OpenAIRE

    Williams, H J; Norton, N; Dwyer, S.; Moskvina, V; Nikolov, I.; Carroll, L.; Georgieva, L; Williams, N. M.; Morris, D.W.; Quinn, E.M.; Giegling, I; M. Ikeda(Kyoto University); Wood, J; Lencz, T; Hultman, C.

    2011-01-01

    Abstract A recent genome wide association study reported evidence for association between rs1344706 within ZNF804A (encoding zinc finger protein 804A) and schizophrenia (P=1.61 x10-7), and stronger evidence when the phenotype was broadened to include bipolar disorder (P=9.96 x10-9). Here we provide additional evidence for association through meta-analysis of a larger dataset (schizophrenia/schizoaffective disorder N = 18945, schizophrenia plus bipolar disorder N =21274, controls N ...

  19. Manipulating Multistage Interconnection Networks Using Fundamental Arrangements

    Directory of Open Access Journals (Sweden)

    E. Gur

    2010-12-01

    Full Text Available Optimizing interconnection networks is a prime object in switching schemes. In this work the authors present a novel approach for obtaining a required channel arrangement in a multi-stage interconnectionnetwork, using a new concept – a fundamental arrangement. The fundamental arrangement is an initial N-1 stage switch arrangement that allows obtaining any required output channel arrangement given an input arrangement, using N/2 binary switches at each stage. The paper demonstrates how a fundamental arrangement can be achieved and how, once this is done, any required arrangement may be obtained within 2(N-1 steps.

  20. Genomic characterization of Listeria monocytogenes strains involved in a multistate listeriosis outbreak associated with cantaloupe in US.

    Directory of Open Access Journals (Sweden)

    Pongpan Laksanalamai

    Full Text Available A multistate listeriosis outbreak associated with cantaloupe consumption was reported in the United States in September, 2011. The outbreak investigation recorded a total of 146 invasive illnesses, 30 deaths and one miscarriage. Subtyping of the outbreak associated clinical, food and environmental isolates revealed two serotypes (1/2a and 1/2b and four pulsed-field gel electrophoresis two-enzyme pattern combinations I, II, III, and IV, including one rarely seen before this outbreak. A DNA-microarray, Listeria GeneChip®, developed by FDA from 24 Listeria monocytogenes genome sequences, was used to further characterize a representative sample of the outbreak isolates. The microarray data (in the form of present or absent calls of specific DNA sequences separated the isolates into two distinct groups as per their serotypes. The gene content of the outbreak-associated isolates was distinct from that of the previously-reported outbreak strains belonging to the same serotypes. Although the 1/2b outbreak associated isolates are closely related to each other, the 1/2a isolates could be further divided into two distinct genomic groups, one represented by pattern combination I strains and the other represented by highly similar pattern combinations III and IV strains. Gene content analysis of these groups revealed unique genomic sequences associated with these two 1/2a genovars. This work underscores the utility of multiple approaches, such as serotyping, PFGE and DNA microarray analysis to characterize the composition of complex polyclonal listeriosis outbreaks.

  1. Genome-wide differential expression reveals candidate genes involved in the pathogenesis of lupus and lupus nephritis.

    Science.gov (United States)

    AlFadhli, Suad; Ghanem, Aqeel A M; Nizam, Rasheeba

    2016-01-01

    Systemic lupus erythematosus (lupus) is an autoimmune disease characterized by multiorgan pathology, accelerated apoptosis and hyper-autoantibody production against self-components. The root cause of lupus remains unknown, although multiple susceptibility factors have been reported in different ethnic group. We aimed to explore the genome-wide differential expression spectrum of lupus and its severe form lupus nephritis (LN) in Arab females. A total of 98 subjects: 40 lupus, 18 LN and 40 age/gender/ethnically matched healthy controls (HC) were recruited. Carefully chosen subjects (n = 11) were employed for whole human-genome expression profiling using high-density Human Exon 1.0.ST arrays (Affymetrix) and statistical analysis was carried out using appropriate software. Validation cohorts (n = 98) were investigated to quantify the expression of the nine selected candidate genes relative to GAPDH as endogenous control. Genome-wide differential analysis revealed seven candidate genes in lupus and 36 in LN, when individually compared to HC (anova Welch t-test, P ≤ 0.005, Tukey's honestly post hoc analysis). Analysis of differentially expressed genes with a fold change of 2, revealed 16 Gene Ontology terms satisfying a P ≤ 0.05. We further detected five distinct inflammatory and metabolic pathways such as TWEAK, osteopontin, endochondral ossification, fluropyrimidine activity and urea cycle and metabolism of amino groups that significantly contribute to the pathogenesis of lupus (P Rheumatology and Wiley Publishing Asia Pty Ltd.

  2. Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

    Science.gov (United States)

    Nugent, Timothy; Jones, David T

    2010-03-19

    Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/.

  3. Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

    Directory of Open Access Journals (Sweden)

    Timothy Nugent

    2010-03-01

    Full Text Available Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/.

  4. Heterotaxy in Caenorhabditis: widespread natural variation in left-right arrangement of the major organs.

    Science.gov (United States)

    Alcorn, Melissa R; Callander, Davon C; López-Santos, Agustín; Torres Cleuren, Yamila N; Birsoy, Bilge; Joshi, Pradeep M; Santure, Anna W; Rothman, Joel H

    2016-12-19

    Although the arrangement of internal organs in most metazoans is profoundly left-right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

  5. Heterotaxy in Caenorhabditis: widespread natural variation in left–right arrangement of the major organs

    Science.gov (United States)

    Callander, Davon C.; López-Santos, Agustín; Torres Cleuren, Yamila N.; Santure, Anna W.

    2016-01-01

    Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821534

  6. Genome-wide retroviral insertional tagging of genes involved in cancer in Cdkn2a-deficient mice

    DEFF Research Database (Denmark)

    Lund, Anders H; Turner, Geoffrey; Trubetskoy, Alla;

    2002-01-01

    retroviral integration sites and mapped them against the mouse genome sequence databases from Celera and Ensembl. In addition to 17 insertions targeting gene loci known to be cancer-related, we identified a total of 37 new common insertion sites (CISs), of which 8 encode components of signaling pathways......-scale retroviral insertional mutagenesis in genetically predisposed mice is useful both as a system for identifying genes underlying cancer and as a genetic framework for the assignment of such genes to specific oncogenic pathways....

  7. Evolutionary aspects of plastid proteins involved in transcription: the transcription of a tiny genome is mediated by a complicated machinery.

    Science.gov (United States)

    Yagi, Yusuke; Shiina, Takashi

    2012-01-01

    Chloroplasts in land plants have a small genome consisting of only 100 genes encoding partial sets of proteins for photosynthesis, transcription and translation. Although it has been thought that chloroplast transcription is mediated by a basically cyanobacterium-derived system, due to the endosymbiotic origin of plastids, recent studies suggest the existence of a hybrid transcription machinery containing non-bacterial proteins that have been newly acquired during plant evolution. Here, we highlight chloroplast-specific non-bacterial transcription mechanisms by which land plant chloroplasts have gained novel functions.

  8. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

    Directory of Open Access Journals (Sweden)

    Ji'an Pan

    Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

  9. Genome wide association mapping in Arabidopsis thaliana identifies novel genes involved in linking allyl glucosinolate to altered biomass and defense

    Directory of Open Access Journals (Sweden)

    Marta Francisco

    2016-07-01

    Full Text Available A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL, may provide direct feedback regulation, linking defense metabolism outputs to the growth and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 µM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

  10. Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications.

    Science.gov (United States)

    Jourda, Cyril; Cardi, Céline; Mbéguié-A-Mbéguié, Didier; Bocs, Stéphanie; Garsmeur, Olivier; D'Hont, Angélique; Yahiaoui, Nabila

    2014-05-01

    Whole-genome duplications (WGDs) are widespread in plants, and three lineage-specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening. Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed. Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1-aminocyclopropane-1-carboxylate synthase (ACS), ethylene-insensitive 3-like (EIL), ethylene-insensitive 3-binding F-box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them. We propose that EIL and EBF genes were co-retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling.

  11. When genome-based approach meets the ‘old but good’: revealing genes involved in the antibacterial activity of Pseudomonas sp. P482 against soft rot pathogens.

    Directory of Open Access Journals (Sweden)

    Dorota Magdalena Krzyżanowska

    2016-05-01

    Full Text Available Dickeya solani and Pectobacterium carotovorum subsp. brasili¬ense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain.Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologues of four nfs genes, that confer production of a nonfluorescent siderophore by P. donghuensis HYST. Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homologue of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability.A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study

  12. Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast

    Directory of Open Access Journals (Sweden)

    Lanthaler Karin

    2011-10-01

    Full Text Available Abstract Background The uptake of drugs into cells has traditionally been considered to be predominantly via passive diffusion through the bilayer portion of the cell membrane. The recent recognition that drug uptake is mostly carrier-mediated raises the question of which drugs use which carriers. Results To answer this, we have constructed a chemical genomics platform built upon the yeast gene deletion collection, using competition experiments in batch fermenters and robotic automation of cytotoxicity screens, including protection by 'natural' substrates. Using these, we tested 26 different drugs and identified the carriers required for 18 of the drugs to gain entry into yeast cells. Conclusions As well as providing a useful platform technology, these results further substantiate the notion that the cellular uptake of pharmaceutical drugs normally occurs via carrier-mediated transport and indicates that establishing the identity and tissue distribution of such carriers should be a major consideration in the design of safe and effective drugs.

  13. Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity

    DEFF Research Database (Denmark)

    Hägg, Sara; Ganna, Andrea; Van Der Laan, Sander W

    2015-01-01

    To date, genome-wide association studies (GWASs) have identified >100 loci with single variants associated with body mass index (BMI). This approach may miss loci with high allelic heterogeneity; therefore, the aim of the present study was to use gene-based meta-analysis to identify regions...... with high allelic heterogeneity to discover additional obesity susceptibility loci. We included GWAS data from 123 865 individuals of European descent from 46 cohorts in Stage 1 and Metabochip data from additional 103 046 individuals from 43 cohorts in Stage 2, all within the Genetic Investigation...... of ANthropometric Traits (GIANT) consortium. Each cohort was tested for association between ∼2.4 million (Stage 1) or ∼200 000 (Stage 2) imputed or genotyped single variants and BMI, and summary statistics were subsequently meta-analyzed in 17 941 genes. We used the ‘VErsatile Gene-based Association Study’ (VEGAS...

  14. Genome mining of the hitachimycin biosynthetic gene cluster: involvement of a phenylalanine-2,3-aminomutase in biosynthesis.

    Science.gov (United States)

    Kudo, Fumitaka; Kawamura, Koichi; Uchino, Asuka; Miyanaga, Akimasa; Numakura, Mario; Takayanagi, Ryuichi; Eguchi, Tadashi

    2015-04-13

    Hitachimycin is a macrolactam antibiotic with (S)-β-phenylalanine (β-Phe) at the starter position of its polyketide skeleton. To understand the incorporation mechanism of β-Phe and the modification mechanism of the unique polyketide skeleton, the biosynthetic gene cluster for hitachimycin in Streptomyces scabrisporus was identified by genome mining. The identified gene cluster contains a putative phenylalanine-2,3-aminomutase (PAM), five polyketide synthases, four β-amino-acid-carrying enzymes, and a characteristic amidohydrolase. A hitA knockout mutant showed no hitachimycin production, but antibiotic production was restored by feeding with (S)-β-Phe. We also confirmed the enzymatic activity of the HitA PAM. The results suggest that the identified gene cluster is responsible for the biosynthesis of hitachimycin. A plausible biosynthetic pathway for hitachimycin, including a unique polyketide skeletal transformation mechanism, is proposed.

  15. Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder.

    Science.gov (United States)

    Williams, H J; Norton, N; Dwyer, S; Moskvina, V; Nikolov, I; Carroll, L; Georgieva, L; Williams, N M; Morris, D W; Quinn, E M; Giegling, I; Ikeda, M; Wood, J; Lencz, T; Hultman, C; Lichtenstein, P; Thiselton, D; Maher, B S; Malhotra, A K; Riley, B; Kendler, K S; Gill, M; Sullivan, P; Sklar, P; Purcell, S; Nimgaonkar, V L; Kirov, G; Holmans, P; Corvin, A; Rujescu, D; Craddock, N; Owen, M J; O'Donovan, M C

    2011-04-01

    A recent genome-wide association study (GWAS) reported evidence for association between rs1344706 within ZNF804A (encoding zinc-finger protein 804A) and schizophrenia (P=1.61 × 10(-7)), and stronger evidence when the phenotype was broadened to include bipolar disorder (P=9.96 × 10(-9)). In this study we provide additional evidence for association through meta-analysis of a larger data set (schizophrenia/schizoaffective disorder N=18 945, schizophrenia plus bipolar disorder N=21 274 and controls N=38 675). We also sought to better localize the association signal using a combination of de novo polymorphism discovery in exons, pooled de novo polymorphism discovery spanning the genomic sequence of the locus and high-density linkage disequilibrium (LD) mapping. The meta-analysis provided evidence for association between rs1344706 that surpasses widely accepted benchmarks of significance by several orders of magnitude for both schizophrenia (P=2.5 × 10(-11), odds ratio (OR) 1.10, 95% confidence interval 1.07-1.14) and schizophrenia and bipolar disorder combined (P=4.1 × 10(-13), OR 1.11, 95% confidence interval 1.07-1.14). After de novo polymorphism discovery and detailed association analysis, rs1344706 remained the most strongly associated marker in the gene. The allelic association at the ZNF804A locus is now one of the most compelling in schizophrenia to date, and supports the accumulating data suggesting overlapping genetic risk between schizophrenia and bipolar disorder.

  16. Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder.

    LENUS (Irish Health Repository)

    Williams, H J

    2011-04-01

    A recent genome-wide association study (GWAS) reported evidence for association between rs1344706 within ZNF804A (encoding zinc-finger protein 804A) and schizophrenia (P=1.61 × 10(-7)), and stronger evidence when the phenotype was broadened to include bipolar disorder (P=9.96 × 10(-9)). In this study we provide additional evidence for association through meta-analysis of a larger data set (schizophrenia\\/schizoaffective disorder N=18 945, schizophrenia plus bipolar disorder N=21 274 and controls N=38 675). We also sought to better localize the association signal using a combination of de novo polymorphism discovery in exons, pooled de novo polymorphism discovery spanning the genomic sequence of the locus and high-density linkage disequilibrium (LD) mapping. The meta-analysis provided evidence for association between rs1344706 that surpasses widely accepted benchmarks of significance by several orders of magnitude for both schizophrenia (P=2.5 × 10(-11), odds ratio (OR) 1.10, 95% confidence interval 1.07-1.14) and schizophrenia and bipolar disorder combined (P=4.1 × 10(-13), OR 1.11, 95% confidence interval 1.07-1.14). After de novo polymorphism discovery and detailed association analysis, rs1344706 remained the most strongly associated marker in the gene. The allelic association at the ZNF804A locus is now one of the most compelling in schizophrenia to date, and supports the accumulating data suggesting overlapping genetic risk between schizophrenia and bipolar disorder.

  17. The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity▿ †

    Science.gov (United States)

    Gartemann, Karl-Heinz; Abt, Birte; Bekel, Thomas; Burger, Annette; Engemann, Jutta; Flügel, Monika; Gaigalat, Lars; Goesmann, Alexander; Gräfen, Ines; Kalinowski, Jörn; Kaup, Olaf; Kirchner, Oliver; Krause, Lutz; Linke, Burkhard; McHardy, Alice; Meyer, Folker; Pohle, Sandra; Rückert, Christian; Schneiker, Susanne; Zellermann, Eva-Maria; Pühler, Alfred; Eichenlaub, Rudolf; Kaiser, Olaf; Bartels, Daniela

    2008-01-01

    Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil. PMID:18192381

  18. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.

    Science.gov (United States)

    Gartemann, Karl-Heinz; Abt, Birte; Bekel, Thomas; Burger, Annette; Engemann, Jutta; Flügel, Monika; Gaigalat, Lars; Goesmann, Alexander; Gräfen, Ines; Kalinowski, Jörn; Kaup, Olaf; Kirchner, Oliver; Krause, Lutz; Linke, Burkhard; McHardy, Alice; Meyer, Folker; Pohle, Sandra; Rückert, Christian; Schneiker, Susanne; Zellermann, Eva-Maria; Pühler, Alfred; Eichenlaub, Rudolf; Kaiser, Olaf; Bartels, Daniela

    2008-03-01

    Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil.

  19. Genomic imbalances are involved in miR-30c and let-7a deregulation in ovarian tumors: implications for HMGA2 expression.

    Science.gov (United States)

    Agostini, Antonio; Brunetti, Marta; Davidson, Ben; Tropé, Claes G; Heim, Sverre; Panagopoulos, Ioannis; Micci, Francesca

    2017-03-28

    The High-mobility group AT-hook 2 protein (HMGA2) is involved in different processes during tumorigenesis. High expression levels of HMGA2 are found in various types of cancer, with recent studies highlighting the important role of miRNAs in the regulation of HMGA2 expression. We report a study of 155 ovarian tumors (30 sex-cord stromal tumors, 22 borderline tumors, and 103 carcinomas) analyzed for HMGA2 expression as well as the expression of two miRNAs targeting this gene, let-7a and miR-30c. We also evaluated the expression of the fragile histidine triad (FHIT) and lin28 homologues (LIN28A/B) genes which are known to be an enhancer of miR-30c expression and a repressor of let-7a, respectively. HMGA2 was found expressed at high levels in most samples analyzed, with clear cell carcinomas as the only exception. let-7a and miR-30c were highly deregulated in all tumor types. LIN28A and FHIT were found overexpressed in all examined tumor types. The chromosomal imbalances that might lead to loss of the genes expressing let-7a and miR-30c could be evaluated on the basis of previously generated karyotypic and high resolution comparative genomic hybridization (CGH) data on 103 tumors. 76% of the samples with an imbalanced genome had at least one chromosomal aberration leading to a deletion of a miRNA cluster for let-7a and miR-30c. FISH using locus specific probes for these clusters validate the aberrations at the gene level. Our study shows that genomic imbalances are involved in miR-30c and let-7a deregulation. One can reasonably assume that dysregulation of these miRNAs is a cause leading to HMGA2 upregulation in ovarian tumors.

  20. The Genome of the Generalist Plant Pathogen Fusarium avenaceum Is Enriched with Genes Involved in Redox, Signaling and Secondary Metabolism

    DEFF Research Database (Denmark)

    Lysøe, Erik; Harris, Linda J.; Walkowiak, Sean

    2014-01-01

    . avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space...

  1. Genome-wide identification and functional analysis of S-RNase involved in the self-incompatibility of citrus.

    Science.gov (United States)

    Liang, Mei; Yang, Wei; Su, Shiying; Fu, Lili; Yi, Hualin; Chen, Chuanwu; Deng, Xiuxin; Chai, Lijun

    2017-04-01

    S-RNase-based self-incompatibility is found in Solanaceae, Rosaceae, and Scrophulariaceae, and is the most widespread mechanism that prevents self-fertilization in plants. Although 'Shatian' pummelo (Citrus grandis), a traditional cultivated variety, possesses the self-incompatible trait, the role of S-RNases in the self-incompatibility of 'Shatian' pummelo is poorly understood. To identify genes associated with self-incompatibility in citrus, we identified 16 genes encoding homologs of ribonucleases in the genomes of sweet orange (Citrus sinensis) and clementine mandarin (Citrus clementine). We preliminarily distinguished S-RNases from S-like RNases with a phylogenetic analysis that classified these homologs into three groups, which is consistent with the previous reports. Expression analysis provided evidence that CsRNS1 and CsRNS6 are S-like RNase genes. The expression level of CsRNS1 was increased during fruit development. The expression of CsRNS6 was increased during the formation of embryogenic callus. In contrast, we found that CsRNS3 possessed several common characteristics of the pistil determinant of self-incompatibility: it has an alkaline isoelectric point (pI), harbors only one intron, and is specifically expressed in style. We obtained a cDNA encoding CgRNS3 from 'Shatian' pummelo and found that it is homolog to CsRNS3 and that CgRNS3 exhibited the same expression pattern as CsRNS3. In an in vitro culture system, the CgRNS3 protein significantly inhibited the growth of self-pollen tubes from 'Shatian' pummelo, but after a heat treatment, this protein did not significantly inhibit the elongation of self- or non-self-pollen tubes. In conclusion, an S-RNase gene, CgRNS3, was obtained by searching the genomes of sweet orange and clementine for genes exhibiting sequence similarity to ribonucleases followed by expression analyses. Using this approach, we identified a protein that significantly inhibited the growth of self-pollen tubes, which is the defining

  2. Genome-Wide Identification of bZIP Family Genes Involved in Drought and Heat Stresses in Strawberry (Fragaria vesca).

    Science.gov (United States)

    Wang, Xiao-Long; Chen, Xinlu; Yang, Tian-Bao; Cheng, Qunkang; Cheng, Zong-Ming

    2017-01-01

    Basic leucine zipper (bZIP) genes are known to play a crucial role in response to various processes in plant as well as abiotic or biotic stress challenges. We have performed an identification and characterization of 50 bZIP genes across the woodland strawberry (Fragaria vesca) genome, which were divided into 10 clades according to the phylogenetic relationship of the strawberry bZIP proteins with those in Arabidopsis and rice. Five categories of intron patterns were observed within basic and hinge regions of the bZIP domains. Some additional conserved motifs have been found with the group specificity. Further, we predicted DNA-binding specificity of the basic and hinge regions as well as dimerization properties of leucine zipper regions, which was consistent with our phylogenetic clade and classified into 20 subfamilies. Across the different developmental stages of 15 organs and two types of fruits, the clade A bZIP members showed different tissue-specific expression patterns and the duplicated genes were differentially regulated, indicating a functional diversification coupled with the expansion of this gene family in strawberry. Under normal growth conditions, mrna11837 and mrna30280 of clade A showed very weak expression levels in organs and fruits, respectively; but higher expression was observed with different set of genes following drought and heat treatment, which may be caused by the separate response pathway between drought and heat treatments.

  3. Genome-Wide Identification of bZIP Family Genes Involved in Drought and Heat Stresses in Strawberry (Fragaria vesca

    Directory of Open Access Journals (Sweden)

    Xiao-Long Wang

    2017-01-01

    Full Text Available Basic leucine zipper (bZIP genes are known to play a crucial role in response to various processes in plant as well as abiotic or biotic stress challenges. We have performed an identification and characterization of 50 bZIP genes across the woodland strawberry (Fragaria vesca genome, which were divided into 10 clades according to the phylogenetic relationship of the strawberry bZIP proteins with those in Arabidopsis and rice. Five categories of intron patterns were observed within basic and hinge regions of the bZIP domains. Some additional conserved motifs have been found with the group specificity. Further, we predicted DNA-binding specificity of the basic and hinge regions as well as dimerization properties of leucine zipper regions, which was consistent with our phylogenetic clade and classified into 20 subfamilies. Across the different developmental stages of 15 organs and two types of fruits, the clade A bZIP members showed different tissue-specific expression patterns and the duplicated genes were differentially regulated, indicating a functional diversification coupled with the expansion of this gene family in strawberry. Under normal growth conditions, mrna11837 and mrna30280 of clade A showed very weak expression levels in organs and fruits, respectively; but higher expression was observed with different set of genes following drought and heat treatment, which may be caused by the separate response pathway between drought and heat treatments.

  4. Genomic identification, phylogeny, and expression analysis of MLO genes involved in susceptibility to powdery mildew in Fragaria vesca.

    Science.gov (United States)

    Miao, L X; Jiang, M; Zhang, Y C; Yang, X F; Zhang, H Q; Zhang, Z F; Wang, Y Z; Jiang, G H

    2016-08-05

    The MLO (powdery mildew locus O) gene family is important in resistance to powdery mildew (PM). In this study, all of the members of the MLO family were identified and analyzed in the strawberry (Fragaria vesca) genome. The strawberry contains at least 20 members of the MLO family, and the protein sequence contained between 171 and 1485 amino acids, with 0-34 introns. Chromosomal localization showed that the MLOs were unevenly distributed on each of the chromosomes, except for chromosome 4. The greatest number of MLOs (seven) was found on chromosome 3. A phylogenetic tree showed that the MLOs were divided into seven groups (I-VII), four of which consisted of MLOs from strawberry, Arabidopsis thaliana, rice, and maize, suggesting that these genes may have evolved after the divergence of monocots and dicots. Multiple sequence alignment showed that strawberry MLO candidates related to powdery mildew resistance possessed seven highly conserved transmembrane domains, a calmodulin-binding domain, and two conserved regions, all of which are important domains for powdery mildew resistance genes. Expressed sequence tag analysis revealed that the MLOs were induced by multiple abiotic stressors, including low and high temperature, drought, and high salinity. These findings will contribute to the functional characterization of MLOs related to PM susceptibility, and will assist in the development of disease resistance in strawberries.

  5. Evidence of two mechanisms involved in Bacillus thuringiensis israelensis decreased toxicity against mosquito larvae: Genome dynamic and toxins stability.

    Science.gov (United States)

    Elleuch, Jihen; Zribi Zghal, Raida; Lacoix, Marie Noël; Chandre, Fabrice; Tounsi, Slim; Jaoua, Samir

    2015-07-01

    Biopesticides based on Bacillus thuringiensis israelensis are the most used and most successful around the world. This bacterium is characterized by a dynamic genome able to win or lose genetic materials which leads to a decrease in its effectiveness. The detection of such phenomena is of great importance to monitor the stability of B. thuringiensis strains in industrial production processes of biopesticides. New local B. thuringiensis israelensis isolates were investigated. They present variable levels of delta-endotoxins production and insecticidal activities against Aedes aegypti larvae. Searching on the origin of this variability, molecular and biochemical analyses were performed. The obtained results describe two main reasons of the decrease of B. thuringiensis israelensis insecticidal activity. The first reason was the deletion of cry4Aa and cry10Aa genes from the 128-kb pBtoxis plasmid as evidenced in three strains (BLB124, BLB199 and BLB506) among five. The second was the early degradation of Cry toxins by proteases in larvae midgut mainly due to some amino acids substitutions evidenced in Cry4Ba and Cry11Aa δ-endotoxins detected in BLB356. Before biological treatment based on B. thuringiensis israelensis, the studies of microflore in each ecosystem have a great importance to succeed pest management programs.

  6. Moduli of weighted hyperplane arrangements

    CERN Document Server

    Lahoz, Martí; Macrí, Emanuele; Stellari, Paolo

    2015-01-01

    This book focuses on a large class of geometric objects in moduli theory and provides explicit computations to investigate their families. Concrete examples are developed that take advantage of the intricate interplay between Algebraic Geometry and Combinatorics. Compactifications of moduli spaces play a crucial role in Number Theory, String Theory, and Quantum Field Theory – to mention just a few. In particular, the notion of compactification of moduli spaces has been crucial for solving various open problems and long-standing conjectures. Further, the book reports on compactification techniques for moduli spaces in a large class where computations are possible, namely that of weighted stable hyperplane arrangements.

  7. A genome-wide immunodetection screen in S. cerevisiae uncovers novel genes involved in lysosomal vacuole function and morphology.

    Directory of Open Access Journals (Sweden)

    Florante Ricarte

    Full Text Available Vacuoles of yeast Saccharomyces cerevisiae are functionally analogous to mammalian lysosomes. Both are cellular organelles responsible for macromolecular degradation, ion/pH homeostasis, and stress survival. We hypothesized that undefined gene functions remain at post-endosomal stage of vacuolar events and performed a genome-wide screen directed at such functions at the late endosome and vacuole interface - ENV genes. The immunodetection screen was designed to identify mutants that internally accumulate precursor form of the vacuolar hydrolase carboxypeptidase Y (CPY. Here, we report the uncovering and initial characterizations of twelve ENV genes. The small size of the collection and the lack of genes previously identified with vacuolar events are suggestive of the intended exclusive functional interface of the screen. Most notably, the collection includes four novel genes ENV7, ENV9, ENV10, and ENV11, and three genes previously linked to mitochondrial processes - MAM3, PCP1, PPE1. In all env mutants, vesicular trafficking stages were undisturbed in live cells as assessed by invertase and active α-factor secretion, as well as by localization of the endocytic fluorescent marker FM4-64 to the vacuole. Several mutants exhibit defects in stress survival functions associated with vacuoles. Confocal fluorescence microscopy revealed the collection to be significantly enriched in vacuolar morphologies suggestive of fusion and fission defects. These include the unique phenotype of lumenal vesicles within vacuoles in the novel env9Δ mutant and severely fragmented vacuoles upon deletion of GET4, a gene recently implicated in tail anchored membrane protein insertion. Thus, our results establish new gene functions in vacuolar function and morphology, and suggest a link between vacuolar and mitochondrial events.

  8. Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity

    Science.gov (United States)

    Hägg, Sara; Ganna, Andrea; Van Der Laan, Sander W.; Esko, Tonu; Pers, Tune H.; Locke, Adam E.; Berndt, Sonja I.; Justice, Anne E.; Kahali, Bratati; Siemelink, Marten A.; Pasterkamp, Gerard; Strachan, David P.; Speliotes, Elizabeth K.; North, Kari E.; Loos, Ruth J.F.; Hirschhorn, Joel N.; Pawitan, Yudi; Ingelsson, Erik

    2015-01-01

    To date, genome-wide association studies (GWASs) have identified >100 loci with single variants associated with body mass index (BMI). This approach may miss loci with high allelic heterogeneity; therefore, the aim of the present study was to use gene-based meta-analysis to identify regions with high allelic heterogeneity to discover additional obesity susceptibility loci. We included GWAS data from 123 865 individuals of European descent from 46 cohorts in Stage 1 and Metabochip data from additional 103 046 individuals from 43 cohorts in Stage 2, all within the Genetic Investigation of ANthropometric Traits (GIANT) consortium. Each cohort was tested for association between ∼2.4 million (Stage 1) or ∼200 000 (Stage 2) imputed or genotyped single variants and BMI, and summary statistics were subsequently meta-analyzed in 17 941 genes. We used the ‘VErsatile Gene-based Association Study’ (VEGAS) approach to assign variants to genes and to calculate gene-based P-values based on simulations. The VEGAS method was applied to each cohort separately before a gene-based meta-analysis was performed. In Stage 1, two known (FTO and TMEM18) and six novel (PEX2, MTFR2, SSFA2, IARS2, CEP295 and TXNDC12) loci were associated with BMI (P gene tests). We confirmed all loci, and six of them were gene-wide significant in Stage 2 alone. We provide biological support for the loci by pathway, expression and methylation analyses. Our results indicate that gene-based meta-analysis of GWAS provides a useful strategy to find loci of interest that were not identified in standard single-marker analyses due to high allelic heterogeneity. PMID:26376864

  9. Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome.

    Science.gov (United States)

    Pierella Karlusich, Juan J; Ceccoli, Romina D; Graña, Martín; Romero, Héctor; Carrillo, Néstor

    2015-02-16

    Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-containing flavodoxin, is a widespread strategy employed by photosynthetic microorganisms to overcome environmental adversities. The flavodoxin gene was lost in the course of plant evolution, but its reintroduction in transgenic plants confers increased tolerance to environmental stress and iron starvation, raising the question as to why a genetic asset with obvious adaptive value was not kept by natural selection. Phylogenetic analyses reveal that the evolutionary history of flavodoxin is intricate, with several horizontal gene transfer events between distant organisms, including Eukarya, Bacteria, and Archaea. The flavodoxin gene is unevenly distributed in most algal lineages, with flavodoxin-containing species being overrepresented in iron-limited regions and scarce or absent in iron-rich environments. Evaluation of cyanobacterial genomic and metagenomic data yielded essentially the same results, indicating that there was little selection pressure to retain flavodoxin in iron-rich coastal/freshwater phototrophs. Our results show a highly dynamic evolution pattern of flavodoxin tightly connected to the bioavailability of iron. Evidence presented here also indicates that the high concentration of iron in coastal and freshwater habitats may have facilitated the loss of flavodoxin in the freshwater ancestor of modern plants during the transition of photosynthetic organisms from the open oceans to the firm land.

  10. Functional genomic analysis of alkaloid biosynthesis in Hyoscyamus niger reveals a cytochrome P450 involved in littorine rearrangement.

    Science.gov (United States)

    Li, Rong; Reed, Darwin W; Liu, Enwu; Nowak, Jacek; Pelcher, Lawrence E; Page, Jonathan E; Covello, Patrick S

    2006-05-01

    Tropane alkaloids are valuable pharmaceutical drugs derived from solanaceous plants such as Hyoscyamus niger (black henbane). The biosynthesis of these molecules, including the nature of the enigmatic rearrangement of (R)-littorine to (S)-hyoscyamine, is not completely understood. To test the hypothesis that a cytochrome P450 enzyme is involved in this rearrangement, we used virus-induced gene silencing to silence a cytochrome P450, CYP80F1, identified from H. niger roots by EST sequencing. Silencing CYP80F1 resulted in reduced hyoscyamine levels and the accumulation of littorine. Hyoscyamine was observed in CYP80F1-expressing tobacco hairy roots supplied with (R)-littorine. Expression in yeast confirmed that CYP80F1 catalyzes the oxidation of (R)-littorine with rearrangement to form hyoscyamine aldehyde, a putative precursor to hyoscyamine, and without rearrangement to form 3'-hydroxylittorine. Our data strongly support the involvement of CYP80F1 in the rearrangement of littorine to hyoscyamine.

  11. 42 CFR 413.241 - Pharmacy arrangements.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Pharmacy arrangements. 413.241 Section 413.241... Disease (ESRD) Services and Organ Procurement Costs § 413.241 Pharmacy arrangements. Effective January 1, 2011, an ESRD facility that enters into an arrangement with a pharmacy to furnish renal dialysis...

  12. Free arrangements and coefficients of characteristic polynomials

    CERN Document Server

    Abe, Takuro

    2011-01-01

    Ziegler showed that free arrangements have free restricted multiarrangements (multirestrictions). After Ziegler's work, several results concerning "reverse direction", namely characterizing freeness of an arrangement via that of multirestriction, have appeared. In this paper, we prove that the second Betti number of the arrangement plays a crucial role.

  13. 45 CFR 302.34 - Cooperative arrangements.

    Science.gov (United States)

    2010-10-01

    ... PLAN REQUIREMENTS § 302.34 Cooperative arrangements. The State plan shall provide that the State will enter into written agreements for cooperative arrangements under § 303.107 with appropriate courts, law... 45 Public Welfare 2 2010-10-01 2010-10-01 false Cooperative arrangements. 302.34 Section...

  14. The physics of custody arrangements

    CERN Document Server

    Gomberoff, Andrés; Romagnoli, Pierre Paul

    2013-01-01

    Divorced individuals face complex situations when they have children with different ex-partners, or even more, when their new partners have children of their own. In such cases, and when kids spend every other weekend with each parent, a practical problem emerges: Is it possible to have such a custody arrangement that every couple has either all of the kids together or no kids at all? We show that in general, it is not possible, but that the number of couples that do can be maximized. The problem turns out to be equivalent to finding the ground state of a spin glass system, which is known to be equivalent to what is called a weighted max-cut problem in graph theory, and hence it is NP-Complete.

  15. Exploring the Genome and Proteome of Desulfitobacterium hafniense DCB2 for its Protein Complexes Involved in Metal Reduction and Dechlorination

    Energy Technology Data Exchange (ETDEWEB)

    Sang-Hoon, Kim; Hardzman, Christina; Davis, John k.; Hutcheson, Rachel; Broderick, Joan B.; Marsh, Terence L.; Tiedje, James M.

    2012-09-27

    Desulfitobacteria are of interest to DOE mission because of their ability to reduce many electron acceptors including Fe(III), U(VI), Cr(VI), As(V), Mn(IV), Se(VI), NO3- and well as CO2, sulfite, fumarate and humates, their ability to colonize more stressful environments because they form spores, fix nitrogen and they have the more protective Gram positive cell walls. Furthermore at least some of them reductively dechlorinate aromatic and aliphatic pollutants. Importantly, most of the metals and the organochlorine reductions are coupled to ATP production and support growth providing for the organism's natural selection at DOE's contaminant sites. This work was undertaken to gain insight into the genetic and metabolic pathways involved in dissimilatory metal reduction and reductive dechlorination, (ii) to discern the commonalities among these electron-accepting processes, (iii) to identify multi-protein complexes catalyzing these functions and (iv) to elucidate the coordination in expression of these pathways and processes.

  16. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

    Directory of Open Access Journals (Sweden)

    Sato Yukuto

    2009-06-01

    Full Text Available Abstract Background Recent genomic studies have revealed a teleost-specific third-round whole genome duplication (3R-WGD event occurred in a common ancestor of teleost fishes. However, it is unclear how the genes duplicated in this event were lost or persisted during the diversification of teleosts, and therefore, how many of the duplicated genes contribute to the genetic differences among teleosts. This subject is also important for understanding the process of vertebrate evolution through WGD events. We applied a comparative evolutionary approach to this question by focusing on the genes involved in long-term potentiation, taste and olfactory transduction, and the tricarboxylic acid cycle, based on the whole genome sequences of four teleosts; zebrafish, medaka, stickleback, and green spotted puffer fish. Results We applied a state-of-the-art method of maximum-likelihood phylogenetic inference and conserved synteny analyses to each of 130 genes involved in the above biological systems of human. These analyses identified 116 orthologous gene groups between teleosts and tetrapods, and 45 pairs of 3R-WGD-derived duplicate genes among them. This suggests that more than half [(45×2/(116+45] = 56.5% of the loci, probably more than ten thousand genes, present in a common ancestor of the four teleosts were still duplicated after the 3R-WGD. The estimated temporal pattern of gene loss suggested that, after the 3R-WGD, many (71/116 of the duplicated genes were rapidly lost during the initial 75 million years (MY, whereas on average more than half (27.3/45 of the duplicated genes remaining in the ancestor of the four teleosts (45/116 have persisted for about 275 MY. The 3R-WGD-derived duplicates that have persisted for a long evolutionary periods of time had significantly larger number of interacting partners and longer length of protein coding sequence, implying that they tend to be more multifunctional than the singletons after the 3R-WGD. Conclusion

  17. Algorithms for Optimally Arranging Multicore Memory Structures

    Directory of Open Access Journals (Sweden)

    Wei-Che Tseng

    2010-01-01

    Full Text Available As more processing cores are added to embedded systems processors, the relationships between cores and memories have more influence on the energy consumption of the processor. In this paper, we conduct fundamental research to explore the effects of memory sharing on energy in a multicore processor. We study the Memory Arrangement (MA Problem. We prove that the general case of MA is NP-complete. We present an optimal algorithm for solving linear MA and optimal and heuristic algorithms for solving rectangular MA. On average, we can produce arrangements that consume 49% less energy than an all shared memory arrangement and 14% less energy than an all private memory arrangement for randomly generated instances. For DSP benchmarks, we can produce arrangements that, on average, consume 20% less energy than an all shared memory arrangement and 27% less energy than an all private memory arrangement.

  18. Efficient genome editing of genes involved in neural crest development using the CRISPR/Cas9 system in Xenopus embryos.

    Science.gov (United States)

    Liu, Zhongzhen; Cheng, Tina Tsz Kwan; Shi, Zhaoying; Liu, Ziran; Lei, Yong; Wang, Chengdong; Shi, Weili; Chen, Xiongfeng; Qi, Xufeng; Cai, Dongqing; Feng, Bo; Deng, Yi; Chen, Yonglong; Zhao, Hui

    2016-01-01

    The RNA guided CRISPR/Cas9 nucleases have been proven to be effective for gene disruption in various animal models including Xenopus tropicalis. The neural crest (NC) is a transient cell population during embryonic development and contributes to a large variety of tissues. Currently, loss-of-function studies on NC development in X. tropicalis are largely based on morpholino antisense oligonucleotide. It is worthwhile establishing targeted gene knockout X. tropicails line using CRISPR/Cas9 system to study NC development. We utilized CRISPR/Cas9 to disrupt genes that are involved in NC formation in X. tropicalis embryos. A single sgRNA and Cas9 mRNA synthesized in vitro, were co-injected into X. tropicalis embryos at one-cell stage to induce single gene disruption. We also induced duplex mutations, large segmental deletions and inversions in X. tropicalis by injecting Cas9 and a pair of sgRNAs. The specificity of CRISPR/Cas9 was assessed in X. tropicalis embryos and the Cas9 nickase was used to reduce the off-target cleavages. Finally, we crossed the G0 mosaic frogs with targeted mutations to wild type frogs and obtained the germline transmission. Total 16 target sites in 15 genes were targeted by CRISPR/Cas9 and resulted in successful indel mutations at 14 loci with disruption efficiencies in a range from 9.3 to 57.8 %. Furthermore, we demonstrated the feasibility of generation of duplex mutations, large segmental deletions and inversions by using Cas9 and a pair of sgRNAs. We observed that CRISPR/Cas9 displays obvious off-target effects at some loci in X. tropicalis embryos. Such off-target cleavages was reduced by using the D10A Cas9 nickase. Finally, the Cas9 induced indel mutations were efficiently passed to G1 offspring. Our study proved that CRISPR/Cas9 could mediate targeted gene mutation in X. tropicalis with high efficiency. This study expands the application of CRISPR/Cas9 platform in X. tropicalis and set a basis for studying NC development using genetic

  19. Genome-wide identification, phylogeny, and expression analyses of the 14-3-3 family reveal their involvement in the development, ripening and abiotic stress response in banana

    Directory of Open Access Journals (Sweden)

    meiying li

    2016-09-01

    Full Text Available Plant 14-3-3 proteins act as critical components of various cellular signaling processes and play an important role in regulating multiple physiological processes. However, less information is known about the 14-3-3 gene family in banana. In this study, 25 14-3-3 genes were identified from the banana genome. Based on the evolutionary analysis, banana 14-3-3 proteins were clustered into ε and non-ε groups. Conserved motif analysis showed that all identified banana 14-3-3 genes had the typical 14-3-3 motif. The gene structure of banana 14-3-3 genes showed distinct class-specific divergence between the ε group and the non-ε group. Most banana 14-3-3 genes showed strong transcript accumulation changes during fruit development and postharvest ripening in two banana varieties, indicating that they might be involved in regulating fruit development and ripening. Moreover, some 14-3-3 genes also showed great changes after osmotic, cold, and salt treatments in two banana varieties, suggested their potential role in regulating banana response to abiotic stress. Taken together, this systemic analysis reveals the involvement of banana 14-3-3 genes in fruit development, postharvest ripening, and response to abiotic stress and provides useful information for understanding the functions of 14-3-3 genes in banana.

  20. Genome-Wide Identification, Phylogeny, and Expression Analyses of the 14-3-3 Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana

    Science.gov (United States)

    Li, Meiying; Ren, Licheng; Xu, Biyu; Yang, Xiaoliang; Xia, Qiyu; He, Pingping; Xiao, Susheng; Guo, Anping; Hu, Wei; Jin, Zhiqiang

    2016-01-01

    Plant 14-3-3 proteins act as critical components of various cellular signaling processes and play an important role in regulating multiple physiological processes. However, less information is known about the 14-3-3 gene family in banana. In this study, 25 14-3-3 genes were identified from the banana genome. Based on the evolutionary analysis, banana 14-3-3 proteins were clustered into ε and non-ε groups. Conserved motif analysis showed that all identified banana 14-3-3 genes had the typical 14-3-3 motif. The gene structure of banana 14-3-3 genes showed distinct class-specific divergence between the ε group and the non-ε group. Most banana 14-3-3 genes showed strong transcript accumulation changes during fruit development and postharvest ripening in two banana varieties, indicating that they might be involved in regulating fruit development and ripening. Moreover, some 14-3-3 genes also showed great changes after osmotic, cold, and salt treatments in two banana varieties, suggested their potential role in regulating banana response to abiotic stress. Taken together, this systemic analysis reveals the involvement of banana 14-3-3 genes in fruit development, postharvest ripening, and response to abiotic stress and provides useful information for understanding the functions of 14-3-3 genes in banana. PMID:27713761

  1. Draft Genome Sequence of Lactobacillus rhamnosus 2166.

    OpenAIRE

    Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.

    2014-01-01

    In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

  2. Draft Genome Sequence of Lactobacillus rhamnosus 2166.

    OpenAIRE

    Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.

    2014-01-01

    In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

  3. Identification of early zygotic genes in the yellow fever mosquito Aedes aegypti and discovery of a motif involved in early zygotic genome activation.

    Directory of Open Access Journals (Sweden)

    James K Biedler

    Full Text Available During early embryogenesis the zygotic genome is transcriptionally silent and all mRNAs present are of maternal origin. The maternal-zygotic transition marks the time over which embryogenesis changes its dependence from maternal RNAs to zygotically transcribed RNAs. Here we present the first systematic investigation of early zygotic genes (EZGs in a mosquito species and focus on genes involved in the onset of transcription during 2-4 hr. We used transcriptome sequencing to identify the "pure" (without maternal expression EZGs by analyzing transcripts from four embryonic time ranges of 0-2, 2-4, 4-8, and 8-12 hr, which includes the time of cellular blastoderm formation and up to the start of gastrulation. Blast of 16,789 annotated transcripts vs. the transcriptome reads revealed evidence for 63 (P<0.001 and 143 (P<0.05 nonmaternally derived transcripts having a significant increase in expression at 2-4 hr. One third of the 63 EZG transcripts do not have predicted introns compared to 10% of all Ae. aegypti genes. We have confirmed by RT-PCR that zygotic transcription starts as early as 2-3 hours. A degenerate motif VBRGGTA was found to be overrepresented in the upstream sequences of the identified EZGs using a motif identification software called SCOPE. We find evidence for homology between this motif and the TAGteam motif found in Drosophila that has been implicated in EZG activation. A 38 bp sequence in the proximal upstream sequence of a kinesin light chain EZG (KLC2.1 contains two copies of the mosquito motif. This sequence was shown to support EZG transcription by luciferase reporter assays performed on injected early embryos, and confers early zygotic activity to a heterologous promoter from a divergent mosquito species. The results of these studies are consistent with the model of early zygotic genome activation via transcriptional activators, similar to what has been found recently in Drosophila.

  4. Genomic organization of the Neurospora crassa gsn gene: possible involvement of the STRE and HSE elements in the modulation of transcription during heat shock.

    Science.gov (United States)

    Freitas, F Zanolli; Bertolini, M C

    2004-12-01

    Glycogen synthase, an enzyme involved in glycogen biosynthesis, is regulated by phosphorylation and by the allosteric ligand glucose-6-phosphate (G6P). In addition, enzyme levels can be regulated by changes in gene expression. We recently cloned a cDNA for glycogen synthase ( gsn) from Neurospora crassa, and showed that gsn transcription decreased when cells were exposed to heat shock (shifted from 30 degrees C to 45 degrees C). In order to understand the mechanisms that control gsn expression, we isolated the gene, including its 5' and 3' flanking regions, from the genome of N. crassa. An ORF of approximately 2.4 kb was identified, which is interrupted by four small introns (II-V). Intron I (482 bp) is located in the 5'UTR region. Three putative Transcription Initiation Sites (TISs) were mapped, one of which lies downstream of a canonical TATA-box sequence (5'-TGTATAAA-3'). Analysis of the 5'-flanking region revealed the presence of putative transcription factor-binding sites, including Heat Shock Elements (HSEs) and STress Responsive Elements (STREs). The possible involvement of these motifs in the negative regulation of gsn transcription was investigated using Electrophoretic Mobility Shift Assays (EMSA) with nuclear extracts of N. crassa mycelium obtained before and after heat shock, and DNA fragments encompassing HSE and STRE elements from the 5'-flanking region. While elements within the promoter region are involved in transcription under heat shock, elements in the 5'UTR intron may participate in transcription during vegetative growth. The results thus suggest that N. crassa possesses trans -acting elements that interact with the 5'-flanking region to regulate gsn transcription during heat shock and vegetative growth.

  5. Chloroplast gene arrangement variation within a closely related group of green algae (Trebouxiophyceae, Chlorophyta).

    Science.gov (United States)

    Letsch, Molly R; Lewis, Louise A

    2012-09-01

    The 22 published chloroplast genomes of green algae, representing sparse taxonomic sampling of diverse lineages that span over one billion years of evolution, each possess a unique gene arrangement. In contrast, many of the >190 published embryophyte (land plant) chloroplast genomes have relatively conserved architectures. To determine the phylogenetic depth at which chloroplast gene rearrangements occur in green algae, a 1.5-4 kb segment of the chloroplast genome was compared across nine species in three closely related genera of Trebouxiophyceae (Chlorophyta). In total, four distinct gene arrangements were obtained for the three genera Elliptochloris, Hemichloris, and Coccomyxa. In Elliptochloris, three distinct chloroplast gene arrangements were detected, one of which is shared with members of its sister genus Hemichloris. Both species of Coccomyxa examined share the fourth arrangement of this genome region, one characterized by very long spacers. Next, the order of genes found in this segment of the chloroplast genome was compared across green algae and land plants. As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared. Well-supported clades possessing a single gene order had similar phylogenetic depth in green algae and embryophytes. When the dominant gene order of this chloroplast segment in embryophytes was assumed to be ancestral for land plants, the maximum molecular divergence was found to be over two times greater in embryophytes than in trebouxiophyte green algae. This study greatly expands information about chloroplast genome variation in green algae, is the first to demonstrate such variation among congeneric green algae, and further illustrates the fluidity of green algal chloroplast genome architecture in comparison to that of many embryophytes.

  6. Flexible Working Time Arrangements in Bulgaria

    OpenAIRE

    Beleva, Iskra

    2009-01-01

    The objective of this paper is to analyze the flexible working time arrangements in Bulgaria, using a life-course perspective. Two important features have to be outlined, namely: underdeveloped flexible forms of employment in the country, including working time arrangement, and lack of previous analysis on flexible working time arrangements from the angle of life-course perspective. The author describes the regulatory framework, collective agreements at national and company level as a frame w...

  7. Living Arrangements of Young Adults in Europe

    Directory of Open Access Journals (Sweden)

    Katrin Schwanitz

    2015-12-01

    Full Text Available Comparative research suggests that there are great cross-national and cross-temporal differences in living arrangements of young adults aged 18-34 in Europe. In this paper, we examine young adults’ living arrangements (1 across several European countries and different national contexts, and (2 by taking into account cross-time variability. In doing so, we pay careful attention to a comprehensive conceptualisation of living arrangements (including extended and non-family living arrangements. The aim of this paper is to deepen our understanding of family structure and household arrangements in Europe by examining and mapping the cross-national and cross-temporal variety of young adults’ living arrangements. For our analysis we use data from the Integrated Public Use Microdata Series International (IPUMSi for the census rounds 1980, 1990, and 2000 for eight European countries (Austria, France, Greece, Hungary, Ireland, Portugal, Romania, and Switzerland. We employ log-linear models to ascertain the influence of individual and contextual factors on living arrangements. The analyses lend further support to a North/West – South/East divide in living arrangements and general gender differentials in extended family living. Other interesting results are the heterogeneity in the living arrangements of single mothers across geographic areas, and the upward trend of extended household living for young men and women between 1980 and 2000.

  8. Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis.

    Science.gov (United States)

    Hanocq, E; Laperche, A; Jaminon, O; Lainé, A-L; Le Gouis, J

    2007-02-01

    Earliness is one of the most important adaptation traits in plant breeding. Our purpose was to identify the genome regions of bread wheat involved in the control of earliness and its three components: photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE). A QTL meta-analysis was carried out to examine the replicability of QTL across 13 independent studies and to propose meta-QTL (MQTL). Initial QTL were projected on a recent consensus map (2004). Quality criteria were proposed to assess the reliability of this projection. These criteria were based on the distances between markers in the QTL regions. Chromosomes of groups 2 and 5 had a greater incidence on earliness control as they carry the known, major genes Ppd and Vrn. Other chromosome regions played an intermediate role in earliness control: 4A [heading date (HD) Meta-QTL], 4B (HD MQTL), 2B (VR MQTL) and 5B (IE MQTL). Markers at this four MQTL should prove helpful in marker-assisted selection, to better control earliness.

  9. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.

    Science.gov (United States)

    Beckenbach, Andrew T

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

  10. Hyperbolic structures on a toric arrangement complement

    NARCIS (Netherlands)

    Shen, Dali

    2015-01-01

    This thesis studies the geometric structures on toric arrangement complements. Inspired by the special hypergeometric functions associated with a root system, we consider a family of connections on a total space which is the product of the complement of a toric arrangement (=finite union of hypertor

  11. Encoding and Decoding Procedures for Arrangements

    Directory of Open Access Journals (Sweden)

    Alexander A. Babaev

    2012-05-01

    Full Text Available This article discusses an algorithm based on the encoding procedure for representing a set of arrangement elements as a single number. Also the author provides the procedure for the inverse transformation of the code into arrangement elements. In addition the Article includes recommendations on the use of the above procedures in combinatorial algorithms of optimization.

  12. Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum).

    Science.gov (United States)

    Wang, Jinyan; Hu, Zhongze; Zhao, Tongmin; Yang, Yuwen; Chen, Tianzi; Yang, Mali; Yu, Wengui; Zhang, Baolong

    2015-02-05

    The basic helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that can bind to specific DNA target sites. They have been well characterized in model plants such as Arabidopsis and rice and have been shown to be important regulatory components in many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in tomatoes. Tomato yellow leaf curl virus (TYLCV) threatens tomato production worldwide by causing leaf yellowing, leaf curling, plant stunting and flower abscission. A total of 152 bHLH transcription factors were identified from the entire tomato genome. Phylogenetic analysis of bHLH domain sequences from Arabidopsis and tomato facilitated classification of these genes into 26 subfamilies. The evolutionary and possible functional relationships revealed during this analysis are supported by other criteria, including the chromosomal distribution of these genes, the conservation of motifs and exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Distribution mapping results showed bHLH genes were localized on the 12 tomato chromosomes. Among the 152 bHLH genes from the tomato genome, 96 bHLH genes were detected in the TYLCV-susceptible and resistant tomato breeding line before (0 dpi) and after TYLCV (357 dpi) infection. As anticipated, gene ontology (GO) analysis indicated that most bHLH genes are related to the regulation of macromolecule metabolic processes and gene expression. Only four bHLH genes were differentially expressed between 0 and 357 dpi. Virus-induced gene silencing (VIGS) of one bHLH genes SlybHLH131 in resistant lines can lead to the cell death. In the present study, 152 bHLH transcription factor genes were identified. One of which bHLH genes, SlybHLH131, was found to be involved in the TYLCV infection through qRT-PCR expression analysis and VIGS validation. The isolation and identification of these bHLH transcription

  13. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships

    Directory of Open Access Journals (Sweden)

    Zhou Kaiya

    2008-11-01

    Full Text Available Abstract Background Snakes as a major reptile group display a variety of morphological characteristics pertaining to their diverse behaviours. Despite abundant analyses of morphological characters, molecular studies using mitochondrial and nuclear genes are limited. As a result, the phylogeny of snakes remains controversial. Previous studies on mitochondrial genomes of snakes have demonstrated duplication of the control region and translocation of trnL to be two notable features of the alethinophidian (all serpents except blindsnakes and threadsnakes mtDNAs. Our purpose is to further investigate the gene organizations, evolution of the snake mitochondrial genome, and phylogenetic relationships among several major snake families. Results The mitochondrial genomes were sequenced for four taxa representing four different families, and each had a different gene arrangement. Comparative analyses with other snake mitochondrial genomes allowed us to summarize six types of mitochondrial gene arrangement in snakes. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (BI, ML, MP, NJ arrived at a similar topology, which was used to reconstruct the evolution of mitochondrial gene arrangements in snakes. Conclusion The phylogenetic relationships among the major families of snakes are in accordance with the mitochondrial genomes in terms of gene arrangements. The gene arrangement in Ramphotyphlops braminus mtDNA is inferred to be ancestral for snakes. After the divergence of the early Ramphotyphlops lineage, three types of rearrangements occurred. These changes involve translocations within the IQM tRNA gene cluster and the duplication of the CR. All phylogenetic methods support the placement of Enhydris plumbea outside of the (Colubridae + Elapidae cluster, providing mitochondrial genomic evidence for the familial rank of Homalopsidae.

  14. Cooling arrangement for a tapered turbine blade

    Science.gov (United States)

    Liang, George

    2010-07-27

    A cooling arrangement (11) for a highly tapered gas turbine blade (10). The cooling arrangement (11) includes a pair of parallel triple-pass serpentine cooling circuits (80,82) formed in an inner radial portion (50) of the blade, and a respective pair of single radial channel cooling circuits (84,86) formed in an outer radial portion (52) of the blade (10), with each single radial channel receiving the cooling fluid discharged from a respective one of the triple-pass serpentine cooling circuit. The cooling arrangement advantageously provides a higher degree of cooling to the most highly stressed radially inner portion of the blade, while providing a lower degree of cooling to the less highly stressed radially outer portion of the blade. The cooling arrangement can be implemented with known casting techniques, thereby facilitating its use on highly tapered, highly twisted Row 4 industrial gas turbine blades that could not be cooled with prior art cooling arrangements.

  15. Rat Genome Database (RGD)

    Data.gov (United States)

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

  16. Genome-Wide Identification of BAHD Acyltransferases and In vivo Characterization of HQT-like Enzymes Involved in Caffeoylquinic Acid Synthesis in Globe Artichoke

    Science.gov (United States)

    Moglia, Andrea; Acquadro, Alberto; Eljounaidi, Kaouthar; Milani, Anna M.; Cagliero, Cecilia; Rubiolo, Patrizia; Genre, Andrea; Cankar, Katarina; Beekwilder, Jules; Comino, Cinzia

    2016-01-01

    Globe artichoke (Cynara cardunculus L. var. scolymus) is a rich source of compounds promoting human health (phytonutrients), among them caffeoylquinic acids (CQAs), mainly represented by chlorogenic acid (CGA), and dicaffeoylquinic acids (diCQAs). The enzymes involved in their biosynthesis belong to the large family of BAHD acyltransferases. Following a survey of the globe artichoke genome, we identified 69 BAHD proteins carrying the catalytic site (HXXXD). Their phylogenetic analysis together with another 43 proteins, from 21 species, representative of the BAHD family, highlighted their grouping in seven major clades. Nine globe artichoke acyltransferases clustered in a sub-group of Clade V, with 3 belonging to hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase (HQT) and 2 to hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) like proteins. We focused our attention on the former, HQT1, HQT2, and HQT3, as they are known to play a key role in CGA biosynthesis. The expression of genes coding for the three HQTs and correlation of expression with the CQA content is reported for different globe artichoke tissues. For the first time in the globe artichoke, we developed and applied the virus-induced gene silencing approach with the goal of assessing in vivo the effect of HQT1 silencing, which resulted in a marked reduction of both CGA and diCQAs. On the other hand, when the role of the three HQTs was assessed in leaves of Nicotiana benthamiana through their transient overexpression, significant increases in mono- and diCQAs content were observed. Using transient GFP fusion proteins expressed in N. benthamiana leaves we also established the sub-cellular localization of these three enzymes. PMID:27721818

  17. Genome-wide transcriptomic and proteomic analyses of bollworm-infested developing cotton bolls revealed the genes and pathways involved in the insect pest defence mechanism.

    Science.gov (United States)

    Kumar, Saravanan; Kanakachari, Mogilicherla; Gurusamy, Dhandapani; Kumar, Krishan; Narayanasamy, Prabhakaran; Kethireddy Venkata, Padmalatha; Solanke, Amolkumar; Gamanagatti, Savita; Hiremath, Vamadevaiah; Katageri, Ishwarappa S; Leelavathi, Sadhu; Kumar, Polumetla Ananda; Reddy, Vanga Siva

    2016-06-01

    Cotton bollworm, Helicoverpa armigera, is a major insect pest that feeds on cotton bolls causing extensive damage leading to crop and productivity loss. In spite of such a major impact, cotton plant response to bollworm infection is yet to be witnessed. In this context, we have studied the genome-wide response of cotton bolls infested with bollworm using transcriptomic and proteomic approaches. Further, we have validated this data using semi-quantitative real-time PCR. Comparative analyses have revealed that 39% of the transcriptome and 35% of the proteome were differentially regulated during bollworm infestation. Around 36% of significantly regulated transcripts and 45% of differentially expressed proteins were found to be involved in signalling followed by redox regulation. Further analysis showed that defence-related stress hormones and their lipid precursors, transcription factors, signalling molecules, etc. were stimulated, whereas the growth-related counterparts were suppressed during bollworm infestation. Around 26% of the significantly up-regulated proteins were defence molecules, while >50% of the significantly down-regulated were related to photosynthesis and growth. Interestingly, the biosynthesis genes for synergistically regulated jasmonate, ethylene and suppressors of the antagonistic factor salicylate were found to be up-regulated, suggesting a choice among stress-responsive phytohormone regulation. Manual curation of the enzymes and TFs highlighted the components of retrograde signalling pathways. Our data suggest that a selective regulatory mechanism directs the reallocation of metabolic resources favouring defence over growth under bollworm infestation and these insights could be exploited to develop bollworm-resistant cotton varieties.

  18. Exchange rate arrangements: From extreme to "normal"

    Directory of Open Access Journals (Sweden)

    Beker Emilija

    2006-01-01

    Full Text Available The paper studies theoretical and empirical location dispersion of exchange rate arrangements - rigid-intermediate-flexible regimes, in the context of extreme arrangements of a currency board, dollarization and monetary union moderate characteristics of intermediate arrangements (adjustable pegs crawling pegs and target zones and imperative-process "normalization" in the form of a managed or clean floating system. It is established that de iure and de facto classifications generate "fear of floating" and "fear of pegging". The "impossible trinity" under the conditions of capital liberalization and globalization creates a bipolar view or hypothesis of vanishing intermediate exchange rate regimes.

  19. Bijections for the Shi and Ish arrangements

    OpenAIRE

    Leven, Emily; Rhoades, Brendon; Wilson, Andrew Timothy

    2013-01-01

    The {\\sf Shi hyperplane arrangement} Shi(n) was introduced by Shi to study the Kazhdan-Lusztig cellular structure of the affine symmetric group. The {\\sf Ish hyperplane arrangement} Ish(n) was introduced by Armstrong in the study of diagonal harmonics. Armstrong and Rhoades discovered a deep combinatorial similarity between the Shi and Ish arrangements. We solve a collection of problems posed by Armstrong and Armstrong-Rhoades by giving bijections between regions of Shi(n) and Ish(n) which pr...

  20. Valve Technology Arrangement of Cryopump: A Review

    Directory of Open Access Journals (Sweden)

    Sanjiv Y. Rajput

    2014-05-01

    Full Text Available A cryopump or a "cryogenic pump" is a vacuum pump that pumps the trap gases and vapours by condensing them on a cold surface. Helium gas which is very light can only be pumped by Cryopump. Cryopump cannot be used when working for continuous operation as it pumps the effluent till the saturation state is achieved. Then the absorbed gases are to be collected through other mechanical pump through regeneration process. Hence, valve technology arrangement is incorporated with the cryopump in order to achieve the continuous pumping when two cryopump are used in alternate processes (i.e. absorption and regeneration. Various design of Valve technology arrangement is proposed by different researcher all over the world. This review paper focuses on the different proposed valve technology arrangement and elaborately explains the various components of valve technology and concludes the best possible arrangement that can be used in Cryopump.

  1. Metacognitive scaffolding in an innovative learning arrangement

    NARCIS (Netherlands)

    Molenaar, I.; Boxtel, C.A.M. van; Sleegers, P.J.C.

    2011-01-01

    This study examined the effects of metacognitive scaffolds on learning outcomes of collaborating students in an innovative learning arrangement. The triads were supported by computerized scaffolds, which were dynamically integrated into the learning process and took a structuring or problematizing

  2. 24 CFR 401.301 - Partnership arrangements.

    Science.gov (United States)

    2010-04-01

    ... (MARK-TO-MARKET) Participating Administrative Entity (PAE) and Portfolio Restructuring Agreement (PRA) § 401.301 Partnership arrangements. If the PAE is in a partnership, the PRA must specify the...

  3. Domestic arrangements at the Grand Master's Palace

    OpenAIRE

    de Piro, Nicholas; Office of the President of Malta

    2012-01-01

    A talk in the Rediscovering the Grandmaster's Palace series entitled: Domestic arrangements at the Grandmaster's Palace. This talk is organised by the Office of the President and delivered by Marquis Nicholas DePiro.

  4. Flexible Employment Arrangements and Workplace Performance

    OpenAIRE

    GIOVANIS, Eleftherios

    2016-01-01

    There is an increasing concern on the quality of jobs and productivity that is witnessed in the flexible employment arrangements. However, the effects of the employment flexible types on workplace performance has not been explored in Britain. In this study the relationship between two employment arrangements and the workplace performance is examined. More specifically, teleworking and compress hours are two main employment types examined using the Workplace Employee R...

  5. Application of arrangement theory to unfolding models

    CERN Document Server

    Kamiya, Hidehiko; Tokushige, Norihide

    2010-01-01

    Arrangement theory plays an essential role in the study of the unfolding model used in many fields. This paper describes how arrangement theory can be usefully employed in solving the problems of counting (i) the number of admissible rankings in an unfolding model and (ii) the number of ranking patterns generated by unfolding models. The paper is mostly expository but also contains some new results such as simple upper and lower bounds for the number of ranking patterns in the unidimensional case.

  6. Optimal hash arrangement of tentacles in jellyfish

    Science.gov (United States)

    Okabe, Takuya; Yoshimura, Jin

    2016-06-01

    At first glance, the trailing tentacles of a jellyfish appear to be randomly arranged. However, close examination of medusae has revealed that the arrangement and developmental order of the tentacles obey a mathematical rule. Here, we show that medusa jellyfish adopt the best strategy to achieve the most uniform distribution of a variable number of tentacles. The observed order of tentacles is a real-world example of an optimal hashing algorithm known as Fibonacci hashing in computer science.

  7. Genome classification by gene distribution: An overlapping subspace clustering approach

    Directory of Open Access Journals (Sweden)

    Halgamuge Saman K

    2008-04-01

    Full Text Available Abstract Background Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods. Results We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2

  8. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  9. Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation.

    Directory of Open Access Journals (Sweden)

    John S K Kauwe

    2014-10-01

    Full Text Available Cerebrospinal fluid (CSF 42 amino acid species of amyloid beta (Aβ42 and tau levels are strongly correlated with the presence of Alzheimer's disease (AD neuropathology including amyloid plaques and neurodegeneration and have been successfully used as endophenotypes for genetic studies of AD. Additional CSF analytes may also serve as useful endophenotypes that capture other aspects of AD pathophysiology. Here we have conducted a genome-wide association study of CSF levels of 59 AD-related analytes. All analytes were measured using the Rules Based Medicine Human DiscoveryMAP Panel, which includes analytes relevant to several disease-related processes. Data from two independently collected and measured datasets, the Knight Alzheimer's Disease Research Center (ADRC and Alzheimer's Disease Neuroimaging Initiative (ADNI, were analyzed separately, and combined results were obtained using meta-analysis. We identified genetic associations with CSF levels of 5 proteins (Angiotensin-converting enzyme (ACE, Chemokine (C-C motif ligand 2 (CCL2, Chemokine (C-C motif ligand 4 (CCL4, Interleukin 6 receptor (IL6R and Matrix metalloproteinase-3 (MMP3 with study-wide significant p-values (p<1.46×10-10 and significant, consistent evidence for association in both the Knight ADRC and the ADNI samples. These proteins are involved in amyloid processing and pro-inflammatory signaling. SNPs associated with ACE, IL6R and MMP3 protein levels are located within the coding regions of the corresponding structural gene. The SNPs associated with CSF levels of CCL4 and CCL2 are located in known chemokine binding proteins. The genetic associations reported here are novel and suggest mechanisms for genetic control of CSF and plasma levels of these disease-related proteins. Significant SNPs in ACE and MMP3 also showed association with AD risk. Our findings suggest that these proteins/pathways may be valuable therapeutic targets for AD. Robust associations in cognitively normal

  10. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  11. Exchange rate regimes and monetary arrangements

    Directory of Open Access Journals (Sweden)

    Ivan Ribnikar

    2005-06-01

    Full Text Available There is a close relationship between a country’s exchange rate regime and monetary arrangement and if we are to examine monetary arrangements then exchange rate regimes must first be analysed. Within the conventional and most widely used classification of exchange rate regimes into rigid and flexible or into polar regimes (hard peg and float on one side, and intermediate regimes on the other there, is a much greater variety among intermediate regimes. A more precise and, as will be seen, more useful classification of exchange rate regimes is the first topic of the paper. The second topic is how exchange rate regimes influence or determine monetary arrangements and monetary policy or monetary policy regimes: monetary autonomy versus monetary nonautonomy and discretion in monetary policy versus commitment in monetary policy. Both topics are important for countries on their path to the EU and the euro area

  12. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes.

    Science.gov (United States)

    Padmalatha, Kethireddy Venkata; Dhandapani, Gurusamy; Kanakachari, Mogilicherla; Kumar, Saravanan; Dass, Abhishek; Patil, Deepak Prabhakar; Rajamani, Vijayalakshmi; Kumar, Krishan; Pathak, Ranjana; Rawat, Bhupendra; Leelavathi, Sadhu; Reddy, Palakolanu Sudhakar; Jain, Neha; Powar, Kasu N; Hiremath, Vamadevaiah; Katageri, Ishwarappa S; Reddy, Malireddy K; Solanke, Amolkumar U; Reddy, Vanga Siva; Kumar, Polumetla Ananda

    2012-02-01

    Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre development. However, not much information is available on cotton genome response in developing fibres under drought stress. In the present study a genome wide transcriptome analysis was carried out to identify differentially expressed genes at various stages of fibre growth under drought stress. Our study identified a number of genes differentially expressed during fibre elongation as compared to other stages. High level up-regulation of genes encoding for enzymes involved in pectin modification and cytoskeleton proteins was observed at fibre initiation stage. While a large number of genes encoding transcription factors (AP2-EREBP, WRKY, NAC and C2H2), osmoprotectants, ion transporters and heat shock proteins and pathways involved in hormone (ABA, ethylene and JA) biosynthesis and signal transduction were up-regulated and genes involved in phenylpropanoid and flavonoid biosynthesis, pentose and glucuronate interconversions and starch and sucrose metabolism pathways were down-regulated during fibre elongation. This study showed that drought has relatively less impact on fibre initiation but has profound effect on fibre elongation by down-regulating important genes involved in cell wall loosening and expansion process. The comprehensive transcriptome analysis under drought stress has provided valuable information on differentially expressed genes and pathways during fibre development that will be useful in developing drought tolerant cotton cultivars without compromising fibre quality.

  13. An array CGH based genomic instability index (G2I is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis

    Directory of Open Access Journals (Sweden)

    Bonnet Françoise

    2012-11-01

    Full Text Available Abstract Background Despite entering complete remission after primary treatment, a substantial proportion of patients with early stage breast cancer will develop metastases. Prediction of such an outcome remains challenging despite the clinical use of several prognostic parameters. Several reports indicate that genomic instability, as reflected in specific chromosomal aneuploidies and variations in DNA content, influences clinical outcome but no precise definition of this parameter has yet been clearly established. Methods To explore the prognostic value of genomic alterations present in primary tumors, we performed a comparative genomic hybridization study on BAC arrays with a panel of breast carcinomas from 45 patients with metastatic relapse and 95 others, matched for age and axillary node involvement, without any recurrence after at least 11 years of follow-up. Array-CGH data was used to establish a two-parameter index representative of the global level of aneusomy by chromosomal arm, and of the number of breakpoints throughout the genome. Results Application of appropriate thresholds allowed us to distinguish three classes of tumors highly associated with metastatic relapse. This index used with the same thresholds on a published set of tumors confirms its prognostic significance with a hazard ratio of 3.24 [95CI: 1.76-5.96] p = 6.7x10-5 for the bad prognostic group with respect to the intermediate group. The high prognostic value of this genomic index is related to its ability to individualize a specific group of breast cancers, mainly luminal type and axillary node negative, showing very high genetic instability and poor outcome. Indirect transcriptomic validation was obtained on independent data sets. Conclusion Accurate evaluation of genetic instability in breast cancers by a genomic instability index (G2I helps individualizing specific tumors with previously unexpected very poor prognosis.

  14. Genetic variation in the non-coding genome : Involvement of micro-RNAs and long non-coding RNAs in disease

    NARCIS (Netherlands)

    Hrdlickova, Barbara; de Almeida, Rodrigo Coutinho; Borek, Zuzanna; Withoff, Sebo

    2014-01-01

    It has been found that the majority of disease-associated genetic variants identified by genome-wide association studies are located outside of protein-coding regions, where they seem to affect regions that control transcription (promoters, enhancers) and non-coding RNAs that also can influence gene

  15. Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning Outbreak in Switzerland

    Science.gov (United States)

    Tobes, Raquel; Manrique, Marina; Brozynska, Marta; Stephan, Roger; Pareja, Eduardo

    2013-01-01

    We present the first complete genome sequence of a Staphylococcus aureus strain assigned to clonal complex 12. The strain was isolated in a food poisoning outbreak due to contaminated potato salad in Switzerland in 2009, and it produces staphylococcal enterotoxin B. PMID:23704175

  16. Genomic Imbalances in Rhabdomyosarcoma Cell Lines Affect Expression of Genes Frequently Altered in Primary Tumors: An Approach to Identify Candidate Genes Involved in Tumor Development

    NARCIS (Netherlands)

    E. Missiaglia; J. Selfe; M. Hamdi; D. Williamson; G. Schaaf; C. Fang; J. Koster; B. Summersgill; B. Messahel; R Versteeg; K. Pritchard-Jones; M. Kool; J. Shipley

    2009-01-01

    Rhabdomyosarcomas (RMS) are the most common pediatric soft tissue sarcomas. They resemble developing skeletal muscle and are histologically divided into two main subtypes; alveolar and embryonal RMS. Characteristic genomic aberrations, including the PAX3- and PAX7-FOXO1 fusion genes in alveolar case

  17. Genome-wide scan for visceral leishmaniasis in mixed-breed dogs identifies candidate genes involved in T helper cells and macrophage signaling

    Science.gov (United States)

    We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2....

  18. A genome-wide search for genes involved in type 2 diabetes in a recently genetically isolated population from the Netherlands

    NARCIS (Netherlands)

    Y.S. Aulchenko (Yurii); N. Vaessen (Norbert); P. Heutink (Peter); J. Pullen (Jan); P.J.L.M. Snijders (Pieter); A. Hofman (Albert); L.A. Sandkuijl (Lodewijk); J.J. Houwing-Duistermaat (Jeanine); S. Bennett (Simon); B.A. Oostra (Ben); C.M. van Duijn (Cock); M. Edwards (Mark)

    2003-01-01

    textabstractMultiple genes, interacting with the environment, contribute to the susceptibility to type 2 diabetes. We performed a genome-wide search to localize type 2 diabetes susceptibility genes in a recently genetically isolated population in the Netherlands. We identified 79 nuclear families wi

  19. Involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of Gordonia polyisoprenivorans strain VH2.

    Science.gov (United States)

    Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Halbsguth, Tobias; Bröker, Daniel; Angelov, Angel; Liebl, Wolfgang; Daniel, Rolf; Steinbüchel, Alexander

    2012-04-01

    The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search.

  20. Arranged matches and mental illness: therapists' dilemmas.

    Science.gov (United States)

    Greenberg, David; Buchbinder, Jacob Tuvia; Witztum, Eliezer

    2012-01-01

    Traditional societies place especial value on marriage and having children, and marriages are often arranged. A series of situations and dilemmas associated with arranged matches and their consequences are described in the course of mental health work with ultra-orthodox Jewish people with severe mental illness. Issues of confidentiality may arise with parents and matchmakers; on the other hand, respectful cooperation with religious authorities, counselors in the community, and family members is important. Information on genetic counseling, contraception, medication during pregnancy, and breastfeeding are considered and interact with communal structures and practices. There is a need for close support and evaluation during the process of marriage, childbearing, and parenthood.

  1. Thermal energy recycling fuel cell arrangement

    Energy Technology Data Exchange (ETDEWEB)

    Hanrahan, Paul R.

    2017-04-11

    An example fuel cell arrangement includes a fuel cell stack configured to receive a supply fluid and to provide an exhaust fluid that has more thermal energy than the supply fluid. The arrangement also includes an ejector and a heat exchanger. The ejector is configured to direct at least some of the exhaust fluid into the supply fluid. The heat exchanger is configured to increase thermal energy in the supply fluid using at least some of the exhaust fluid that was not directed into the supply fluid.

  2. The Monodromy Conjecture for hyperplane arrangements

    CERN Document Server

    Budur, Nero; Teitler, Zach

    2009-01-01

    The Monodromy Conjecture asserts that if c is a pole of the local topological zeta function of a hypersurface, then exp(2\\pi c) is an eigenvalue of the monodromy on the cohomology of the Milnor fiber. A stronger version of the conjecture asserts that every pole is a root of the Bernstein-Sato polynomial of the hypersurface. In this note we prove the weak version of the conjecture for hyperplane arrangements. Furthermore, we reduce the strong version to the following conjecture: -n/d is always a root of the Bernstein-Sato polynomial of an indecomposable essential central hyperplane arrangement of d hyperplanes in the affine n-space.

  3. People management implications of virtual workplace arrangements

    Directory of Open Access Journals (Sweden)

    K. Ortlepp

    2006-12-01

    Full Text Available Purpose: The purpose of this paper is to investigate the factors that led to an organisation implementing a particular form of virtual workplace arrangement, namely, home-based work. The benefits and disadvantages associated with this form of work arrangement are explored from both the managers' and home-based employees' perspectives. Design/Methodology/Approach: Given the exploratory nature of the empirical study on which this paper is based, a qualitative research design was adopted so as to ensure that the data collection process was dynamic and probing in nature. Semi-structured in-depth interviews were therefore used as instruments for data collection. Findings: The research findings indicate that virtual work arrangements such as home-based work arrangements have advantages for both employers and employees. For instance, reduction of costs associated with office space and facilities, decrease in absenteeism rates, increased employee job satisfaction and improvements in employees' general quality of life. However, a number of negative experiences related to this form of virtual work arrangement are also evident, for example, feelings of isolation as well as stress related to the inability to have firm boundaries between work and family responsibilities. Implications: Based on the insights gained from the findings in the empirical study, a number of areas that need to be given specific attention when organisations are introducing virtual workplace arrangements of this nature are identified. Recommendations made in this article are important for human resource management specialists as well as core business policy makers considering different forms of organisational design. Originality/Value: Maximising the quality of production and service provided has become the prime objective in most organisations in the 21st century. Technology has made it possible for some jobs to be performed at any place at any time and has facilitated the

  4. Thermal energy recycling fuel cell arrangement

    Science.gov (United States)

    Hanrahan, Paul R.

    2017-04-11

    An example fuel cell arrangement includes a fuel cell stack configured to receive a supply fluid and to provide an exhaust fluid that has more thermal energy than the supply fluid. The arrangement also includes an ejector and a heat exchanger. The ejector is configured to direct at least some of the exhaust fluid into the supply fluid. The heat exchanger is configured to increase thermal energy in the supply fluid using at least some of the exhaust fluid that was not directed into the supply fluid.

  5. Cooling arrangement for a gas turbine component

    Science.gov (United States)

    Lee, Ching-Pang; Heneveld, Benjamin E

    2015-02-10

    A cooling arrangement (82) for a gas turbine engine component, the cooling arrangement (82) having a plurality of rows (92, 94, 96) of airfoils (98), wherein adjacent airfoils (98) within a row (92, 94, 96) define segments (110, 130, 140) of cooling channels (90), and wherein outlets (114, 134) of the segments (110, 130) in one row (92, 94) align aerodynamically with inlets (132, 142) of segments (130, 140) in an adjacent row (94, 96) to define continuous cooling channels (90) with non continuous walls (116, 120), each cooling channel (90) comprising a serpentine shape.

  6. Review of arrangements for the recent transportation of radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Codd, M.H.

    1995-07-01

    The terms of reference of this review were: to examine the adequacy of the arrangements made for the transport of contaminated material from Lucas Heights and St Marys to Woomera, in terms of compliance with the Australian Code for the Safe Transport of Radioactive Substances 1990; to report to the Minister for Industry, Science and Technology on the quality of the planning and preparation for the move; the safety and effectiveness of the move itself; the adequacy of response to any `incidents` involved in the move, and of contingency arrangements; whether planning and transport arrangements might be improved for the future. Thus, the Review was focussed on movements of material in two specific cases - material owned by the CSIRO and stored at Lucas Heights and material owned by the Department of Defence and stored at St Marys. The report concludes that the movements of wastes were carried out consistent with the Transport Code, without any risk to public safety. Additional relevant information in support of the review is contained in 8 appendixes.

  7. The effect of alternative work arrangements on women's well-being: a demand-control model.

    Science.gov (United States)

    Kelloway, E K; Gottlieb, B H

    1998-01-01

    The growth of women's participation in the labor force and evidence of the conflict they experience between job and family demands have spurred many employers to introduce alternative work arrangements such as flextime, job sharing, and telecommuting. Drawing on data gained from a sample of women (N = 998) in two large Canadian organizations, this study evaluates two mediational models of the impact of alternative work arrangements on women's stress and family role competence. Specifically, it tests and finds support for the hypotheses that (a) work arrangements involving scheduling flexibility (telecommuting and flextime) promote these aspects of women's well-being by increasing their perceived control over their time, and (b) arrangements involving reduced hours of employment (part-time employment and job sharing) promote well-being by reducing perceived job overload. Discussion of these findings centers on their implications for employed women, their employers, and future research.

  8. 75 FR 25150 - NVOCC Negotiated Rate Arrangements

    Science.gov (United States)

    2010-05-07

    ... requirement inhibits the beneficial effects of competition for shippers (NYNJFFF&BA at 3); that the tariff... shippers can rely on tariff rates to be accurate, complete and in effect for 30 days; in the event of a... exemption for non-vessel-operating common carriers agreeing to negotiated rate arrangements from...

  9. Arranging a Library to Support Adolescent Development

    Science.gov (United States)

    Cesari, Lindsay

    2014-01-01

    When designing a school library space and deciding how to arrange resources, it is important to consider multiple components of adolescent development, including social, emotional, and behavioral aspects. Acknowledging these developmental facets and their importance can provide additional justification for some of the more controversial aspects of…

  10. Partnership Arrangements: Governmental Rhetoric or Governance Scheme?

    NARCIS (Netherlands)

    G.R. Teisman (Geert); E-H. Klijn (Erik-Hans)

    2002-01-01

    textabstractIt has become popular to advocate partnership arrangements. Such partnerships may be seen as new forms of governance, which fit in with the imminent network society. However, the idea of partnership is often introduced without much reflection on the need to reorganize policy-making proce

  11. Characterisation of a large complex intragenic re-arrangement in the FVII gene (F7) avoiding misdiagnosis in inherited factor VII deficiency.

    Science.gov (United States)

    Giansily-Blaizot, Muriel; Thorel, Delphine; Khau Van Kien, Philippe; Behar, Catherine; Romey, Marie-Catherine; Mugneret, Francine; Schved, Jean-François; Claustres, Mireille

    2007-08-01

    Inherited factor VII (FVII) deficiency is a rare autosomal recessive bleeding disorder mostly caused by point mutations. Large genomic re-arrangements at F7 locus could account for a fraction of mutant alleles that remain unidentified after DNA sequencing, because they escape conventional polymerase chain reaction (PCR)-based techniques. We report the first systematic screening of F7 for large re-arrangements, by semi-quantitative multiplex PCR of fluorescent fragments targeting the 9 exons and the promoter region. A well-characterised cohort of 43 unrelated patients either apparently homozygous for a F7 point mutation or carrying at least one unidentified F7 mutant allele participated in this study. Two large F7 re-arrangements were identified in two FVII-deficient pedigrees, including a discontinuous deletion involving two distinct portions of F7 whose proximal and distal end junctions were characterised. A simple and efficient method for the routine detection of gross alterations of F7, which accounted for 2.3% of mutant alleles in our sample, is now available in inherited FVII deficiency. This test should complement conventional PCR-based techniques not only in unsolved cases, but also where inheritance pattern analysis is not achievable.

  12. Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection.

    Science.gov (United States)

    Butterbach, Patrick; Verlaan, Maarten G; Dullemans, Annette; Lohuis, Dick; Visser, Richard G F; Bai, Yuling; Kormelink, Richard

    2014-09-02

    Tomato yellow leaf curl virus (TYLCV) and related begomoviruses are a major threat to tomato production worldwide and, to protect against these viruses, resistance genes from different wild tomato species are introgressed. Recently, the Ty-1 resistance gene was identified, shown to code for an RNA-dependent RNA polymerase and to be allelic with Ty-3. Here we show that upon TYLCV challenging of resistant lines carrying Ty-1 or Ty-3, low virus titers were detected concomitant with the production of relatively high levels of siRNAs whereas, in contrast, susceptible tomato Moneymaker (MM) revealed higher virus titers but lower amounts of siRNAs. Comparative analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the V1 and C3 genes in Ty-1 and Ty-3. In plants containing Ty-2 resistance the virus was hardly detectable, but the siRNA profile resembled the one observed in TYLCV-challenged susceptible tomato (MM). Furthermore, a relative hypermethylation of the TYLCV V1 promoter region was observed in genomic DNA collected from Ty-1 compared with that from (MM). The resistance conferred by Ty-1 was also effective against the bipartite tomato severe rugose begomovirus, where a similar genome hypermethylation of the V1 promoter region was discerned. However, a mixed infection of TYLCV with cucumber mosaic virus compromised the resistance. The results indicate that Ty-1 confers resistance to geminiviruses by increasing cytosine methylation of viral genomes, suggestive of enhanced transcriptional gene silencing. The mechanism of resistance and its durability toward geminiviruses under natural field conditions is discussed.

  13. Analysis of the genome of a Korean isolate of the Pieris rapae granulovirus enabled by its separation from total host genomic DNA by pulse-field electrophoresis.

    Directory of Open Access Journals (Sweden)

    Yong Hun Jo

    Full Text Available BACKGROUND: Most traditional genome sequencing projects involving viruses include the culture and purification of the virus particles. However, purification of virions may yield insufficient material for traditional sequencing. The electrophoretic method described here provides a strategy whereby the genomic DNA of the Korean isolate of Pieris rapae granulovirus (PiraGV-K could be recovered in sufficient amounts for sequencing by purifying it directly from total host DNA by pulse-field gel electrophoresis (PFGE. METHODOLOGY/PRINCIPAL FINDINGS: The total genomic DNA of infected P. rapae was embedded in agarose plugs, treated with restriction nuclease and methylase, and then PFGE was used to separate PiraGV-K DNA from the DNA of P. rapae, followed by mapping of fosmid clones of the purified viral DNA. The double-stranded circular genome of PiraGV-K was found to encode 120 open reading frames (ORFs, which covered 92% of the sequence. BLAST and ORF arrangement showed the presence of 78 homologs to other genes in the database. The mean overall amino acid identity of PiraGV-K ORFs was highest with the Chinese isolate of PiraGV (~99%, followed up with Choristoneura occidentalis ORFs at 58%. PiraGV-K ORFs were grouped, according to function, into 10 genes involved in transcription, 11 involved in replication, 25 structural protein genes, and 15 auxiliary genes. Genes for Chitinase (ORF 10 and cathepsin (ORF 11, involved in the liquefaction of the host, were found in the genome. CONCLUSIONS/SIGNIFICANCE: The recovery of PiraGV-K DNA genome by pulse-field electrophoretic separation from host genomic DNA had several advantages, compared with its isolation from particles harvested as virions or inclusions from the P. rapae host. We have sequenced and analyzed the 108,658 bp PiraGV-K genome purified by the electrophoretic method. The method appears to be generally applicable to the analysis of genomes of large viruses.

  14. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival.

    Science.gov (United States)

    Weigman, Victor J; Chao, Hann-Hsiang; Shabalin, Andrey A; He, Xiaping; Parker, Joel S; Nordgard, Silje H; Grushko, Tatyana; Huo, Dezheng; Nwachukwu, Chika; Nobel, Andrew; Kristensen, Vessela N; Børresen-Dale, Anne-Lise; Olopade, Olufunmilayo I; Perou, Charles M

    2012-06-01

    Breast cancer is a heterogeneous disease with known expression-defined tumor subtypes. DNA copy number studies have suggested that tumors within gene expression subtypes share similar DNA Copy number aberrations (CNA) and that CNA can be used to further sub-divide expression classes. To gain further insights into the etiologies of the intrinsic subtypes, we classified tumors according to gene expression subtype and next identified subtype-associated CNA using a novel method called SWITCHdna, using a training set of 180 tumors and a validation set of 359 tumors. Fisher's exact tests, Chi-square approximations, and Wilcoxon rank-sum tests were performed to evaluate differences in CNA by subtype. To assess the functional significance of loss of a specific chromosomal region, individual genes were knocked down by shRNA and drug sensitivity, and DNA repair foci assays performed. Most tumor subtypes exhibited specific CNA. The Basal-like subtype was the most distinct with common losses of the regions containing RB1, BRCA1, INPP4B, and the greatest overall genomic instability. One Basal-like subtype-associated CNA was loss of 5q11-35, which contains at least three genes important for BRCA1-dependent DNA repair (RAD17, RAD50, and RAP80); these genes were predominantly lost as a pair, or all three simultaneously. Loss of two or three of these genes was associated with significantly increased genomic instability and poor patient survival. RNAi knockdown of RAD17, or RAD17/RAD50, in immortalized human mammary epithelial cell lines caused increased sensitivity to a PARP inhibitor and carboplatin, and inhibited BRCA1 foci formation in response to DNA damage. These data suggest a possible genetic cause for genomic instability in Basal-like breast cancers and a biological rationale for the use of DNA repair inhibitor related therapeutics in this breast cancer subtype.

  15. MOX fuel arrangement for nuclear core

    Science.gov (United States)

    Kantrowitz, Mark L.; Rosenstein, Richard G.

    1998-01-01

    In order to use up a stockpile of weapons-grade plutonium, the plutonium is converted into a mixed oxide (MOX) fuel form wherein it can be disposed in a plurality of different fuel assembly types. Depending on the equilibrium cycle that is required, a predetermined number of one or more of the fuel assembly types are selected and arranged in the core of the reactor in accordance with a selected loading schedule. Each of the fuel assemblies is designed to produce different combustion characteristics whereby the appropriate selection and disposition in the core enables the resulting equilibrium cycle to closely resemble that which is produced using urania fuel. The arrangement of the MOX rods and burnable absorber rods within each of the fuel assemblies, in combination with a selective control of the amount of plutonium which is contained in each of the MOX rods, is used to tailor the combustion characteristics of the assembly.

  16. Financial arrangement selection for energy management projects

    Science.gov (United States)

    Woodroof, Eric Aubrey

    Scope and method of study. The purpose of this study was to develop a model (E-FUND) to help facility managers select financial arrangements for energy management projects (EMPs). The model was developed with the help of a panel of expert financiers. The panel also helped develop a list of key objectives critical to the decision process. The E-FUND model was tested by a population of facility managers in four case studies. Findings and conclusions. The results may indicate that having a high economic benefit (from an EMP) is not overwhelmingly important, when compared to other qualitative objectives. The results may also indicate that the true lease and performance contract may be the most applicable financial arrangements for EMPs.

  17. Child Care Arrangements Of Working Mothers

    Directory of Open Access Journals (Sweden)

    Singh H

    1993-01-01

    Full Text Available Children arrangements for infants and preschool children and the reasons for working outside the home were studied in 300 mothers of whom 100 were teachers (Group. I 100 clerks (groups II and 100 tabourers (Group III. The interview method was used. The most common (80% reason for working was financial needs, the next most frequent was utilization of specialized skills. In 58.7% of the cases, substitute childcare was provided by one of the family members, usually the grandmother. Sixty six percent of caretakers were illiterate. Most (93% of the working mothers had also to perform certain household chores. Bottle-feeding was stated at birth by 80% of these mothers: Childcare arrangements for children of working mothers must be considered in the future.

  18. Creating flexible work arrangements through idiosyncratic deals.

    Science.gov (United States)

    Hornung, Severin; Rousseau, Denise M; Glaser, Jürgen

    2008-05-01

    A survey of 887 employees in a German government agency assessed the antecedents and consequences of idiosyncratic arrangements individual workers negotiated with their supervisors. Work arrangements promoting the individualization of employment conditions, such as part-time work and telecommuting, were positively related to the negotiation of idiosyncratic deals ("i-deals"). Worker personal initiative also had a positive effect on i-deal negotiation. Two types of i-deals were studied: flexibility in hours of work and developmental opportunities. Flexibility i-deals were negatively related and developmental i-deals positively related to work-family conflict and working unpaid overtime. Developmental i-deals were also positively related to increased performance expectations and affective organizational commitment, while flexibility i-deals were unrelated to either.

  19. Valve Technology Arrangement of Cryopump: A Review

    OpenAIRE

    Sanjiv Y. Rajput

    2014-01-01

    A cryopump or a "cryogenic pump" is a vacuum pump that pumps the trap gases and vapours by condensing them on a cold surface. Helium gas which is very light can only be pumped by Cryopump. Cryopump cannot be used when working for continuous operation as it pumps the effluent till the saturation state is achieved. Then the absorbed gases are to be collected through other mechanical pump through regeneration process. Hence, valve technology arrangement is incorporated with the c...

  20. Optimum Arrangement of Taxi Drivers’ Working Hours

    OpenAIRE

    TANIZAKI, Takashi

    2014-01-01

    Part 2: Knowledge Discovery and Sharing; International audience; We propose optimum arrangement of taxi drivers’ working hours. In Japan, income of taxi vehicle is decreasing about 11 thousand yen in the past 15 years. Then some taxi companies are investing to gain more customers. But there are many small taxi companies that are difficult to invest with much money. Therefore we have been researching the other method to gain more customers by little investment for small companies. In this pape...

  1. Simple Euclidean arrangements with one (>=5)-gon

    CERN Document Server

    Leaños, Jesus; Rivera-Martinez, Luis Manuel

    2010-01-01

    Let L be a simple Euclidean arrangement of n pseudolines. It is shown that if L has exactly one (>=5)=gon P, and k is the number of edges of P that are adjacent to an unbounded cell of the subarrangement of L induced by the pseudolines in P, then L has exactly n-k triangles and k+n(n-5)/2 quadrilaterals. We also prove that if each pseudoline of L is adjacent to P then L is stretchable.

  2. Hyperplane arrangements and Lefschetz's hyperplane section theorem

    OpenAIRE

    Yoshinaga, Masahiko

    2005-01-01

    The Lefschetz hyperplane section theorem asserts that a complex affine variety is homotopy equivalent to a space obtained from its generic hyperplane section by attaching some cells. The purpose of this paper is to give an explicit description of attaching maps of these cells for the complement of a complex hyperplane arrangement defined over real numbers. The cells and attaching maps are described in combinatorial terms of chambers. We also discuss the cellular chain complex with coefficient...

  3. Generalized Lantern Relations and Planar Line Arrangements

    CERN Document Server

    Hironaka, Eriko

    2011-01-01

    In this paper we show that to each planar line arrangement defined over the real numbers, for which no two lines are parallel, one can write down a corresponding relation on Dehn twists that can be read off from the combinatorics and relative locations of intersections. This leads to an alternate proof of Wajnryb's generalized lantern relations, and of Endo, Mark and Horn-Morris' daisy relations.

  4. Frequency Arrangement For 700 MHz Band

    Directory of Open Access Journals (Sweden)

    Ancans G.

    2015-02-01

    Full Text Available The 694-790 MHz (700 MHz band was allocated by the 2012 World Radiocommunication Conference (WRC-12 in ITU Region 1 (Europe included, to the mobile service on a co-primary basis with other services to which this band was allocated on the primary basis and identified for the International Mobile Telecommunications (IMT. At the same time, the countries of Region 1 will be able also to continue using these frequencies for their broadcasting services if necessary. This allocation will be effective immediately after 2015 World Radiocommunication Conference (WRC-15. In order to make the best possible use of this frequency band for mobile service, a worldwide harmonized frequency arrangement is to be prepared to allow for large economies of scale and international roaming as well as utilizing the available spectrum in the best possible way, minimizing possible interference between services, facilitating deployment and cross-border coordination. The authors analyze different possible frequency arrangements and conclude on the frequency arrangement most suitable for Europe.

  5. Recurring part arrangements in shape collections

    KAUST Repository

    Zheng, Youyi

    2014-05-01

    Extracting semantically related parts across models remains challenging, especially without supervision. The common approach is to co-analyze a model collection, while assuming the existence of descriptive geometric features that can directly identify related parts. In the presence of large shape variations, common geometric features, however, are no longer sufficiently descriptive. In this paper, we explore an indirect top-down approach, where instead of part geometry, part arrangements extracted from each model are compared. The key observation is that while a direct comparison of part geometry can be ambiguous, part arrangements, being higher level structures, remain consistent, and hence can be used to discover latent commonalities among semantically related shapes. We show that our indirect analysis leads to the detection of recurring arrangements of parts, which are otherwise difficult to discover in a direct unsupervised setting. We evaluate our algorithm on ground truth datasets and report advantages over geometric similarity-based bottom-up co-segmentation algorithms. © 2014 The Author(s) Computer Graphics Forum © 2014 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.

  6. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

    Science.gov (United States)

    Undabarrena, Agustina; Ugalde, Juan A; Seeger, Michael; Cámara, Beatriz

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  7. Early events in the generation of autophagosomes are required for the formation of membrane structures involved in hepatitis C virus genome replication.

    Science.gov (United States)

    Mohl, Bjorn-Patrick; Bartlett, Christopher; Mankouri, Jamel; Harris, Mark

    2016-03-01

    Hepatitis C virus (HCV) infection has been shown to induce autophagy but the mechanisms underpinning this process remain to be elucidated. Induction of autophagy requires the class III phosphatidylinositol 3-kinase, Vps34, which produces phosphatidylinositol 3-phosphate (PI3P) within the endoplasmic reticulum (ER) membrane. This recruits proteins with PI3P binding domains such as the double-FYVE-containing protein 1 (DFCP1). DFCP1 generates cup-shaped protrusions from the ER membrane, termed omegasomes, which provide a platform for the production of autophagosomes. Here we present data demonstrating that both Vps34 and DFCP1 are required for HCV genome replication, in the context of both a subgenomic replicon and virus infection, but did not affect virus entry or initial translation. Using live cell fluorescence microscopy we demonstrated that early during HCV infection the nascent viral genome replication complexes (identified by using non-structural protein NS5A as a marker) transiently colocalize with DFCP1-positive punctae (omegasomes), before the two structures move apart from each other. This observation is reminiscent of the transient association of LC3 and DFCP1 during omegasome formation, and therefore we propose that omegasomes are utilized by HCV to generate the double-membrane vesicles which are the hallmark of HCV replication complexes.

  8. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

    Directory of Open Access Journals (Sweden)

    Katarina Truvé

    2016-05-01

    Full Text Available Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA 26 (p = 2.8 x 10-8. Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.

  9. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus

    Science.gov (United States)

    Dickinson, Peter; Xiong, Anqi; York, Daniel; Jayashankar, Kartika; Pielberg, Gerli; Koltookian, Michele; Murén, Eva; Fuxelius, Hans-Henrik; Weishaupt, Holger; Andersson, Göran; Hedhammar, Åke; Bongcam-Rudloff, Erik; Forsberg-Nilsson, Karin

    2016-01-01

    Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10−8). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility. PMID:27171399

  10. Histone H2AX Is Involved in FoxO3a-Mediated Transcriptional Responses to Ionizing Radiation to Maintain Genome Stability

    Directory of Open Access Journals (Sweden)

    Stephane Tarrade

    2015-12-01

    Full Text Available Histone H2AX plays a crucial role in molecular and cellular responses to DNA damage and in the maintenance of genome stability. It is downstream of ataxia telangiectasia mutated (ATM damage signaling pathway and there is an emerging role of the transcription factor FoxO3a, a regulator of a variety of other pathways, in activating this signaling. We asked whether H2AX may feedback to FoxO3a to affect respective FoxO3a-dependent pathways. We used a genetically matched pair of mouse embryonic fibroblast H2AX+/+ and H2AX−/− cell lines to carry out comprehensive time-course and dose-response experiments and to show that the expression of several FoxO3a-regulated genes was altered in H2AX−/− compared to H2AX+/+ cells at both basal and irradiated conditions. Hspa1b and Gadd45a were down-regulated four- to five-fold and Ddit3, Cdkn1a and Sod2 were up-regulated 2–3-fold in H2AX−/− cells. Using the luciferase reporter assay, we directly demonstrated that transcriptional activity of FoxoO3a was reduced in H2AX−/− cells. FoxO3a localization within the nuclear phospho-ATM (Ser1981 foci in irradiated cells was affected by the H2AX status, as well as its posttranslational modification (phospho-Thr32. These differences were associated with genomic instability and radiosensitivity in H2AX−/− cells. Finally, knockdown of H2AX in H2AX+/+ cells resulted in FoxO3a-dependent gene expression patterns and increased radiosensitivity that partially mimicked those found in H2AX−/− cells. Taken together, our data suggest a role for FoxO3a in the maintenance of genome integrity in response to DNA damage that is mediated by H2AX via yet unknown mechanisms.

  11. Accumulation of point mutations and reassortment of genomic RNA segments are involved in the microevolution of Puumala hantavirus in a bank vole (Myodes glareolus) population.

    Science.gov (United States)

    Razzauti, Maria; Plyusnina, Angelina; Henttonen, Heikki; Plyusnin, Alexander

    2008-07-01

    The genetic diversity of Puumala hantavirus (PUUV) was studied in a local population of its natural host, the bank vole (Myodes glareolus). The trapping area (2.5 x 2.5 km) at Konnevesi, Central Finland, included 14 trapping sites, at least 500 m apart; altogether, 147 voles were captured during May and October 2005. Partial sequences of the S, M and L viral genome segments were recovered from 40 animals. Seven, 12 and 17 variants were detected for the S, M and L sequences, respectively; these represent new wild-type PUUV strains that belong to the Finnish genetic lineage. The genetic diversity of PUUV strains from Konnevesi was 0.2-4.9 % for the S segment, 0.2-4.8 % for the M segment and 0.2-9.7 % for the L segment. Most nucleotide substitutions were synonymous and most deduced amino acid substitutions were conservative, probably due to strong stabilizing selection operating at the protein level. Based on both sequence markers and phylogenetic clustering, the S, M and L sequences could be assigned to two groups, 'A' and 'B'. Notably, not all bank voles carried S, M and L sequences belonging to the same group, i.e. S(A)M(A)L(A) or S(B)M(B)L(B). A substantial proportion (8/40, 20 %) of the newly characterized PUUV strains possessed reassortant genomes such as S(B)M(A)L(A), S(A)M(B)L(B) or S(B)M(A)L(B). These results suggest that at least some of the PUUV reassortants are viable and can survive in the presence of their parental strains.

  12. Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses

    Science.gov (United States)

    Lafarge, Tanguy; Bueno, Crisanta; Frouin, Julien; Jacquin, Laval; Courtois, Brigitte; Ahmadi, Nourollah

    2017-01-01

    Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait. PMID:28152098

  13. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    Full Text Available Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings

  14. Membrane-impermeable estrogen is involved in regulation of calbindin-D9k expression via non-genomic pathways in a rat pituitary cell line, GH3 cells.

    Science.gov (United States)

    Dang, Vu Hoang; Choi, Kyung-Chul; Jeung, Eui-Bae

    2010-06-01

    Estrogen (E2) has been shown to regulate various functions for many pituitary hormones. Recently, the potential roles of non-genomic pathways in E2-induced actions have been proposed in the previous studies, however, the effects of E2 remain to be elucidated in regard to non-genomic induction of cytosolic protein calbindin-D9k (CaBP-9k). To gain a better understanding of the molecular events underlying E2-induced expression of CaBP-9k, rat pituitary tumor cells (GH3 cells) were treated with E-BSA (membrane impermeable E2-conjugated with BSA). Non-genomic induction of CaBP-9k by E-BSA was determined using RT-PCR and western blot analysis. The significant increase in CaBP-9k mRNA level was observed as early as 15 min following treatment with a high concentration of E-BSA (10(-6)M), whereas rapid and significant induction of CaBP-9k protein was noted at 5, 15 and 30 min after E-BSA exposure (p<0.05). In order to determine the potential involvement of different signaling pathways, several inhibitors were employed, i.e., ICI 182,780 for the estrogen receptor (ER) pathway, pertussis toxin (PTX) for the G-protein-coupled signaling pathway, U0126 (U) for the ERK (extracellular regulated kinase) and wortmannin (W) for the Akt (protein kinase B). Co-treatment with ICI 182, 780 and PTX reversed an E-BSA-induced increase in CaBP-9k mRNA and protein. Although neither U nor W alone attenuated E-BSA-induced effects, these inhibitors together abolished E-BSA-induced CaBP-9k expression, suggesting their involvement in its regulation. Taken together, these results demonstrate the involvement of various signaling pathways in E2-induced regulation of CaBP-9k. In addition, ER and G-protein-coupled signaling pathways may play central roles in the non-genomic activities of E2 and that downstream signaling via ERK and Akt are required to evoke ER-mediated induction of CaBP-9k in vitro. Copyright 2010 Elsevier Ltd. All rights reserved.

  15. Developing Breast Cancer Program at Xavier; Genomic and Proteomic Analysis of Signaling Pathways Involved in Xenohormone and MEK5 Regulation of Breast Cancer

    Science.gov (United States)

    2007-05-01

    focus on breast and prostate cancer. The two additional XU faculty involved will develop a mini-proposal in Y1-2 and carry out pilot studies with...department. Dr. Wiese is now PI of both the Xavier DOD Breast Cancer and the Prostate Cancer programs as well as manager of the new NCI P20 grant at...potentially involved in difference sin the MEK5 and VEC cels suggested a role for metalloproteinases and Cox2 . Using Western blot analysis we demonstrate

  16. Minimum Energy Requirements in Complex Distillation Arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Halvorsen, Ivar J.

    2001-07-01

    Distillation is the most widely used industrial separation technology and distillation units are responsible for a significant part of the total heat consumption in the world's process industry. In this work we focus on directly (fully thermally) coupled column arrangements for separation of multicomponent mixtures. These systems are also denoted Petlyuk arrangements, where a particular implementation is the dividing wall column. Energy savings in the range of 20-40% have been reported with ternary feed mixtures. In addition to energy savings, such integrated units have also a potential for reduced capital cost, making them extra attractive. However, the industrial use has been limited, and difficulties in design and control have been reported as the main reasons. Minimum energy results have only been available for ternary feed mixtures and sharp product splits. This motivates further research in this area, and this thesis will hopefully give some contributions to better understanding of complex column systems. In the first part we derive the general analytic solution for minimum energy consumption in directly coupled columns for a multicomponent feed and any number of products. To our knowledge, this is a new contribution in the field. The basic assumptions are constant relative volatility, constant pressure and constant molar flows and the derivation is based on Underwood's classical methods. An important conclusion is that the minimum energy consumption in a complex directly integrated multi-product arrangement is the same as for the most difficult split between any pair of the specified products when we consider the performance of a conventional two-product column. We also present the Vmin-diagram, which is a simple graphical tool for visualisation of minimum energy related to feed distribution. The Vmin-diagram provides a simple mean to assess the detailed flow requirements for all parts of a complex directly coupled arrangement. The main purpose in

  17. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  18. Improved shock-detection pin arrangement

    Energy Technology Data Exchange (ETDEWEB)

    Erskine, D.J.

    1995-08-01

    Shockwave speeds are often measured by comparing arrival times at the tips of electrical shorting pins in a hexagonal array over two elevations (called up and down). In the conventional arrangement, the center pin is solely responsible for measuring the curvature of the wavefront. Without this datum the shock speed cannot be precisely determined. In some experiments this pin fail frequently enough to be a problem. We report a simple rearrangement between up and down designated pins which eliminates the critical reliance on a single.

  19. Ventricular torsional relation to ventricular fiber arrangement

    CERN Document Server

    Ranjbar, Saeed; Meybodi, Mahmood Emami

    2014-01-01

    Left ventricular torsion from helically oriented myofibers is a key parameter of cardiac performance. Physicians observing heart motion on echocardiograms, during cardiac catheterization, or in the operating room, are impressed by the twisting or rotary motion of the left ventricle during systole. Conceptually, the heart has been treated as a pressure chamber. The rotary or torsional deformation has been poorly understood by basic scientists and has lacked clinical relevance. The aim of this paper attempts to discuss about this question: Is ventricular twisting related to ventricular fiber arrangement? That is dependent to an assumed model of the left ventricular structure.

  20. Waveguide arrangements based on adiabatic elimination

    Energy Technology Data Exchange (ETDEWEB)

    Suchowski, Haim; Mrejen, Michael; Wu, Chihhui; Zhang, Xiang

    2016-09-13

    This disclosure provides systems, methods, and apparatus related to nanophotonics. In one aspect, an arrangement of waveguides includes a substrate and three waveguides. Each of the three waveguides may be a linear waveguide. A second waveguide is positioned between a first waveguide and a third waveguide. The dimensions and positions of the first, the second, and the third waveguides are specified to substantially eliminate coupling between the first waveguide and the third waveguide over a distance of about 1 millimeter to 2 millimeters along lengths of the first waveguide, the second waveguide, and the third waveguide.

  1. A regional arrangement proposal for the UNASUR

    Directory of Open Access Journals (Sweden)

    Fernando Ferrari-Filho

    2014-09-01

    Full Text Available The article analyses the current process of economic integration in South America. Thus, concentrating our attention on the UNASUR regional integration process, two questions arise: First, is UNASUR the most viable institution to achieve a consistent economic integration process in South America? Second, what model of economic integration should be adopted in the case of UNASUR, which would ensure macroeconomic stability and avoid financial and exchange rate crises in the South America? To answer these questions, the article proposes, based on the Keynes (1944/1980's revolutionary analysis presented in his International Clearing Union, during the Bretton Woods Conference in 1944, a regional arrangement to UNASUR.

  2. 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.

  3. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate.

    Science.gov (United States)

    de Crécy-Lagard, Valérie; Phillips, Gabriela; Grochowski, Laura L; El Yacoubi, Basma; Jenney, Francis; Adams, Michael W W; Murzin, Alexey G; White, Robert H

    2012-11-16

    C-1 carriers are essential cofactors in all domains of life, and in Archaea, these can be derivatives of tetrahydromethanopterin (H(4)-MPT) or tetrahydrofolate (H(4)-folate). Their synthesis requires 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) as the precursor, but the nature of pathways that lead to its formation were unknown until the recent discovery of the GTP cyclohydrolase IB/MptA family that catalyzes the first step, the conversion of GTP to dihydroneopterin 2',3'-cyclic phosphate or 7,8-dihydroneopterin triphosphate [El Yacoubi, B.; et al. (2006) J. Biol. Chem., 281, 37586-37593 and Grochowski, L. L.; et al. (2007) Biochemistry46, 6658-6667]. Using a combination of comparative genomics analyses, heterologous complementation tests, and in vitro assays, we show that the archaeal protein families COG2098 and COG1634 specify two of the missing 6-HMDP synthesis enzymes. Members of the COG2098 family catalyze the formation of 6-hydroxymethyl-7,8-dihydropterin from 7,8-dihydroneopterin, while members of the COG1634 family catalyze the formation of 6-HMDP from 6-hydroxymethyl-7,8-dihydropterin. The discovery of these missing genes solves a long-standing mystery and provides novel examples of convergent evolutions where proteins of dissimilar architectures perform the same biochemical function.

  4. Molecular mechanisms and pathways involved in bovine embryonic genome activation and their regulation by alternative in vivo and in vitro culture conditions.

    Science.gov (United States)

    Gad, Ahmed; Hoelker, Michael; Besenfelder, Urban; Havlicek, Vitezslav; Cinar, Ulas; Rings, Franca; Held, Eva; Dufort, Isabelle; Sirard, Marc-André; Schellander, Karl; Tesfaye, Dawit

    2012-10-01

    Understanding gene expression patterns in response to altered environmental conditions at different time points of the preimplantation period would improve our knowledge on regulation of embryonic development. Here we aimed to examine the effect of alternative in vivo and in vitro culture conditions at the time of major embryonic genome activation (EGA) on the development and transcriptome profile of bovine blastocysts. Four different blastocyst groups were produced under alternative in vivo and in vitro culture conditions before or after major EGA. Completely in vitro- and in vivo-produced blastocysts were used as controls. We compared gene expression patterns between each blastocyst group and in vivo blastocyst control group using EmbryoGENE's bovine microarray. The data showed that changing culture conditions from in vivo to in vitro or vice versa, either before or after the time of major EGA, had no effect on the developmental rates; however, in vitro conditions during that time critically influenced the transcriptome of the blastocysts produced. The source of oocyte had a critical effect on developmental rates and the ability of the embryo to react to changing culture conditions. Ontological classification highlighted a marked contrast in expression patterns for lipid metabolism and oxidative stress response between blastocysts generated in vivo versus in vitro, with opposite trends. Molecular mechanisms and pathways that are influenced by altered culture conditions during EGA were defined. These results will help in the development of new strategies to modify culture conditions at this critical stage to enhance the development of competent blastocysts.

  5. Radiotherapy for glioblastoma: reorganization of genome maintenance mechanisms involved in the process of inhibiting cancer; Radioterapia de glioblastoma: reorganizacao das vias de manutencao do genoma

    Energy Technology Data Exchange (ETDEWEB)

    Ludwig, J.K.; Santos, C.L. dos [Centro Universitario Franciscano, Santa Maria, RS (Brazil). Curso de Fisica Medica; Simao, E.M., E-mail: edersimao@gmail.com [Centro Universitario Franciscano, Santa Maria, RS (Brazil). Programa de Pos-Graduacao em Nanociencias

    2014-11-01

    Glioblastoma is a very aggressive brain tumor, which occurs in Glial cells. The treatment consists in chemotherapy, surgery and radiotherapy. The radiotherapy is a treatment method that uses ionizing radiation to kill cancer cells. The cells have genome maintenance mechanisms (MMG) distributed in apoptosis, DNA damage response, and cell cycle pathways. These pathways are formed by sets of proteins and perform specific functions within the cell (example: induce cell death). The mutation of these proteins associated with the failure of the MMG can cause the activation of mutations and consequently induce the development of cancer. This work, objective has to identify pathways and proteins expressed in cancer treatment using free software of the statistical analysis, developed in Fortran and R platforms to show the effects caused by radiation in the proteins of cancerous tissues. The results, were fond to pathways of glioblastoma treated with radiotherapy, activation of apoptosis and response to DNA damage pathways, indicating that there is death of carcinogenic tissue caused by radiation and that some cells are triggering a process of DNA repair. (author)

  6. Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.

    Science.gov (United States)

    Arefin, Badrul; Kucerova, Lucie; Dobes, Pavel; Markus, Robert; Strnad, Hynek; Wang, Zhi; Hyrsl, Pavel; Zurovec, Michal; Theopold, Ulrich

    2014-01-01

    Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) which infects its host by accessing the hemolymph where it releases endosymbiotic bacteria of the species Photorhabdus luminescens. We performed a genome-wide transcriptional analysis of the Drosophila response to EPN infection at the time point at which the nematodes reached the hemolymph either via the cuticle or the gut and the bacteria had started to multiply. Many of the most strongly induced genes have been implicated in immune responses in other infection models. Mapping of the complete set of differentially regulated genes showed the hallmarks of a wound response, but also identified a large fraction of EPN-specific transcripts. Several genes identified by transcriptome profiling or their homologues play protective roles during nematode infections. Genes that positively contribute to controlling nematobacterial infections encode: a homolog of thioester-containing complement protein 3, a basement membrane component (glutactin), a recognition protein (GNBP-like 3) and possibly several small peptides. Of note is that several of these genes have not previously been implicated in immune responses.

  7. Genome-wide gene expression analysis of Bordetella pertussis isolates associated with a resurgence in pertussis: elucidation of factors involved in the increased fitness of epidemic strains.

    Science.gov (United States)

    King, Audrey J; van der Lee, Saskia; Mohangoo, Archena; van Gent, Marjolein; van der Ark, Arno; van de Waterbeemd, Bas

    2013-01-01

    Bordetella pertussis (B. pertussis) is the causative agent of whooping cough, which is a highly contagious disease in the human respiratory tract. Despite vaccination since the 1950s, pertussis remains the most prevalent vaccine-preventable disease in developed countries. A recent resurgence pertussis is associated with the expansion of B. pertussis strains with a novel allele for the pertussis toxin (ptx) promoter ptxP3 in place of resident ptxP1 strains. The recent expansion of ptxP3 strains suggests that these strains carry mutations that have increased their fitness. Compared to the ptxP1 strains, ptxP3 strains produce more Ptx, which results in increased virulence and immune suppression. In this study, we investigated the contribution of gene expression changes of various genes on the increased fitness of the ptxP3 strains. Using genome-wide gene expression profiling, we show that several virulence genes had higher expression levels in the ptxP3 strains compared to the ptxP1 strains. We provide the first evidence that wildtype ptxP3 strains are better colonizers in an intranasal mouse infection model. This study shows that the ptxP3 mutation and the genetic background of ptxP3 strains affect fitness by contributing to the ability to colonize in a mouse infection model. These results show that the genetic background of ptxP3 strains with a higher expression of virulence genes contribute to increased fitness.

  8. [Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

    Science.gov (United States)

    Katsy, E I; Petrova, L P

    2015-12-01

    Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

  9. Functional genomics analysis of low concentration of ethanol in human hepatocellular carcinoma (HepG2 cells. Role of genes involved in transcriptional and translational processes

    Directory of Open Access Journals (Sweden)

    Francisco Castaneda, Sigrid Rosin-Steiner, Klaus Jung

    2007-01-01

    Full Text Available We previously found that ethanol at millimolar level (1 mM activates the expression of transcription factors with subsequent regulation of apoptotic genes in human hepatocellular carcinoma (HCC HepG2 cells. However, the role of ethanol on the expression of genes implicated in transcriptional and translational processes remains unknown. Therefore, the aim of this study was to characterize the effect of low concentration of ethanol on gene expression profiling in HepG2 cells using cDNA microarrays with especial interest in genes with transcriptional and translational function. The gene expression pattern observed in the ethanol-treated HepG2 cells revealed a relatively similar pattern to that found in the untreated control cells. The pairwise comparison analysis demonstrated four significantly up-regulated (COBRA1, ITGB4, STAU2, and HMGN3 genes and one down-regulated (ANK3 gene. All these genes exert their function on transcriptional and translational processes and until now none of these genes have been associated with ethanol. This functional genomic analysis demonstrates the reported interaction between ethanol and ethanol-regulated genes. Moreover, it confirms the relationship between ethanol-regulated genes and various signaling pathways associated with ethanol-induced apoptosis. The data presented in this study represents an important contribution toward the understanding of the molecular mechanisms of ethanol at low concentration in HepG2 cells, a HCC-derived cell line.

  10. High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway

    OpenAIRE

    2014-01-01

    Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae , phylum Bacteroidetes . Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitien...

  11. The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

    DEFF Research Database (Denmark)

    Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben;

    2013-01-01

    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...

  12. On the connectivity of the realization spaces of line arrangements

    CERN Document Server

    Nazir, Shaheen

    2010-01-01

    We prove that under certain combinatorial conditions, the realization spaces of line arrangements on the complex projective plane are connected. We also give several examples of arrangements with eight, nine and ten lines which have disconnected realization spaces.

  13. CHD6 regulates the topological arrangement of the CFTR locus.

    Science.gov (United States)

    Sancho, Ana; Li, SiDe; Paul, Thankam; Zhang, Fan; Aguilo, Francesca; Vashisht, Ajay; Balasubramaniyan, Natarajan; Leleiko, Neal S; Suchy, Frederick J; Wohlschlegel, James A; Zhang, Weijia; Walsh, Martin J

    2015-05-15

    The control of transcription is regulated through the well-coordinated spatial and temporal interactions between distal genomic regulatory elements required for specialized cell-type and developmental gene expression programs. With recent findings CFTR has served as a model to understand the principles that govern genome-wide and topological organization of distal intra-chromosomal contacts as it relates to transcriptional control. This is due to the extensive characterization of the DNase hypersensitivity sites, modification of chromatin, transcription factor binding sites and the arrangement of these sites in CFTR consistent with the restrictive expression in epithelial cell types. Here, we identified CHD6 from a screen among several chromatin-remodeling proteins as a putative epigenetic modulator of CFTR expression. Moreover, our findings of CTCF interactions with CHD6 are consistent with the role described previously for CTCF in CFTR regulation. Our results now reveal that the CHD6 protein lies within the infrastructure of multiple transcriptional complexes, such as the FACT, PBAF, PAF1C, Mediator, SMC/Cohesion and MLL complexes. This model underlies the fundamental role CHD6 facilitates by tethering cis-acting regulatory elements of CFTR in proximity to these multi-subunit transcriptional protein complexes. Finally, we indicate that CHD6 structurally coordinates a three-dimensional stricture between intragenic elements of CFTR bound by several cell-type specific transcription factors, such as CDX2, SOX18, HNF4α and HNF1α. Therefore, our results reveal new insights into the epigenetic regulation of CFTR expression, whereas the manipulation of CFTR gene topology could be considered for treating specific indications of cystic fibrosis and/or pancreatitis.

  14. Genome-wide gene expression analysis of Bordetella pertussis isolates associated with a resurgence in pertussis: elucidation of factors involved in the increased fitness of epidemic strains.

    Directory of Open Access Journals (Sweden)

    Audrey J King

    Full Text Available Bordetella pertussis (B. pertussis is the causative agent of whooping cough, which is a highly contagious disease in the human respiratory tract. Despite vaccination since the 1950s, pertussis remains the most prevalent vaccine-preventable disease in developed countries. A recent resurgence pertussis is associated with the expansion of B. pertussis strains with a novel allele for the pertussis toxin (ptx promoter ptxP3 in place of resident ptxP1 strains. The recent expansion of ptxP3 strains suggests that these strains carry mutations that have increased their fitness. Compared to the ptxP1 strains, ptxP3 strains produce more Ptx, which results in increased virulence and immune suppression. In this study, we investigated the contribution of gene expression changes of various genes on the increased fitness of the ptxP3 strains. Using genome-wide gene expression profiling, we show that several virulence genes had higher expression levels in the ptxP3 strains compared to the ptxP1 strains. We provide the first evidence that wildtype ptxP3 strains are better colonizers in an intranasal mouse infection model. This study shows that the ptxP3 mutation and the genetic background of ptxP3 strains affect fitness by contributing to the ability to colonize in a mouse infection model. These results show that the genetic background of ptxP3 strains with a higher expression of virulence genes contribute to increased fitness.

  15. Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation.

    Directory of Open Access Journals (Sweden)

    Vasundhara Paliwal

    Full Text Available Pseudomonas putida CSV86, a plasmid-free strain possessing capability to transfer the naphthalene degradation property, has been explored for its metabolic diversity through genome sequencing. The analysis of draft genome sequence of CSV86 (6.4 Mb revealed the presence of genes involved in the degradation of naphthalene, salicylate, benzoate, benzylalcohol, p-hydroxybenzoate, phenylacetate and p-hydroxyphenylacetate on the chromosome thus ensuring the stability of the catabolic potential. Moreover, genes involved in the metabolism of phenylpropanoid and homogentisate, as well as heavy metal resistance, were additionally identified. Ability to grow on vanillin, veratraldehyde and ferulic acid, detection of inducible homogentisate dioxygenase and growth on aromatic compounds in the presence of heavy metals like copper, cadmium, cobalt and arsenic confirm in silico observations reflecting the metabolic versatility. In silico analysis revealed the arrangement of genes in the order: tRNA(Gly, integrase followed by nah operon, supporting earlier hypothesis of existence of a genomic island (GI for naphthalene degradation. Deciphering the genomic architecture of CSV86 for aromatic degradation pathways and identification of elements responsible for horizontal gene transfer (HGT suggests that genetic bioaugmentation strategies could be planned using CSV86 for effective bioremediation.

  16. Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Shan Dan

    Full Text Available Fetal chromosomal abnormalities are the most common reasons for invasive prenatal testing. Currently, G-band karyotyping and several molecular genetic methods have been established for diagnosis of chromosomal abnormalities. Although these testing methods are highly reliable, the major limitation remains restricted resolutions or can only achieve limited coverage on the human genome at one time. The massively parallel sequencing (MPS technologies which can reach single base pair resolution allows detection of genome-wide intragenic deletions and duplication challenging karyotyping and microarrays as the tool for prenatal diagnosis. Here we reported a novel and robust MPS-based method to detect aneuploidy and imbalanced chromosomal arrangements in amniotic fluid (AF samples. We sequenced 62 AF samples on Illumina GAIIx platform and with averagely 0.01× whole genome sequencing data we detected 13 samples with numerical chromosomal abnormalities by z-test. With up to 2× whole genome sequencing data we were able to detect microdeletion/microduplication (ranged from 1.4 Mb to 37.3 Mb of 5 samples from chorionic villus sampling (CVS using SeqSeq algorithm. Our work demonstrated MPS is a robust and accurate approach to detect aneuploidy and imbalanced chromosomal arrangements in prenatal samples.

  17. Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.

    Science.gov (United States)

    Kim, Byoung-Chan; Postier, Bradley L; Didonato, Raymond J; Chaudhuri, Swades K; Nevin, Kelly P; Lovley, Derek R

    2008-06-01

    Geobacter sulfurreducens effectively produces electricity in microbial fuel cells by oxidizing acetate with an electrode serving as the sole electron acceptor. Deletion of the gene encoding OmcF, a monoheme outer membrane c-type cytochrome, substantially decreased current production. Previous studies demonstrated that inhibition of Fe(III) reduction in the OmcF-deficient mutant could be attributed to poor transcription of the gene for OmcB, an outer membrane c-type cytochrome that is required for Fe(III) reduction. However, a mutant in which omcB was deleted produced electricity as well as wild type. Microarray analysis of the OmcF-deficient mutant versus the wild type revealed that many of the genes with the greatest decreases in transcript levels were genes whose expression was previously reported to be upregulated in cells grown with an electrode as the sole electron acceptor. These included genes with putative functions related to metal efflux and/or type I secretion and two hypothetical proteins. The outer membrane cytochromes, OmcS and OmcE, which previous studies have demonstrated are required for optimal current generation, were not detected on the outer surface of the OmcF-deficient mutant even though the omcS and omcE genes were still transcribed, suggesting that the putative secretion system could be involved in the export of outer membrane proteins necessary for electron transfer to the fuel cell anode. These results suggest that the requirement for OmcF for optimal current production is not because OmcF is directly involved in extracellular electron transfer but because OmcF is required for the appropriate transcription of other genes either directly or indirectly involved in electricity production.

  18. Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids.

    Science.gov (United States)

    Kurabayashi, Atsushi; Yoshikawa, Natsuhiko; Sato, Naoki; Hayashi, Yoko; Oumi, Shohei; Fujii, Tamotsu; Sumida, Masayuki

    2010-08-01

    We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

  19. 48 CFR 252.239-7008 - Reuse arrangements.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Reuse arrangements. 252... Provisions And Clauses 252.239-7008 Reuse arrangements. As prescribed in 239.7411(a), use the following clause: Reuse Arrangements (DEC 1991) (a) When feasible, the Contractor shall reuse canceled...

  20. European top managers' support for work-life arrangements

    NARCIS (Netherlands)

    Been, W.M.

    2015-01-01

    In recent decades, work-life arrangements increasingly became an integral part of the organization of work. Arrangements such as telecommuting, flextime, part-time hours, and various types of leave arrangements are available to employees in many organizations. Top managers, such as CEOs, CFOs and me

  1. Evaluation of alternative institutional arrangements in public utilities

    Directory of Open Access Journals (Sweden)

    Ermishina Anna, V.

    2015-06-01

    Full Text Available Since early 2000s a policy of attracting private operators to public utilities, which should help to increase productivity, reduce costs, and as a result, reduce utility prices takes place in Russia. The aim of the study is to identify the relationship between institutional arrangements and pricing for water and wastewater services. Applying statistical and cluster analysis to empirical data on water utilities in 13 largest cities has revealed the differences in the level and dynamics of prices for water and wastewater services in the group of public utilities and public private water utilities. In 2011-2014 the level and growth price rates in the group of public private partnerships were higher than in group of municipal water utilities. Thus, the involvement of private operators has not yet lead to the expected reduction in prices.

  2. The spatial arrangement of chromosomes during prometaphase facilitates spindle assembly.

    Science.gov (United States)

    Magidson, Valentin; O'Connell, Christopher B; Lončarek, Jadranka; Paul, Raja; Mogilner, Alex; Khodjakov, Alexey

    2011-08-19

    Error-free chromosome segregation requires stable attachment of sister kinetochores to the opposite spindle poles (amphitelic attachment). Exactly how amphitelic attachments are achieved during spindle assembly remains elusive. We employed photoactivatable GFP and high-resolution live-cell confocal microscopy to visualize complete 3D movements of individual kinetochores throughout mitosis in nontransformed human cells. Combined with electron microscopy, molecular perturbations, and immunofluorescence analyses, this approach reveals unexpected details of chromosome behavior. Our data demonstrate that unstable lateral interactions between kinetochores and microtubules dominate during early prometaphase. These transient interactions lead to the reproducible arrangement of chromosomes in an equatorial ring on the surface of the nascent spindle. A computational model predicts that this toroidal distribution of chromosomes exposes kinetochores to a high density of microtubules which facilitates subsequent formation of amphitelic attachments. Thus, spindle formation involves a previously overlooked stage of chromosome prepositioning which promotes formation of amphitelic attachments.

  3. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C

    2009-04-01

    Full Text Available Abstract The draft genome sequence of cattle (Bos taurus has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries.

  4. Genome-wide comparison of genes involved in the biosynthesis, metabolism, and signaling of juvenile hormone between silkworm and other insects

    Directory of Open Access Journals (Sweden)

    Daojun Cheng

    2014-06-01

    Full Text Available Juvenile hormone (JH contributes to the regulation of larval molting and metamorphosis in insects. Herein, we comprehensively identified 55 genes involved in JH biosynthesis, metabolism and signaling in the silkworm (Bombyx mori as well as 35 in Drosophila melanogaster, 35 in Anopheles gambiae, 36 in Apis mellifera, 47 in Tribolium castaneum, and 44 in Danaus plexippus. Comparative analysis showed that each gene involved in the early steps of the mevalonate (MVA pathway, in the neuropeptide regulation of JH biosynthesis, or in JH signaling is a single copy in B. mori and other surveyed insects, indicating that these JH-related pathways or steps are likely conserved in all surveyed insects. However, each gene participating in the isoprenoid branch of JH biosynthesis and JH metabolism, together with the FPPS genes for catalyzing the final step of the MVA pathway of JH biosynthesis, exhibited an obvious duplication in Lepidoptera, including B. mori and D. plexippus. Microarray and real-time RT-PCR analysis revealed that different copies of several JH-related genes presented expression changes that correlated with the dynamics of JH titer during larval growth and metamorphosis. Taken together, the findings suggest that duplication-derived copy variation of JH-related genes might be evolutionarily associated with the variation of JH types between Lepidoptera and other insect orders. In conclusion, our results provide useful clues for further functional analysis of JH-related genes in B. mori and other insects.

  5. Tendons Arrangement Effects on Reinforced Concrete Frames

    Directory of Open Access Journals (Sweden)

    Ayad B. Bahnam

    2013-05-01

    Full Text Available  The tendons arrangement effects on the response of reinforced concrete frame experiencing blast loads is investigated in this paper. The structure is modeled using nonlinear finite elements employing a bilinear hysteretic model. So that elements are used so that yielding of the structures could be accurately modeled and captured. The frame is analyzed using a non-linear, elastic-plastic finite element program written in code MATLAB. Six tendon architectures were investigated. A single tendon was placed between different floors and its effects investigated. From the obtained results, the ideal case which causes a reduction in the maximum displacement and the amount of permanent deflection without increase in the maximum structural shear forces greatly is obtained.

  6. Rim seal arrangement having pumping feature

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ching-Pang; Myers, Caleb

    2017-04-25

    A rim seal arrangement for a gas turbine engine includes a first seal face on a rotor component, and a second seal face on a stationary annular rim centered about a rotation axis of the rotor component. The second seal face is spaced from the first seal face along an axial direction to define a seal gap. The seal gap is located between a radially outer hot gas path and a radially inner rotor cavity. The first seal face has a plurality of circumferentially spaced depressions, each having a depth in an axial direction and extending along a radial extent of the first seal face. The depressions influence flow in the seal gap such that during rotation of the rotor component, fluid in the seal gap is pumped in a radially outward direction to prevent ingestion of a gas path fluid from the hot gas path into the rotor cavity.

  7. Factored Facade Acquisition using Symmetric Line Arrangements

    KAUST Repository

    Ceylan, Duygu

    2012-05-01

    We introduce a novel framework for image-based 3D reconstruction of urban buildings based on symmetry priors. Starting from image-level edges, we generate a sparse and approximate set of consistent 3D lines. These lines are then used to simultaneously detect symmetric line arrangements while refining the estimated 3D model. Operating both on 2D image data and intermediate 3D feature representations, we perform iterative feature consolidation and effective outlier pruning, thus eliminating reconstruction artifacts arising from ambiguous or wrong stereo matches. We exploit non-local coherence of symmetric elements to generate precise model reconstructions, even in the presence of a significant amount of outlier image-edges arising from reflections, shadows, outlier objects, etc. We evaluate our algorithm on several challenging test scenarios, both synthetic and real. Beyond reconstruction, the extracted symmetry patterns are useful towards interactive and intuitive model manipulations.

  8. Arrangement Computation for Planar Algebraic Curves

    CERN Document Server

    Berberich, Eric; Kobel, Alexander; Sagraloff, Michael

    2011-01-01

    We present a new certified and complete algorithm to compute arrangements of real planar algebraic curves. Our algorithm provides a geometric-topological analysis of the decomposition of the plane induced by a finite number of algebraic curves in terms of a cylindrical algebraic decomposition of the plane. Compared to previous approaches, we improve in two main aspects: Firstly, we significantly reduce the amount of exact operations, that is, our algorithms only uses resultant and gcd as purely symbolic operations. Secondly, we introduce a new hybrid method in the lifting step of our algorithm which combines the usage of a certified numerical complex root solver and information derived from the resultant computation. Additionally, we never consider any coordinate transformation and the output is also given with respect to the initial coordinate system. We implemented our algorithm as a prototypical package of the C++-library CGAL. Our implementation exploits graphics hardware to expedite the resultant and gcd...

  9. Re-Presenting Subversive Songs: Applying Strategies for Invention and Arrangement to Nontraditional Speech Texts

    Science.gov (United States)

    Charlesworth, Dacia

    2010-01-01

    Invention deals with the content of a speech, arrangement involves placing the content in an order that is most strategic, style focuses on selecting linguistic devices, such as metaphor, to make the message more appealing, memory assists the speaker in delivering the message correctly, and delivery ideally enables great reception of the message.…

  10. Beginning teachers' self-efficacy and stress and the supposed effects of induction arrangements

    NARCIS (Netherlands)

    Helms-Lorenz, Michelle; Slof, Bert; Vermue, Carlien E.; Canrinus, Esther. T.

    2012-01-01

    Induction arrangements are implemented in schools all over the world to support beginning teachers (BTs) (novices) in gradually growing into their profession. The aim of this study is to gain more insight into two key psychological processes involved in the work of a qualified beginning teacher, nam

  11. Re-Presenting Subversive Songs: Applying Strategies for Invention and Arrangement to Nontraditional Speech Texts

    Science.gov (United States)

    Charlesworth, Dacia

    2010-01-01

    Invention deals with the content of a speech, arrangement involves placing the content in an order that is most strategic, style focuses on selecting linguistic devices, such as metaphor, to make the message more appealing, memory assists the speaker in delivering the message correctly, and delivery ideally enables great reception of the message.…

  12. Social Workers' Final Act of Service: Respectful Burial Arrangements for Indigent, Unclaimed, and Unidentified People

    Science.gov (United States)

    Castex, Graciela M.

    2007-01-01

    Social workers have long been involved in identifying resources and making final arrangements for clients who die without an estate or have no heirs, who may be institutionalized or unknown to the community, or whose body may be unclaimed for burial. Absent quick intervention, these individuals are often at risk for an anonymous potter's field…

  13. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

    Science.gov (United States)

    Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

    2012-07-01

    This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

  14. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications.

    Science.gov (United States)

    Akasaki, Tetsuya; Nikaido, Masato; Tsuchiya, Kotaro; Segawa, Susumu; Hasegawa, Masami; Okada, Norihiro

    2006-03-01

    We determined the complete mitochondrial genomes of five cephalopods of the Subclass Coleoidea (Suborder Oegopsida: Watasenia scintillans, Todarodes pacificus, Suborder Myopsida: Sepioteuthis lessoniana, Order Sepiida: Sepia officinalis, and Order Octopoda: Octopus ocellatus) and used them to infer phylogenetic relationships. In our Maximum Likelihood (ML) tree, sepiids (cuttlefish) are at the most basal position of all decapodiformes, and oegopsids and myopsids form a monophyletic clade, thus supporting the traditional classification of the Order Teuthida. We detected extensive gene rearrangements in the mitochondrial genomes of broad cephalopod groups. It is likely that the arrangements of mitochondrial genes in Oegopsida and Sepiida were derived from those of Octopoda, which is thought to be the ancestral order, by entire gene duplication and random gene loss. Oegopsida in particular has undergone long-range gene duplications. We also found that the mitochondrial gene arrangement of Sepioteuthis lessoniana differs from that of Loligo bleekeri, although they belong to the same family. Analysis of both the phylogenetic tree and mitochondrial gene rearrangements of coleoid Cephalopoda suggests that each mitochondrial gene arrangement was acquired after the divergence of each lineage.

  15. Environmentally triggered genomic plasticity and capsular polysaccharide formation are involved in increased ethanol and acetic acid tolerance in Kozakia baliensis NBRC 16680.

    Science.gov (United States)

    Brandt, Julia U; Born, Friederike-Leonie; Jakob, Frank; Vogel, Rudi F

    2017-08-10

    Kozakia baliensis NBRC 16680 secretes a gum-cluster derived heteropolysaccharide and forms a surface pellicle composed of polysaccharides during static cultivation. Furthermore, this strain exhibits two colony types on agar plates; smooth wild-type (S) and rough mutant colonies (R). This switch is caused by a spontaneous transposon insertion into the gumD gene of the gum-cluster, resulting in a heteropolysaccharide secretion deficient, rough phenotype. To elucidate, whether this is a directed switch triggered by environmental factors, we checked the number of R and S colonies under different growth conditions including ethanol and acetic acid supplementation. Furthermore, we investigated the tolerance of R and S strains against ethanol and acetic acid in shaking and static growth experiments. To get new insights into the composition and function of the pellicle polysaccharide, the polE gene of the R strain was additionally deleted, as it was reported to be involved in pellicle formation in other acetic acid bacteria. The number of R colonies was significantly increased upon growth on acetic acid and especially ethanol. The morphological change from K. baliensis NBRC 16680 S to R strain was accompanied by changes in the sugar contents of the produced pellicle EPS. The R:ΔpolE mutant strain was not able to form a regular pellicle anymore, but secreted an EPS into the medium, which exhibited a similar sugar monomer composition as the pellicle polysaccharide isolated from the R strain. The R strain had a markedly increased tolerance towards acetic acid and ethanol compared to the other NBRC 16680 strains (S, R:ΔpolE). A relatively high intrinsic acetic acid tolerance was also observable for K. baliensis DSM 14400(T), which might indicate diverse adaptation mechanisms of different K. baliensis strains in altering natural habitats. The results suggest that the genetically triggered R phenotype formation is directly related to increased acetic acid and ethanol

  16. A functional genomic screen combined with time-lapse microscopy uncovers a novel set of genes involved in dorsal closure of Drosophila embryos.

    Directory of Open Access Journals (Sweden)

    Ferenc Jankovics

    Full Text Available Morphogenesis, the establishment of the animal body, requires the coordinated rearrangement of cells and tissues regulated by a very strictly-determined genetic program. Dorsal closure of the epithelium in the Drosophila melanogaster embryo is one of the best models for such a complex morphogenetic event. To explore the genetic regulation of dorsal closure, we carried out a large-scale RNA interference-based screen in combination with in vivo time-lapse microscopy and identified several genes essential for the closure or affecting its dynamics. One of the novel dorsal closure genes, the small GTPase activator pebble (pbl, was selected for detailed analysis. We show that pbl regulates actin accumulation and protrusion dynamics in the leading edge of the migrating epithelial cells. In addition, pbl affects dorsal closure dynamics by regulating head involution, a morphogenetic process mechanically coupled with dorsal closure. Finally, we provide evidence that pbl is involved in closure of the adult thorax, suggesting its general requirement in epithelial closure processes.

  17. Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-kappaB activation.

    Science.gov (United States)

    Ng, P W; Iha, H; Iwanaga, Y; Bittner, M; Chen, Y; Jiang, Y; Gooden, G; Trent, J M; Meltzer, P; Jeang, K T; Zeichner, S L

    2001-07-27

    The Tax protein of human T-lymphotropic virus type 1 (HTLV-1), an oncoprotein that transactivates viral and cellular genes, plays a key role in HTLV-1 replication and pathogenesis. We used cDNA microarrays to examine Tax-mediated transcriptional changes in the human Jurkat T-cell lines JPX-9 and JPX-M which express Tax and Tax-mutant protein, respectively, under the control of an inducible promoter. Approximately 300 of the over 2000 genes examined were differentially expressed in the presence of Tax. These genes were grouped according to their function and are discussed in the context of existing findings in the literature. There was strong agreement between our results and genes previously reported as being Tax-responsive. Genes that were differentially expressed in the presence of Tax included those related to apoptosis, the cell cycle and DNA repair, signaling factors, immune modulators, cytokines and growth factors, and adhesion molecules. Functionally, we provide evidence that one of these genes, the mixed-lineage kinase MLK-3, is involved in Tax-mediated NF-kappa-B signaling. Our current results provide additional insights into Tax-mediated signaling.

  18. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

    Directory of Open Access Journals (Sweden)

    Cremer Thomas

    2005-12-01

    Full Text Available Abstract Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.

  19. Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.)

    Science.gov (United States)

    Wang, Chen-Yang; Liu, Sheng-Rui; Zhang, Xiao-Yu; Ma, Yu-Jiao; Hu, Chun-Gen; Zhang, Jin-Zhi

    2017-01-01

    Long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in post-transcriptional and transcriptional regulation in Arabidopsis. However, lncRNAs and their functional roles remain poorly characterized in woody plants, including citrus. To identify lncRNAs and investigate their role in citrus flowering, paired-end strand-specific RNA sequencing was performed for precocious trifoliate orange and its wild-type counterpart. A total of 6,584 potential lncRNAs were identified, 51.6% of which were from intergenic regions. Additionally, 555 lncRNAs were significantly up-regulated and 276 lncRNAs were down-regulated in precocious trifoliate orange, indicating that lncRNAs could be involved in the regulation of trifoliate orange flowering. Comparisons between lncRNAs and coding genes indicated that lncRNAs tend to have shorter transcripts and lower expression levels and that they display significant expression specificity. More importantly, 59 and 7 lncRNAs were identified as putative targets and target mimics of citrus miRNAs, respectively. In addition, the targets of Pt-miR156 and Pt-miR396 were confirmed using the regional amplification reverse-transcription polymerase chain reaction method. Furthermore, overexpression of Pt-miR156a1 and Pt-miR156a1 in Arabidopsis resulted in an extended juvenile phase, short siliques, and smaller leaves in transgenic plants compared with control plants. These findings provide important insight regarding citrus lncRNAs, thus enabling in-depth functional analyses. PMID:28233798

  20. The Chlamydomonas genome project: a decade on

    Science.gov (United States)

    Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

    2014-01-01

    The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

  1. Identification of potential genetic components involved in the deviant quorum-sensing signaling pathways of Burkholderia glumae through a functional genomics approach

    Directory of Open Access Journals (Sweden)

    Ruoxi eChen

    2015-03-01

    Full Text Available Burkholderia glumae is the chief causal agent for bacterial panicle blight of rice. The acyl-homoserine lactone (AHL-mediated quorum-sensing (QS system dependent on a pair of luxI and luxR homologs, tofI and tofR, is the primary cell-to-cell signaling mechanism determining the virulence of this bacterium. Production of toxoflavin, a major virulence factor of B. glumae, is known to be dependent on the tofI/tofR QS system. In our previous study, however, it was observed that B. glumae mutants defective in tofI or tofR produced toxoflavin if they grew on the surface of a solid medium, suggesting that alternative signaling pathways independent of tofI or tofR are activated in that growth condition for the production of toxoflavin. In this study, potential genetic components involved in the tofI- and tofR-independent signaling pathways for toxoflavin production were sought through screening random mini-Tn5 mutants of B. glumae to better understand the intercellular signaling pathways of this pathogen. Fifteen and three genes were initially identified as the potential genetic elements of the tofI- and tofR-independent pathways, respectively. Especially, the ORF (bglu_2g06320 divergently transcribed from toxJ, which encodes an orphan LuxR protein and controls toxoflavin biosynthesis, was newly identified in this study as a gene required for the tofR-independent toxoflavin production and named as toxK. Among those genes, flhD, dgcB, and wyzB were further studied to validate their functions in the tofI-independent toxoflavin production, and similar studies were also conducted with qsmR and toxK for their functions in the tofR-independent toxoflavin production. This work provides a foundation for future comprehensive studies of the intercellular signaling systems of B. glumae and other related pathogenic bacteria.

  2. Strike a balance with flexible working arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Madison, Alison L.

    2012-12-15

    Monthly Economic Diversity column for the Tri-City Herald - Topic: Telworking - Excerpt below: As the holiday season kicks into high gear, work-life balance is on many of our minds. How can I meet all of my work commitments this month when no one will be in the office, and still strategically use very little vacation time to stretch the holiday break from four days to fourteen? Am I right? I think most all of us want to stay engaged with our professional lives while maintaining the freedom to prioritize our personal lives. And many employers have come up with ways to help us achieve that balance. Teleworking is not a brand new concept, but is certainly gaining steam as employers and employees alike try to find ways to meet a variety of wants and needs. There are benefits to both sides when it comes to offering flexible working arrangements such as teleworking. For businesses attempting to meet sustainability targets by reducing employee commuting and associated impacts to energy and environment, the benefits of this option can really add up.

  3. Nonstandard work arrangements and worker health and safety.

    Science.gov (United States)

    Howard, John

    2017-01-01

    Arrangements between those who perform work and those who provide jobs come in many different forms. Standard work arrangements now exist alongside several nonstandard arrangements: agency work, contract work, and gig work. While standard work arrangements are still the most prevalent types, the rise of nonstandard work arrangements, especially temporary agency, contract, and "gig" arrangements, and the potential effects of these new arrangements on worker health and safety have captured the attention of government, business, labor, and academia. This article describes the major work arrangements in use today, profiles the nonstandard workforce, discusses several legal questions about how established principles of labor and employment law apply to nonstandard work arrangements, summarizes findings published in the past 20 years about the health and safety risks for workers in nonstandard work arrangements, and outlines current research efforts in the area of healthy work design and worker well-being. Am. J. Ind. Med. 60:1-10, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  5. Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling.

    Science.gov (United States)

    Inoue, Jun; Sato, Yukuto; Sinclair, Robert; Tsukamoto, Katsumi; Nishida, Mutsumi

    2015-12-01

    Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post-teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70-80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.

  6. Th17 response and autophagy - main pathways implicated in the development of inflammatory bowel disease by genome-wide association studies: new factors involved in inflammatory bowel disease susceptibility

    Directory of Open Access Journals (Sweden)

    Roberto Díaz-Peña

    2015-09-01

    Full Text Available Inflammatory bowel disease (IBD is an entity that mainly includes ulcerative colitis (UC and Crohn's disease (CD. Improved health care, diet changes, and higher industrialization are associated with an increase in IBD prevalence. This supports the central role of environmental factors in the pathology of this disease. However, IBD also shows a relevant genetic component as shown by high heritability. Classic genetic studies showed relevant associations between IBD susceptibility and genes involved in the immune response. This is consistent with prior theories about IBD development. According to these, contact of the immune system with a high number of harmless antigens from the diet and the bacterial flora should originate tolerance while preserving response against pathogens. Failure to achieve this balance may originate the typical inflammatory response associated with IBD. Recently, genome-wide association studies (GWASs have confirmed the implication of the immune system, particularly the Th17 immune response, previously associated to other autoimmune diseases, and of autophagy. In this paper, the mechanisms involved in these two relevant pathways and their potential role in the pathogenesis of IBD are reviewed.

  7. The genomic region of rbcLS in Synechococcus sp. PCC 7942 contains genes involved in the ability to grow under low CO2 concentration and in chlorophyll biosynthesis.

    Science.gov (United States)

    Ronen-Tarazi, M; Lieman-Hurwitz, J; Gabay, C; Orus, M I; Kaplan, A

    1995-08-01

    Several genes involved in the ability of Synechococcus sp. PCC 7942 to grow under different CO2 concentrations were mapped in the genomic region of rbcLS (the operon encoding the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase). Insertion of a cartridge encoding kanamycin resistance within open reading frame (ORF) 78, designated ccmJ, located 7 kb upstream of rbcLS, resulted in a kanamycin-resistant, high-CO2-requiring mutant, M3, which does not contain normal carboxysomes. ccmJ shows significant homology to csoS1 encoding a carboxysomal shell polypeptide in Thiobacillus neopolitanus. Analysis of the polypeptide pattern of a carboxysome-enriched fraction indicated several differences between the wild type and the mutant. The amount of the ribulose-1,5-bisphosphate carboxylase/oxygenase subunits was considerably smaller in the carboxysomal fraction of the mutant when compared to the wild type. On the basis of the sequence analyses, ORF286 and ORF466, located downstream of ccmJ, were identified as chlL and chlN, respectively, which are involved in chlorophyll biosynthesis in the dark.

  8. Diversification of seed arrangement induced by ovule rotation and septum formation in Leguminosae.

    Science.gov (United States)

    Endo, Yasuhiko; Ohashi, Hiroyoshi

    2009-09-01

    The plants of Leguminosae, which comprises 731 genera, bear monocarpellary flowers. The fruit, known as a pod, generally contains a row of seeds, and the internal structure appears to be simple. In Leguminosae, the seeds are generally arranged longitudinally along the suture of the pod but, in a few genera, namely, Cassia, Indigofera, and Senna, they are arranged transversely. Transverse seed arrangement facilitates the accommodation of a considerable number of seeds and has been considered to be established by rotation of seeds during development. We studied the development both these patterns of seed arrangement, i.e., longitudinal and transverse, in Senna and Indigofera in order to elucidate the structural changes occurring in ovaries (or pods) and determine the forces responsible for rotation of ovules (or seeds) by dissecting ovaries and pods at different developmental stages. Our results showed that at an early developmental stage the ovules were obliquely oriented or transversely arranged; later, the direction of their growth was restricted by the ovary walls or neighboring ovules, and therefore the obliquely oriented ovules rotated inward or outward. Thus, it was clarified that the processes involved in the formation of the internal structure of pods are regulated in a complex manner.

  9. Optical properties of quasiperiodically arranged semiconductor nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Werchner, Marco

    2009-12-18

    This work consists of two parts which are entitled ''One-Dimensional Resonant Fibonacci Quasicrystals'' and ''Resonant Tunneling of Light in Silicon Nanostructures''. A microscopic theory has been applied to investigate the optical properties of the respective semiconductor nanostructures. The studied one-dimensional resonant Fibonacci quasicrystals consist of GaAs quantum wells (QW) that are separated by either a large spacer L or a small one S. These spacers are arranged according to the Fibonacci sequence LSLLSLSL.. The average spacing satisfies a generalized Bragg condition with respect to the 1s-exciton resonance of the QWs. A theory, that makes use of the transfer-matrix method and that allows for the microscopic description of many-body effects such as excitation-induced dephasing caused by the Coulomb scattering of carriers, has been applied to compute the optical spectra of such structures. A pronounced sharp reflectivity minimum is found in the vicinity of the heavy-hole resonance both in the measured as well as in the calculated linear 54-QW spectra. Specifically, the influence of the carrier density, of the QW arrangement, of a detuning away from the exact Bragg condition, of the average spacing as well as of the ratio of the optical path lengths of the large and small spacers L and S, respectively, and of the QW number on the optical properties of the samples have been studied. Additionally, self-similarity among reflection spectra corresponding to different QW numbers that exceed a Fibonacci number by one is observed, which identifies certain spectral features as true fingerprints of the Fibonacci spacing. In the second part, resonant tunneling of light in stacked structures consisting of alternating parallel layers of silicon and air have been studied theoretically.Light may tunnel through the air barrier due to the existence of evanescent waves inside the air layers if the neighboring silicon layer is close

  10. Human Rights Arrangement on Indonesian Law

    Directory of Open Access Journals (Sweden)

    S. Masribut Sardol

    2014-01-01

    Full Text Available Article 1 paragraph (3 of the Constitution of 1945 (UUD 1945 stated that Indonesia is a Rule of Law. One feature of the Rule of Law is the existence of human rights in the state administration. Indonesia, since independence on August 17, 1945 has asserted the defense of human rights as stated in the opening clause and in the torso of the 1945 Constitution Article 27-34. In the era of reform, on the Government of President Habibie, the President and the Parliament ratified the UN convention against torture and other cruel, inhuman, or degrading human dignity into Law number 5 of 1998. Then the MPR also publishes the statutes of MPR No. XVII/MPR/1998 on Human Rights, which was followed up with the appearance of Law No. 39 of 1999 on human rights. In accordance with the law in Indonesia based on the sort of Law No. 12 of 2011, the actual products that have been issued by the Government (the MPR, DPR and President that follow up the substance of Human Rights in the Constitution with established Assembly and the law is already correct. But when the MPR then does the second amendment to the Constitution on August 18, 2000 by adding a special article chapters and contains about Human Rights (as mentioned in Chapter X-A section 28 A-J, have made the complexity hierarchy of law in Indonesia because it is not in accordance with the substance of article 7 of Law No. 12 of 2011. How To Cite: Sardol, S. (2014. Human Rights Arrangement on Indonesian Law. Rechtsidee, 1(1, 85-100. doi:http://dx.doi.org/10.21070/jihr.v1i1.105

  11. Multiple childcare arrangements and health outcomes in early childhood.

    Science.gov (United States)

    Chen, Jen-Hao

    2013-04-01

    This study examined the associations between multiple childcare arrangements and young children's health problems. This study used three waves of the Early Childhood Longitudinal Study-Birth Cohort, collected from a nationally representative sample of children when they were 9 months old, 2 years old, and 4 years old (N = 7,150). 'Multiple childcare arrangements' was defined and measured by the number of non-parental childcare arrangements that occurred on a regular basis. During each wave of the data collection, the mother reported the number of regular childcare arrangements by three types: relative care, non-relative care, and center-based care. These numbers were summed to calculate the total number of arrangements. The mother also reported the incidence of ear infections, gastrointestinal illnesses, asthma diagnosis, and unintentional injuries of the child. Random effects and fixed effects regression models were used to estimate the association between the number of childcare arrangements and measures of early childhood health problems. Increases in the total number of childcare arrangements were associated with an elevated risk of ear infections, gastrointestinal illnesses, and diagnosed asthma in children. Further analysis indicates that increases in both the number of center-based care and non-relative care (but not relative care) arrangements can lead to a greater chance of health problems in young children. Multiple childcare arrangements are associated with communicable illness and diagnosed asthma in early childhood and appear to be a risk factor for health problems in early childhood.

  12. Arithmetic matroids, the Tutte polynomial and toric arrangements

    National Research Council Canada - National Science Library

    D’Adderio, Michele; Moci, Luca

    2013-01-01

    .... Guided by the geometry of generalized toric arrangements, we provide a combinatorial interpretation of the associated arithmetic Tutte polynomial, which can be seen as a generalization of Crapo's...

  13. Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome.

    OpenAIRE

    1992-01-01

    A 23-kb fragment of the Streptomyces coelicolor chromosome spanning the dnaA region has been isolated as a cosmid clone. Nucleotide sequence analysis of a 5-kb portion shows that the genes for the RNase P protein (rnpA), ribosomal protein L34 (rpmH), the replication initiator protein (dnaA), and the beta subunit of DNA polymerase III (dnaN) are present in the highly conserved gene arrangement found in all eubacterial genomes studied so far. The dnaA-dnaN intergenic region is approximately 1 k...

  14. Determinants of Child Custody Arrangements at Divorce.

    Science.gov (United States)

    Fox, Greer Litton; Kelly, Robert F.

    1995-01-01

    Using data on 509 cases from a census of a large Michigan county's divorces involving minor children filed in the early 1980s, modeled the likelihood that mothers versus fathers would receive sole custody. Found substantial gender differences in the effects of socioeconomic and legal process variables on custody outcomes. (JBJ)

  15. Sales Promotion Arrangements in the FMCG Channel

    NARCIS (Netherlands)

    V. Immink; B. Wierenga (Berend)

    2004-01-01

    textabstractSales promotions in FMCG involve some form of coordination/cooperation between manufacturer and retailer. The result is a sales promotion agreement (SPA). First, we examine which elements are agreed upon in SPAs (e.g. goals, budgets, etc.). Second, we explain the differences in SPAs (e.g

  16. [Genomics and functional genomics in microbiology].

    Science.gov (United States)

    Encarnación-Guevara, Sergio

    2006-01-01

    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  17. 29 CFR 779.230 - Franchise and other arrangements.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Franchise and other arrangements. 779.230 Section 779.230... Coverage Leased Departments, Franchise and Other Business Arrangements § 779.230 Franchise and other.... The quotation in § 779.229 from the Senate Report shows that Congress recognized that some...

  18. Living Arrangements and Family Formation Attitudes in Early Adulthood.

    Science.gov (United States)

    Axinn, William G.; Barber, Jennifer S.

    1997-01-01

    Examines the impact of nonfamily living arrangements and cohabitation on changes in family formation attitudes at the individual level. Results indicate that both the experience and duration of cohabiting arrangements have significant effects on family formation attitudes but fail to show significant consequences of premarital, nonfamily living…

  19. Exploring living arrangements of divorced families in the Netherlands

    NARCIS (Netherlands)

    Bakker, W.; Mulder, C.H.

    2009-01-01

    We aim to gain more insight into the characteristics of divorced families with different types of post-divorce living arrangements, and in particular with co-parenting arrangements in which the child alternates between the parents’ residences. Empirical evidence comes from a mixed- method research,

  20. Territoriality: Seat Preferences in Different Types of Classroom Arrangements

    Science.gov (United States)

    Kaya, Naz; Burgess, Brigitte

    2007-01-01

    Students' degree of territoriality based on gender and seat preferences in different types of classroom arrangements was studied. The types of classroom arrangements included rows of tablet-arm chairs, U-shaped, clusters, and rows of tables with individual chairs. The study was carried out through a survey at a large public institution in the…

  1. Do Knowledge Arrangements Affect Student Reading Comprehension of Genetics?

    Science.gov (United States)

    Wu, Jen-Yi; Tung, Yu-Neng; Hwang, Bi-Chi; Lin, Chen-Yung; Che-Di, Lee; Chang, Yung-Ta

    2014-01-01

    Various sequences for teaching genetics have been proposed. Three seventh-grade biology textbooks in Taiwan share similar key knowledge assemblages but have different knowledge arrangements. To investigate the influence of knowledge arrangements on student understanding of genetics, we compared students' reading comprehension of the three texts…

  2. Arrangement for carrying out and studying chemical reactions

    NARCIS (Netherlands)

    Langeveld, A.D.; Makkee, M.; Moulijn, J.A.

    1993-01-01

    Abstract of NL 9102029 (A) Described is an arrangement for carrying out TAP experiments. Such an arrangement comprises a reaction chamber in which a very short-lived beam of molecules is directed at a target to produce a short-lived beam of intermediate-product molecules, and a vacuum chamber wher

  3. Minimality of hyperplane arrangements and basis of local system cohomology

    CERN Document Server

    Yoshinaga, Masahiko

    2010-01-01

    The purpose of this paper is applying minimality of hyperplane arrangements to local system cohomology groups. It is well known that twisted cohomology groups with coefficients in a generic rank one local system vanish except in the top degree, and bounded chambers form a basis of the remaining cohomology group. We determine precisely when this phenomenon happens for two dimensional arrangements.

  4. 33 CFR 157.222 - Pump and piping arrangements.

    Science.gov (United States)

    2010-07-01

    ... OIL IN BULK Dedicated Clean Ballast Tanks on Tank Vessels Design and Equipment § 157.222 Pump and piping arrangements. (a) Dedicated clean ballast tanks must be connected to the least practicable: (1... each dedicated clean ballast tank must be arranged so that oily water does not enter any...

  5. 22 CFR 92.63 - Arrangement of papers.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Arrangement of papers. 92.63 Section 92.63... and Letters Rogatory § 92.63 Arrangement of papers. Unless special instructions to the contrary are received, the various papers comprising the completed record of the depositions should usually be...

  6. On capital allocation for stochastic arrangement increasing actuarial risks

    Directory of Open Access Journals (Sweden)

    Pan Xiaoqing

    2017-01-01

    Full Text Available This paper studies the increasing convex ordering of the optimal discounted capital allocations for stochastic arrangement increasing risks with stochastic arrangement decreasing occurrence times. The application to optimal allocation of policy limits is presented as an illustration as well.

  7. Do Knowledge Arrangements Affect Student Reading Comprehension of Genetics?

    Science.gov (United States)

    Wu, Jen-Yi; Tung, Yu-Neng; Hwang, Bi-Chi; Lin, Chen-Yung; Che-Di, Lee; Chang, Yung-Ta

    2014-01-01

    Various sequences for teaching genetics have been proposed. Three seventh-grade biology textbooks in Taiwan share similar key knowledge assemblages but have different knowledge arrangements. To investigate the influence of knowledge arrangements on student understanding of genetics, we compared students' reading comprehension of the three…

  8. Do Knowledge Arrangements Affect Student Reading Comprehension of Genetics?

    Science.gov (United States)

    Wu, Jen-Yi; Tung, Yu-Neng; Hwang, Bi-Chi; Lin, Chen-Yung; Che-Di, Lee; Chang, Yung-Ta

    2014-01-01

    Various sequences for teaching genetics have been proposed. Three seventh-grade biology textbooks in Taiwan share similar key knowledge assemblages but have different knowledge arrangements. To investigate the influence of knowledge arrangements on student understanding of genetics, we compared students' reading comprehension of the three texts…

  9. A Unit Cell Laboratory Experiment: Marbles, Magnets, and Stacking Arrangements

    Science.gov (United States)

    Collins, David C.

    2011-01-01

    An undergraduate first-semester general chemistry laboratory experiment introducing face-centered, body-centered, and simple cubic unit cells is presented. Emphasis is placed on the stacking arrangement of solid spheres used to produce a particular unit cell. Marbles and spherical magnets are employed to prepare each stacking arrangement. Packing…

  10. 28 CFR 550.44 - Procedures for arranging drug counseling.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Procedures for arranging drug counseling... MANAGEMENT DRUG PROGRAMS Drug Services (Urine Surveillance and Counseling for Sentenced Inmates in Contract CTCs) § 550.44 Procedures for arranging drug counseling. The contract center staff shall hold a...

  11. Mitochondrial genome organization and phylogeny of two vespid wasps.

    Science.gov (United States)

    Cameron, Stephen L; Dowton, Mark; Castro, Lyda R; Ruberu, Kalani; Whiting, Michael F; Austin, Andy D; Diement, Kieren; Stevens, Julia

    2008-10-01

    We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data.

  12. Biocommunication and natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther; Witzany

    2010-01-01

    The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,i.e.language-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative perspective is competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to(re-)combine and(re-)regulate them according to context-dependent(i.e.adaptational) purposes of the host organism.

  13. How children arrange social communities across contexts

    DEFF Research Database (Denmark)

    Højholt, Charlotte

    different life contexts, contradictory demands and social conflicts. One point in the paper will be to illustrate that they are doing this together. Children’s developmental contexts are societal and historical structured and in the same time the children themselves are involved in organising, negotiating...... and contributing to different activities of their life. Following children in their everyday life across contexts has highlighted a theme about how children ‘arrange’ their social communities and their personal participation in varying and shifting activities. In this way the paper will emphasize the active...... seems closely connected to analysis of the social practices where children are taking part....

  14. Combining Geomatics and Conventional Methods for Monitoring Forest Conditions under Different Governance Arrangements

    Institute of Scientific and Technical Information of China (English)

    Ambika P. Gautam

    2006-01-01

    This study employed an innovative methodological framework that combines geomatics and conventional survey methods to monitor changes in forest conditions and examine their associations with local forest governance parameters in a mountain watershed covering 153.3 km2 in the middle mountains of Nepal. The study involved two spatial scales and analytical steps. First, geomatics techniques were used to map and detect changes in major land cover types in the watershed between 1976 and 2000 and to analyze relationships between forest cover changes and governance arrangements. This was followed by micro-level analysis of the relationships between the biological conditions of selected forests within the watershed and their governance arrangements, using conventional survey methods and analytical tools. The findings show that forest cover in the watershed increased by about 15 per cent during the period. The rate of increase in forest cover was highest in areas under a semi-government type of governance arrangement, while the community forests were generally better in terms of current biological conditions compared to the semi-government forests. This inconsistency between the findings from the two analyscs does not allow us to draw any firm conclusions regarding the role of property rights in determining forest condition, but it indicates that the outcomes of local forest management initiatives may be more dependent on local institutional arrangements regulating forest use and maintenance of forest resources than on the type of property rights arrangements. The findings also provide evidence of the methodological suitability of the research approach adopted, which may be useful for addressing many other research questions related to forestry and natural resources management, particularly those involving multiple spatial scales.

  15. Expression of mature micro-RNA involved in the functioning of p53-dependent system of maintaining the genome stability of the individuals exposed to radiation at clinically relevant doses

    Directory of Open Access Journals (Sweden)

    Shulenina L.V.

    2014-12-01

    Full Text Available Purpose: to explore the content of mature micro-RNA involved in the functioning of p53-dependent system of maintaining the genome stability in the blood of patients in distant time after irradiation at clinically relevant doses and to compare these micro-RNA with the development of malignant tumors in the period of late consequences of radiation injury. Materials and methods. We used the blood samples of patients with acute radiation syndrome (ARS, acute radiation syndrome with the development of local radiation injury (ARS+LRI and local radiation injury (LRI obtained through 1-51 year after radiation injury. The mature mir34a, mir21, mir145, mir16, mir125b, Iet7a which contained in the common fractions of RNA were reverse transcribed by using specific "stem-loop" — primers. The relative amount of micro-RNA in blood of patients by real-time PCR. Statistical analysis of the results was carried out using the non-parametric Mann —Whitney test. Data are presented as median and quartiles, normalized to median of control group accepted for 1. Results. We found a significant reduction of content of mir34a, mir21 in the blood of patients with a diagnosis ARS and the increase of content of mir145 in patients with LRI. Analysis of the individual values of micro-RNA expression in the blood of patients whose cancer was detected, except for patients with a bazalioma, showed consistency of changes with risk of carcinogenesis. Conclusion. For the first time was investigated the functional activity of p53-dependent system of maintaining the genome stability by measuring of micro-RNA in the blood of patients after many years post radiation injury. We found a significant reduction of content of mir34a, mir21 in blood of patients with ARS, and increased mir145 in patients with LRI. Our results suggest that further research with groups of patients, and analysis the dynamics of micro-RNA content would allow for use the micro-RNA as indicators of risk of late

  16. In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the enzymes involved in GDP-L-fucose synthesis and Golgi import.

    Science.gov (United States)

    Peterson, Nathan A; Anderson, Tavis K; Wu, Xiao-Jun; Yoshino, Timothy P

    2013-07-09

    fucosylated glycotopes. This study is the first to identify and characterize three key genes that are putatively involved in the synthesis and Golgi import of GDP-L-fucose in S. mansoni and provides fundamental information regarding their genomic organization, genetic variation, molecular phylogenetics, and developmental expression in intramolluscan larval stages.

  17. METHOD FOR DETERMINING THE MAXIMUM ARRANGEMENT FACTOR OF FOOTWEAR PARTS

    Directory of Open Access Journals (Sweden)

    DRIŞCU Mariana

    2014-05-01

    Full Text Available By classic methodology, designing footwear is a very complex and laborious activity. That is because classic methodology requires many graphic executions using manual means, which consume a lot of the producer’s time. Moreover, the results of this classical methodology may contain many inaccuracies with the most unpleasant consequences for the footwear producer. Thus, the costumer that buys a footwear product by taking into consideration the characteristics written on the product (size, width can notice after a period that the product has flaws because of the inadequate design. In order to avoid this kind of situations, the strictest scientific criteria must be followed when one designs a footwear product. The decisive step in this way has been made some time ago, when, as a result of powerful technical development and massive implementation of electronical calculus systems and informatics, This paper presents a product software for determining all possible arrangements of a footwear product’s reference points, in order to automatically acquire the maximum arrangement factor. The user multiplies the pattern in order to find the economic arrangement for the reference points. In this purpose, the user must probe few arrangement variants, in the translation and rotate-translation system. The same process is used in establishing the arrangement factor for the two points of reference of the designed footwear product. After probing several variants of arrangement in the translation and rotation and translation systems, the maximum arrangement factors are chosen. This allows the user to estimate the material wastes.

  18. Building a data sharing model for global genomic research.

    Science.gov (United States)

    Kosseim, Patricia; Dove, Edward S; Baggaley, Carman; Meslin, Eric M; Cate, Fred H; Kaye, Jane; Harris, Jennifer R; Knoppers, Bartha M

    2014-08-11

    Data sharing models designed to facilitate global business provide insights for improving transborder genomic data sharing. We argue that a flexible, externally endorsed, multilateral arrangement, combined with an objective third-party assurance mechanism, can effectively balance privacy with the need to share genomic data globally.

  19. Complete mitochondrial genome of a Asian lion (Panthera leo goojratensis).

    Science.gov (United States)

    Li, Yu-Fei; Wang, Qiang; Zhao, Jian-ning

    2016-01-01

    The entire mitochondrial genome of this Asian lion (Panthera leo goojratensis) was 17,183 bp in length, gene composition and arrangement conformed to other lions, which contained the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and a non-coding region. The characteristic of the mitochondrial genome was analyzed in detail.

  20. Issues Associated with IAEA Involvement in Assured Nuclear Fuel Supply Arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Kessler, Carol E.; Mathews, Carrie E.

    2008-02-08

    Assured nuclear fuel supply has been discussed at various times as a mechanism to help limit expansion of enrichment and reprocessing (E&R) capability beyond current technology holders. Given the events in the last few years in North Korea and Iran, concern over weapons capabilities gained from acquisition of E&R capabilities has heightened and brought assured nuclear fuel supply (AFS) again to the international agenda. Successful AFS programs can be valuable contributions to strengthening the nonproliferation regime and helping to build public support for expanding nuclear energy.

  1. Laser-driven deflection arrangements and methods involving charged particle beams

    Science.gov (United States)

    Plettner, Tomas [San Ramon, CA; Byer, Robert L [Stanford, CA

    2011-08-09

    Systems, methods, devices and apparatus are implemented for producing controllable charged particle beams. In one implementation, an apparatus provides a deflection force to a charged particle beam. A source produces an electromagnetic wave. A structure, that is substantially transparent to the electromagnetic wave, includes a physical structure having a repeating pattern with a period L and a tilted angle .alpha., relative to a direction of travel of the charged particle beam, the pattern affects the force of the electromagnetic wave upon the charged particle beam. A direction device introduces the electromagnetic wave to the structure to provide a phase-synchronous deflection force to the charged particle beam.

  2. Optimal arrangements of scanning heads for self-calibration of angle encoders

    Science.gov (United States)

    Jiao, Yang; Dong, Zeguang; Ding, Ye; Liu, Pinkuan

    2017-10-01

    The calibration of the angle encoder is necessary to improve the accuracy of angle measurement in precision rotating devices. Due to the characteristics of in situ calibration of encoders, self-calibration methods depending on special arrangements of multiple scanning heads have been widely used. Conventional works usually arrange the scanning heads in a regularly distributed way, generally involving too many scanning heads, especially when more high order Fourier components of the encoder error are calibrated. This paper presents an optimization-based arrangement method for self-calibration of angle encoders. Fourier approaches are used to determine the error of encoder from the angle differences measured between scanning heads. The relations between detectable Fourier components of the error and angular intervals of the heads are obtained from the properties of transfer functions. The optimal arrangements for two and three scanning heads, including the adjustment tolerances of the heads with the range of tested Fourier orders, are presented. The results of simulations and experiments demonstrate that the proposed optimal schemes can realize the same performance of calibration but with fewer scanning heads, compared to the conventional methods.

  3. William Barlow and the Determination of Atomic Arrangement in Crystals.

    Science.gov (United States)

    Mauskopf, Seymour H

    2015-04-01

    William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

  4. Complements and higher resonance varieties of hyperplane arrangements

    CERN Document Server

    Budur, Nero

    2011-01-01

    Hyperplane arrangements form the geometric counterpart of combinatorial objects such as matroids. The shape of the sequence of Betti numbers of the complement of a hyperplane arrangement is of particular interest in combinatorics, where they are known, up to a sign, as Whitney numbers of the first kind, and appear as the coefficients of chromatic, or characteristic, polynomials. We show that certain combinations, some nonlinear, of these Betti numbers satisfy Schur positivity. At the same time, we study the higher degree resonance varieties of the arrangement. We draw some consequences, using homological algebra results and vector bundles techniques, of the fact that all resonance varieties are determinantal.

  5. Designing a Miniature Wheel Arrangement for Mobile Robot Platforms

    CERN Document Server

    Kayani, Saheeb Ahmed

    2011-01-01

    In this research report details of design of a miniature wheel arrangement are presented. This miniature wheel arrangement is essentially a direction control mechanism intended for use on a mobile robot platform or base. The design is a specific one employing a stepper motor as actuator and as described can only be used on a certain type of wheeled robots. However as a basic steering control element, more than one of these miniature wheel arrangements can be grouped together to implement more elaborate and intelligent direction control schemes on varying configurations of wheeled mobile robot platforms.

  6. Partial mitochondrial gene arrangements support a close relationship between Tardigrada and Arthropoda.

    Science.gov (United States)

    Ryu, Shi Hyun; Lee, Ji Min; Jang, Kuem-Hee; Choi, Eun Hwa; Park, Shin Ju; Chang, Cheon Young; Kim, Won; Hwang, Ui Wook

    2007-12-31

    Regions (about 3.7-3.8 kb) of the mitochondrial genomes (rrnL-cox1) of two tardigrades, a heterotardigrade, Batillipes pennaki, and a eutardigrade, Pseudobiotus spinifer, were sequenced and characterized. The gene order in Batillipes was rrnL-V-rrnS-Q-I-M-nad2-W-C-Y-cox1, and in Pseudobiotus it was rrnL-V-rrnS-Q-M-nad2-W-C-Y-cox1. With the exception of the trnI gene, the two tardigrade regions have the same gene content and order. Their gene orders are strikingly similar to that of the chelicerate Limulus polyphemus (rrnL-V-rrnS-CR-I-Q-M-nad2-W-C-Y-cox1), which is considered to be ancestral for arthropods. Although the tardigrades do not have a distinct control region (CR) within this segment, the trnI gene in Pseudobiotus is located between rrnL-trnL1 and trnL2-nad1, and the trnI gene in Batillipes is located between trnQ and trnM. In addition, the 106-bp region between trnQ and trnM in Batillipes not only contains two plausible trnI genes with opposite orientations, but also exhibits some CR-like characteristics. The mitochondrial gene arrangements of 183 other protostomes were compared. 60 (52.2%) of the 115 arthropods examined have the M-nad2-W-C-Y-cox1 arrangement, and 88 (76.5%) the M-nad2-W arrangement, as found in the tardigrades. In contrast, no such arrangement was seen in the 70 non-arthropod protostomes studied. These are the first non-sequence molecular data that support the close relationship of tardigrades and arthropods.

  7. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

    Directory of Open Access Journals (Sweden)

    Michael B Walker

    Full Text Available Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

  8. Cancer genomics

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  9. A Genome-wide Association Study Provides Evidence of Sex-specific Involvement of Chr1p35.1 (ZSCAN20-TLR12P and Chr8p23.1 (HMGB1P46 With Diabetic Neuropathic Pain

    Directory of Open Access Journals (Sweden)

    Weihua Meng

    2015-10-01

    Full Text Available Neuropathic pain is defined as pain arising as a direct consequence of a lesion or a disease affecting the somatosensory system and it affects around 1 in 4 diabetic patients in the UK. The purpose of this genome-wide association study (GWAS was to identify genetic contributors to this disorder. Cases of neuropathic pain were defined as diabetic patients with a multiple prescription history of at least one of five drugs specifically indicated for the treatment of neuropathic pain. Controls were diabetic individuals who were not prescribed any of these drugs, nor amitriptyline, carbamazepine, or nortriptyline. Overall, 961 diabetic neuropathic pain cases and 3260 diabetic controls in the Genetics of Diabetes Audit and Research Tayside (GoDARTS cohort were identified. We found a cluster in the Chr1p35.1 (ZSCAN20-TLR12P with a lowest P value of 2.74 × 10−7 at rs71647933 in females and a cluster in the Chr8p23.1, next to HMGB1P46 with a lowest P value of 8.02 × 10−7 at rs6986153 in males. Sex-specific narrow sense heritability was higher in males (30.0% than in females (14.7%. This GWAS on diabetic neuropathic pain provides evidence for the sex-specific involvement of Chr1p35.1 (ZSCAN20-TLR12P and Chr8p23.1 (HMGB1P46 with the disorder, indicating the need for further research.

  10. The primitive derivation and freeness of multi-Coxeter arrangements

    OpenAIRE

    Yoshinaga, Masahiko

    2002-01-01

    We will prove the freeness of multi-Coxeter arrangements by constructing a basis of the module of vector fields which contact to each reflecting hyperplanes with some multiplicities using K. Saito's theory of primitive derivation.

  11. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Directory of Open Access Journals (Sweden)

    Neni Mariana

    2010-07-01

    Full Text Available Few researches have been concerned about relation between children’s spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was conducted in Indonesia in which we investigated pre-school children’s (between 2 and 3.5 years old ability in making structured arrangement and their ability to determine the quantities by looking at the arrangements. The result shows us that some of the children were able to make such arrangement. However, the children found difficulties either to determine quantities from those arrangements or to compare some structures to easily recognize number of objects.

  12. Children's postdivorce residence arrangements and parental experienced time pressure

    NARCIS (Netherlands)

    van der Heijden, Franciëlla; Poortman, Anne Rigt; van der Lippe, Tanja

    2016-01-01

    Although the rise in postdivorce joint physical custody has fueled scholarly interest in its impact on children, consequences for parents remain understudied. Because children's residence arrangements determine time and coordination demands associated with child care, this study investigated the rel

  13. Children's postdivorce residence arrangements and parental experienced time pressure

    NARCIS (Netherlands)

    van der Heijden, Franciëlla; Poortman, Anne Rigt; van der Lippe, Tanja

    2016-01-01

    Although the rise in postdivorce joint physical custody has fueled scholarly interest in its impact on children, consequences for parents remain understudied. Because children's residence arrangements determine time and coordination demands associated with child care, this study investigated the

  14. Children's postdivorce residence arrangements and parental experienced time pressure

    NARCIS (Netherlands)

    van der Heijden, Franciëlla; Poortman, Anne Rigt; van der Lippe, Tanja

    2016-01-01

    Although the rise in postdivorce joint physical custody has fueled scholarly interest in its impact on children, consequences for parents remain understudied. Because children's residence arrangements determine time and coordination demands associated with child care, this study investigated the rel

  15. Parental Involvement

    OpenAIRE

    Ezra S Simon

    2008-01-01

    This study was conducted in Ghana to investigate, (1) factors that predict parental involvement, (2) the relationship between parental home and school involvement and the educational achievement of adolescents, (3) the relationship between parental authoritativeness and the educational achievement of adolescent students, (4) parental involvement serving as a mediator between their authoritativeness and the educational achievement of the students, and (5) whether parental involvement decreases...

  16. Arranging transient process used in iterative learning control system

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Considering the same initial state error in each repetitive operation in the iterative learning system, a method of arranging the transient process is given. During the current iteration, the system will track the transient function firstly, and then the expected trajectory. After several iterations, the learning system output will trend to the arranged curve, which has avoided the effect of the initial error on the controller. Also the transient time can be changed as you need, which makes the designing si...

  17. Contractual Arrangement and Marketing Practices in the Indirect Export Channel

    OpenAIRE

    Daniel C Bello; Nicholas C Williamson

    1985-01-01

    The association between contractual arrangement and the marketing practices of export intermediaries and domestic supplies is examined. Based on data collected from a national sample of export management companies, the effect of structuring the export arrangement as a contractual, administrative, or conventional channel is analyzed. Prior research suggests that contractual form establishes the framework within which all the economic and sociopolitical interactions between the supplier and exp...

  18. Modelling and arrangement of composite panels in modernized freight cars

    Directory of Open Access Journals (Sweden)

    Płaczek Marek

    2017-01-01

    Full Text Available A process of modelling in a CAD system and designing of arrangement of composite panels used for freight cars’ body shell protection against corrosion and for easier unloading of transported cargo in winter conditions is presented in this work. Arrangement of used composite panels was designing in order to fulfil assumed criteria and thus to improve the process of freight cars modernization during periodic repairs.

  19. Islamic versus conventional banking: A comparative analysis of financial arrangements

    OpenAIRE

    Marinković, Srđan

    2013-01-01

    The paper explores the concept of Islamic banking by making comparison between the basic features of some key conventional and Islamic financial arrangements. Paradigm version of Islamic banking forbids arrangements based on a predetermined rate of return on financial investments, instead it proposes equity based modes of finance which promote partnership between financier and an entrepreneur. Nevertheless, the theoretically suggested concepts in current practice are faced with serious diffic...

  20. Labour Arrangements in Cassava Production in Oyo State, Nigeria

    Directory of Open Access Journals (Sweden)

    Abila, N.

    2012-01-01

    Full Text Available The study examined the effects of labour arrangements on the profitability of cassava enterprises in Oyo North Area of Oyo State, Nigeria. A multi-stage sampling technique was adopted for data collection, while data were analysed using descriptive statistics and budgetary analysis. The results show that the prevalent labour arrangements for cassava enterprises are: a combination of Family, Hired and Contract labour (38.9%; Family-Hired labour (27.8%; Family-Contract labour (31.1%. The gross margin per hectares across labour arrangements are N279481.99 (all-labour, N286044.24 (family-hired, N216940.10 (familycontract, and N235000.00 (family only. The returns on a naira invested on variable costs across different labour arrangements for cassava enterprises are N2.04 (all-labour, N3.66 (family-hired, N2.37 (familycontract, and N2.61 (family only. This implies that a unit (N1 variable cost in the various labour arrangements of all-labour, family/hired, family/contract and family only in cassava production will yield a marginal return of N3.04, N3.66, N2.37 and N2.61 respectively. Family-hired labour arrangement yields higher marginal return per unit of manday and one naira spent than all other arrangements. The study recommends among others the application of laboursaving technologies and an optimum combination of various labour arrangements to reduce the cost of labour used in cassava production.

  1. Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

    Directory of Open Access Journals (Sweden)

    Ritland Carol

    2009-08-01

    Full Text Available Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs and full-length (FLcDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR and a cytochrome P450 (CYP720B4 from a non-arrayed genomic BAC library of white spruce (Picea glauca. Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR and 94 kbp (CYP720B4 long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs, high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene

  2. Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae.

    Science.gov (United States)

    Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

    2014-12-01

    Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

  3. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

    Science.gov (United States)

    Rong, Junkang; Bowers, John E.; Schulze, Stefan R.; Waghmare, Vijay N.; Rogers, Carl J.; Pierce, Gary J.; Zhang, Hua; Estill, James C.; Paterson, Andrew H.

    2005-01-01

    Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons (Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (α) in Arabidopsis. At least 59% of the cotton map and 53% of the Arabidopsis transcriptome showed correspondence in multilocus gene arrangements based on one or both of two software packages (CrimeStatII, FISH). Genomic regions in which chromosome structural rearrangement has been rapid (obscuring gene order correspondence) have also been subject to greater divergence of individual gene sequences. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes. PMID:16109973

  4. Governance arrangements for health systems in low-income countries: an overview of systematic reviews.

    Science.gov (United States)

    Herrera, Cristian A; Lewin, Simon; Paulsen, Elizabeth; Ciapponi, Agustín; Opiyo, Newton; Pantoja, Tomas; Rada, Gabriel; Wiysonge, Charles S; Bastías, Gabriel; Garcia Marti, Sebastian; Okwundu, Charles I; Peñaloza, Blanca; Oxman, Andrew D

    2017-09-12

    Governance arrangements include changes in rules or processes that determine authority and accountability for health policies, organisations, commercial products and health professionals, as well as the involvement of stakeholders in decision-making. Changes in governance arrangements can affect health and related goals in numerous ways, generally through changes in authority, accountability, openness, participation and coherence. A broad overview of the findings of systematic reviews can help policymakers, their technical support staff and other stakeholders to identify strategies for addressing problems and improving the governance of their health systems. To provide an overview of the available evidence from up-to-date systematic reviews about the effects of governance arrangements for health systems in low-income countries. Secondary objectives include identifying needs and priorities for future evaluations and systematic reviews on governance arrangements and informing refinements of the framework for governance arrangements outlined in the overview. We searched Health Systems Evidence in November 2010 and PDQ Evidence up to 17 December 2016 for systematic reviews. We did not apply any date, language or publication status limitations in the searches. We included well-conducted systematic reviews of studies that assessed the effects of governance arrangements on patient outcomes (health and health behaviours), the quality or utilisation of healthcare services, resource use (health expenditures, healthcare provider costs, out-of-pocket payments, cost-effectiveness), healthcare provider outcomes (such as sick leave), or social outcomes (such as poverty, employment) and that were published after April 2005. We excluded reviews with limitations that were important enough to compromise the reliability of the findings of the review. Two overview authors independently screened reviews, extracted data and assessed the certainty of evidence using GRADE. We prepared

  5. Modelling the development and arrangement of the primary vascular structure in plants.

    Science.gov (United States)

    Cartenì, Fabrizio; Giannino, Francesco; Schweingruber, Fritz Hans; Mazzoleni, Stefano

    2014-09-01

    The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive. This study presents a spatially explicit reaction-diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells. Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele). The results presented demonstrate, as a proof of concept, that a common genetic-molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues.

  6. DNA double-strand breaks alter the spatial arrangement of homologous loci in plant cells.

    Science.gov (United States)

    Hirakawa, Takeshi; Katagiri, Yohei; Ando, Tadashi; Matsunaga, Sachihiro

    2015-06-05

    Chromatin dynamics and arrangement are involved in many biological processes in nuclei of eukaryotes including plants. Plants have to respond rapidly to various environmental stimuli to achieve growth and development because they cannot move. It is assumed that the alteration of chromatin dynamics and arrangement support the response to these stimuli; however, there is little information in plants. In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO/LacI-EGFP system and simulation analysis. It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. These results suggest that homologous loci approach each other to repair DSBs, and AtRAD54 mediates these phenomena.

  7. Practices and material arrangements in urban planning - a practice theoretical perspective

    DEFF Research Database (Denmark)

    Buch, Anders; Harders, Anne Katrine Braagaard

    2016-01-01

    that the realization of visions is contingent on the involved practices and the prefiguration of the dominant practice architectures by material arrangements. It is the main argument of the paper, that by focusing on practices and material arrangements we can understand better what happens in urban development......A sustainable transition of our cities is more urgent than ever. For that reason, many urban development projects worldwide are assigned ambitious visions about contributing to the sustainable transition. However, it seems that the projects often lack ability to realize these visions...... and to actually contribute to a sustainable transition. On the contrary, the projects seem to strengthen the already unsustainable configuration of our cities. In this paper we will argue that there is no causal relationship between vision and reality in urban planning. With reference to a Schatzkian practice...

  8. Practices and material arrangements in urban planning - a practice theoretical perspective

    DEFF Research Database (Denmark)

    Buch, Anders; Harders, Anne Katrine Braagaard

    that the realization of visions is contingent on the involved practices and the prefiguration of the dominant practice architectures by material arrangements. It is the main argument of the paper, that by focusing on practices and material arrangements we can understand better what happens in urban development......A sustainable transition of our cities is more urgent than ever. For that reason, many urban development projects worldwide are assigned ambitious visions about contributing to the sustainable transition. However, it seems that the projects often lack ability to realize these visions...... and to actually contribute to a sustainable transition. On the contrary, the projects seem to strengthen the already unsustainable configuration of our cities. In this paper we will argue that there is no causal relationship between vision and reality in urban planning. With reference to a Schatzkian practice...

  9. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  10. AC losses in circular arrangements of parallel superconducting tapes

    DEFF Research Database (Denmark)

    Kühle (fratrådt), Anders Van Der Aa; Træholt, Chresten; Däumling, Manfred

    1998-01-01

    The DC and AC properties of superconducting tapes connected in parellel and arranged in a single closed layer on two tubes (correspondig to power cable models with infinite pitch) with different diameters are compared. We find that the DC properties, i.e. the critical currents of the two arrangem......The DC and AC properties of superconducting tapes connected in parellel and arranged in a single closed layer on two tubes (correspondig to power cable models with infinite pitch) with different diameters are compared. We find that the DC properties, i.e. the critical currents of the two...... arrangements, scale with the number of tapes and hence appear to be independent of the diameter.However, the AC loss per tape (for a given current per tape) appears to decrease with increasing diameter of the circular arrangement. Compared to a model for the AC loss in a continuous superconducting layer...... (Monoblock model) the measured values are about half an order of magnitude higher than expected for the small diameter arrangement. When compared to the AC loss calculated for N individual superconducting tapes using a well known model ( Norris elliptical) the difference is slightly smaller....

  11. BUTYRATE-MEDIATED GENOMIC CHANGES INVOLVED IN NON-SPECIFIC HOST DEFENSES, MATRIX REMODELING AND THE IMMUNE RESPONSE IN THE RUMEN EPITHELIUM OF COWS AFFLICTED WITH SUBACUTE RUMINAL ACIDOSIS

    Directory of Open Access Journals (Sweden)

    Louis Dionissopoulos

    2013-01-01

    Full Text Available Subacute Ruminal Acidosis (SARA is a disorder in cattle which can lead to chronic inflammation in the rumen epithelium, known as rumenitis. Butyrate has been shown to attenuate some of the detrimental effects of inflammatory gastroenteral disorders but the molecular mechanisms mediated by butyrate have not been defined. The objective of this study was to define the inflammatory-related genomic changes responsible for the beneficial effects of butyrate. Experimentally, 16 fistulated dairy cows at mid-lactation were fed a SARA-inducing (45% non-fiber carbohydrate diet beginning 2 days before the beginning of treatment and continuing throughout the experiment. Cows were then evenly divided into treatment groups where a carrier with (n = 8 or without (n = 8 supplemental butyrate (2.5% initial DM intake was deposited into the rumen daily for 7 days. The minimum rumen pH was higher in cows with supplemental butyrate (4.96±0.09 to 5.20±0.05, p = 0.040, but mean pH, maximum pH and the duration for which rumen pH was below 5.6 was unaffected. Free plasma Lipopolysaccharide (LPS concentration was unaffected by treatment as was the concentration of Serum Amyloid A (SAA, although the LPS Binding Protein (LBP concentration was increased by the addition of butyrate to the rumen (6.91±0.29 to 7.93±0.29 μg mL-1, p = 0.024. Of the rumen Short Chain Fatty Acids (SCFA tested, only butyrate showed a pronounced treatment effect, rising from 8.60±0.94 to 21.60±0.94 mM (p≤0.0001. Plasma Beta-Hydroxybutyrate (BHBA concentration also increased (799.50±265.24 to 3261.63±265.24 μM, p≤0.001. Butyrate infusion did not affect milk parameters (total fat, lactose, total protein and LOS; however, when related to dry matter intake, milk production efficiency was increased (p = 0.035. Microarray and qRT-PCR analyses of rumen papillae biopsies collected on day 7 found that butyrate administration affected (p≤0.05 the expression of genes

  12. Inverse design of LED arrangement for visible light communication systems

    Science.gov (United States)

    Zheng, Huanhuan; Chen, Jian; Yu, Changyuan; Gurusamy, Mohan

    2017-01-01

    In this paper, an optimal LED arrangement for indoor visible light communications (VLC) is proposed and numerically investigated. By using the concept of inverse design, the LED distribution can be formulated as a convex optimization problem and resolved accordingly. We show that sufficient brightness and uniform signal to noise ratio (SNR) can be achieved within the indoor coverage by using the proposed optimal LED arrangement, thus enabling the terminal mobility for indoor VLC. In addition, the analysis of delay spread distribution over the receiving plane shows that the design exhibits enhanced tolerance of inter-symbol interference (ISI). With the consideration of cabling cost for practical implementation, the suboptimal LED arrangement design is also investigated. Numerical results indicate that the suboptimal design can reduce the power consumption of the system with acceptable performance degradation.

  13. Do organizational and political-legal arrangements explain financial wrongdoing?

    Science.gov (United States)

    Prechel, Harland; Zheng, Lu

    2016-12-01

    The 2008 financial crisis was a systemic problem with deep-rooted structural causes that created opportunities to engage in financial malfeasance, a form of corporate wrongdoing. However, few quantitative studies exist on the effects of organizational and political-legal arrangements on financial malfeasance. In this paper, we examine the effects of organizational and political-legal arrangements that emerged in the 1990s in the FIRE sector (i.e., financial, insurance, and real estate) on financial malfeasance. Our historical contextualization demonstrates how changes in the political-legal arrangements facilitate the emergence of new corporate structures and opportunities for financial malfeasance. Our longitudinal quantitative analysis demonstrates that US FIRE sector corporations with a more complex organizational structure, larger size, lower dividend payment, and higher executive compensation are more prone to commit financial malfeasance. © London School of Economics and Political Science 2016.

  14. Orientations of linear stone arrangements in New South Wales

    CERN Document Server

    Hamacher, Duane W; Norris, Ray P

    2012-01-01

    We test the hypothesis that Aboriginal linear stone arrangements in New South Wales (NSW) are oriented to cardinal directions. We accomplish this by measuring the azimuths of stone arrangements described in site cards from the NSW Aboriginal Heritage Information Management System. We then survey a subset of these sites to test the accuracy of information recorded on the site cards. We find a preference recorded in the site cards for cardinal orientations among azimuths. The field surveys show that the site cards are reasonably accurate, but the surveyors probably did not correct for magnetic declinations. Using Monte Carlo statistics, we show that these preferred orientations did not occur by chance and that Aboriginal people deliberately aligned these arrangements to the approximate cardinal directions. We briefly explore possible reasons for these preferred orientations and highlight the need for future work.

  15. [Analysis of cell arrangements in Biota orientalis using Fourier transformation].

    Science.gov (United States)

    Duo, Hua-Qiong; Wang, Xi-Ming

    2009-10-01

    Fourier transform image-processing technology is applied for determining the cross section cell arrangement of early-wood in Biota orientalis. In this method, the disc-convoluted dot map from each cell radius with 10 pixels is transformed by Fourier transform, generating the angle distribution function in the power spectral pattern. The maximum value is the arrangement of the cell. The results of Fourier transform image-processing technology indicated that the arrangements of the cell of Biota orientalis are 15 degrees in oblique direction, respectively. This method provides a new basis for the digitized identification of the wood, and also the new theoretical research direction for the digitized identification and examination of the wood species.

  16. Genomics, Obesity and the Struggle over Responsibilities

    NARCIS (Netherlands)

    Korthals, M.J.J.A.A.

    2011-01-01

    This volume addresses the overlapping aspects of the fields of genomics, obesity and (non- ) medical ethics. It is unique in its examination of the implications of genomics for obesity from an ethical perspective. Genomics covers the sciences and technologies involved in the pathways that DNA takes

  17. 29 CFR 779.228 - Types of arrangements contemplated by exception.

    Science.gov (United States)

    2010-07-01

    ... Coverage Leased Departments, Franchise and Other Business Arrangements § 779.228 Types of arrangements... section 3(s) would not otherwise apply: (a) Any arrangement, whether by agreement, franchise or...

  18. Comparative Microbial Genomics and Forensics.

    Science.gov (United States)

    Massey, Steven E

    2016-08-01

    Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

  19. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  20. Developing physician pay arrangements: the cash and care equation.

    Science.gov (United States)

    Levitch, J H

    1998-11-01

    Developing physician compensation packages that help a healthcare organization meet its business objectives while satisfying physician pay expectations requires new ways of linking pay to physician performance. Such compensation arrangements specifically should include pay tied to defined performance standards, compensation linked to group performance, performance incentives based on realistic, achievable goals, work performance measured by common criteria, and similar pay ensured for similar work. Final pay arrangements also should include items that are sometimes overlooked, such as fully delineated job responsibilities, performance measures aligned correctly with performance areas, and the value of benefits considered in the cash compensation levels.

  1. Inorganic arrangement crystal beryllium, lithium, selenium and silicon

    CERN Document Server

    Gobato, Ricardo; Fedrigo, Desire Francine Gobato

    2015-01-01

    The use of inorganic crystals technology has been widely date. Since quartz crystals for watches in the nineteenth century, and common way radio in the early twentieth century, to computer chips with new semiconductor materials. Chemical elements such as beryllium, lithium, selenium and silicon, are widely used in technology. The development of new crystals arising from that arrangement can bring technological advances in several areas of knowledge. The likely difficulty of finding such crystals in nature or synthesized, suggest an advanced study of the subject. A study using computer programs with ab initio method was applied. As a result of the likely molecular structure of the arrangement of a crystal was obtained.

  2. Ladder Arrangement Method for Stealth Design of Vivaldi Antenna Array

    Directory of Open Access Journals (Sweden)

    XiaoXiang He

    2013-01-01

    Full Text Available A novel stealth design method for X-band Vivaldi antenna arrays is proposed in this paper by ladder arrangement along radiation direction. Two-element array, eight-element array, and 3 × 7-element array are investigated in this paper. S parameters, RCSs, and radiation patterns are studied, respectively. According to the ladder arrangement of Vivaldi antennas presented, 16.3 dBsm maximal RCS reduction is achieved with satisfied radiation performance. As simulated and measured, results demonstrate that the effectiveness of the presented low RCS design method is validated.

  3. Linking better shiftwork arrangements with safety and health management systems

    Directory of Open Access Journals (Sweden)

    Kazutaka Kogi

    2004-12-01

    Full Text Available OBJECTIVE: Various support measures useful for promoting joint change approaches to the improvement of both shiftworking arrangements and safety and health management systems were reviewed. A particular focus was placed on enterprise-level risk reduction measures linking working hours and management systems. METHODS: Voluntary industry-based guidelines on night and shift work for department stores and the chemical, automobile and electrical equipment industries were examined. Survey results that had led to the compilation of practicable measures to be included in these guidelines were also examined. The common support measures were then compared with ergonomic checkpoints for plant maintenance work involving irregular nightshifts. On the basis of this analysis, a new night and shift work checklist was designed. RESULTS: Both the guidelines and the plant maintenance work checkpoints were found to commonly cover multiple issues including work schedules and various job-related risks. This close link between shiftwork arrangements and risk management was important as shiftworkers in these industries considered teamwork and welfare services to be essential for managing risks associated with night and shift work. Four areas found suitable for participatory improvement by managers and workers were work schedules, ergonomic work tasks, work environment and training. The checklist designed to facilitate participatory change processes covered all these areas. CONCLUSIONS: The checklist developed to describe feasible workplace actions was suitable for integration with comprehensive safety and health management systems and offered valuable opportunities for improving working time arrangements and job content together.OBJETIVOS: Foram revisados diversas medidas de apoio úteis para incentivar abordagens conjuntas para a melhoria na organização do trabalho por turnos e os processos de gestão de saúde e segurança. As medidas para redução de risco em n

  4. Diffeomorphic types of complements of nice point arrangements in CP~l

    Institute of Scientific and Technical Information of China (English)

    YAU Stephen S.-T.; YE Fei

    2009-01-01

    We use a new method to study arrangement in CP~l,define a class of nice point arrangements and show that if two nice point arrangements have the same combinatorics,then their complements are diffeomorphic to each other. In particular,the moduli space of nice point arrangements with same combinatorics in CP~l is connected. It generalizes the result on point arrangements in CP~3 to point arrangements in CP~l for any l.

  5. Diffeomorphic types of complements of nice point arrangements in CP~l

    Institute of Scientific and Technical Information of China (English)

    YAU; Stephen; S.-T.

    2009-01-01

    We use a new method to study arrangement in CPl,define a class of nice point arrangements and show that if two nice point arrangements have the same combinatorics,then their complements are diffeomorphic to each other.In particular,the moduli space of nice point arrangements with same combinatorics in CPl is connected.It generalizes the result on point arrangements in CP3 to point arrangements in CPl for any l.

  6. Domestication genomics: evidence from animals.

    Science.gov (United States)

    Wang, Guo-Dong; Xie, Hai-Bing; Peng, Min-Sheng; Irwin, David; Zhang, Ya-Ping

    2014-02-01

    Animal domestication has far-reaching significance for human society. The sequenced genomes of domesticated animals provide critical resources for understanding the genetic basis of domestication. Various genomic analyses have shed a new light on the mechanism of artificial selection and have allowed the mapping of genes involved in important domestication traits. Here, we summarize the published genomes of domesticated animals that have been generated over the past decade, as well as their origins, from a phylogenomic point of view. This review provides a general description of the genomic features encountered under a two-stage domestication process. We also introduce recent findings for domestication traits based on results from genome-wide association studies and selective-sweep scans for artificially selected genomic regions. Particular attention is paid to issues relating to the costs of domestication and the convergent evolution of genes between domesticated animals and humans.

  7. Frontex Working Arrangements: Legitimacy and Human Rights Concerns Regarding ‘Technical Relationships’

    Directory of Open Access Journals (Sweden)

    Melanie Fink

    2012-06-01

    Full Text Available Practices of extraterritorialisation have become cornerstones of the European Union member states' border control. Most of them are highly dependent on the willingness of third countries to cooperate. An increasingly important phenomenon is that cooperation is secured through relationships established by administrative authorities. This article deals with the challenges arising from the active engagement of Frontex in setting up cooperation structures.It is argued that the so-called working arrangements concluded between Frontex and the respective authorities of third countries, in their current form, show considerable deficiencies from the perspectives of the rule of law, democracy and human rights protection. They are not open to judicial review, the Parliament is not involved in their conclusion and they are not disclosed to the public. Furthermore, the human rights record of cooperating authorities is not considered. Concerns in this respect are frequently attempted to be dispelled by recourse to the 'technical' as opposed to 'political' nature of working arrangements. Likewise, it is assumed that merely 'technical relationships' cannot affect individuals. These arguments are not convincing. Quite the contrary, the political implications of working arrangements and their operation in a highly human rights sensitive field demand conformity with the fundamental values the European Union is based on.

  8. Mitochondrial genome of Micrura bella (Nemertea: Heteronemertea), the largest mitochondrial genome known to phylum Nemertea.

    Science.gov (United States)

    Shen, Chunyang; Shi-Chun, Sun

    2016-07-01

    The complete mitochondrial genome (mitogenome) of Micrura bella was sequenced and analyzed. Being the largest mitogenome known to phylum Nemertea, the genome is 16 847 bp in length. It encodes 37 genes typical to metazoan mitogenomes and has the same gene arrangement with the other Heteronemertea mitogenomes sequenced to date. The genome has the maximal number of non-coding nucleotides (2037 bp at 25 sites) in Nemertea mitogenomes, among which two large non-coding regions were found (507 and 508 bp, respectively).

  9. Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

    KAUST Repository

    Graham, Kenneth

    2014-07-09

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

  10. Importance of the donor:fullerene intermolecular arrangement for high-efficiency organic photovoltaics.

    Science.gov (United States)

    Graham, Kenneth R; Cabanetos, Clement; Jahnke, Justin P; Idso, Matthew N; El Labban, Abdulrahman; Ngongang Ndjawa, Guy O; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F; Amassian, Aram; Beaujuge, Pierre M; McGehee, Michael D

    2014-07-09

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b']dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) (13)C{(1)H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material

  11. 33 CFR 157.11 - Pumping, piping and discharge arrangements.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Pumping, piping and discharge... CARRYING OIL IN BULK Design, Equipment, and Installation § 157.11 Pumping, piping and discharge arrangements. (a) Each tank vessel must have a fixed piping system for transferring oily mixtures from...

  12. 29 CFR 780.126 - Contract arrangements for raising poultry.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Contract arrangements for raising poultry. 780.126 Section 780.126 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR STATEMENTS OF GENERAL POLICY OR INTERPRETATION NOT DIRECTLY RELATED TO REGULATIONS EXEMPTIONS APPLICABLE TO AGRICULTURE, PROCESSING OF AGRICULTURAL...

  13. Parents' experiences of flexible work arrangements in changing European workplaces

    NARCIS (Netherlands)

    S. Lewis (Suzan); L. den Dulk (Laura)

    2009-01-01

    textabstractVarious leaves and other forms of flexible working arrangements have been implemented in workplaces to support employees with family commitments. Some are a response to public policy, others developed voluntarily. However, research examining the effectiveness of these policies in a searc

  14. Arrangement of library materials models in Slovene public libraries

    Directory of Open Access Journals (Sweden)

    Marija Kobal

    2009-01-01

    Full Text Available The classification and the alignment of library material represent an important part of the library science from its early beginnings onwards. The introduction of UDC into Slovene public libraries coincided with the alteration of the open access library collection.In Slovenia the public libraries in average take into account the references and recommendations for the arrangement of the free access library collection, considering the age groups of the users, adults and juniors. The next division is connected with the functional type of the material, which is divided into fiction, and scientific material,and then there is the UDC label for the arrangement of the material on the shelves or word systematic in one of the public libraries. In the junior department there is a need for a further division into four age/reading groups of books instead of three.Within the formed groups there is the further arrangement of books in an alphabetical order by means of author or subject headings. The public library is a unit, which services all the residents in its local area. The different needs and interests of users should take into account in the formation of a library material arrangement.

  15. Flexible Work Arrangements: Accessibility in a University Environment

    Science.gov (United States)

    Sharafizad, Fleur; Paull, Megan; Omari, Maryam

    2011-01-01

    Attraction and retention of highly qualified employees has become an area of concern for Australian universities. It has been suggested that flexible work arrangements can be utilised to achieve this goal once the factors affecting their uptake have been identified. This mixed-method study of 495 academic and general staff at an Australian…

  16. A taxonomy of management challenges for developing shared services arrangements

    NARCIS (Netherlands)

    Knol, A.J.; Janssen, M.F.W.H.A.; Sol, H.G.

    Shared service centres (SSCs) are an organisational arrangement to deliver services. During SSC development organisations encounter a variety of challenges affecting its success or failure. Yet in this embryonic research field a systematic insight into management challenges is absent. Drawing on

  17. Arrangement of collagen fibers in human placental stem villi

    NARCIS (Netherlands)

    Sati, Leyla; Demir, Ayse Yasemin; Sarikcioglu, Levent; Demir, Ramazan

    2008-01-01

    The aim of the study was to investigate the arrangements and related localization patterns of different collagen types in the stroma of placental stem villi by immunohistochemistry and electron microscopy. A total of 14 normal human term placental tissue samples were studied. Immunohistochemistry wa

  18. Arrangement of collagen fibers in human placental stem villi

    NARCIS (Netherlands)

    Sati, Leyla; Demir, Ayse Yasemin; Sarikcioglu, Levent; Demir, Ramazan

    2008-01-01

    The aim of the study was to investigate the arrangements and related localization patterns of different collagen types in the stroma of placental stem villi by immunohistochemistry and electron microscopy. A total of 14 normal human term placental tissue samples were studied. Immunohistochemistry

  19. Leaf arrangements are invalid in the taxonomy of orchid species

    Directory of Open Access Journals (Sweden)

    Anna Jakubska-Busse

    2017-07-01

    Full Text Available The selection and validation of proper distinguishing characters are of crucial importance in taxonomic revisions. The modern classifications of orchids utilize the molecular tools, but still the selection and identification of the material used in these studies is for the most part related to general species morphology. One of the vegetative characters quoted in orchid manuals is leaf arrangement. However, phyllotactic diversity and ontogenetic changeability have not been analysed in detail in reference to particular taxonomic groups. Therefore, we evaluated the usefulness of leaf arrangements in the taxonomy of the genus Epipactis Zinn, 1757. Typical leaf arrangements in shoots of this genus are described as distichous or spiral. However, in the course of field research and screening of herbarium materials, we indisputably disproved the presence of distichous phyllotaxis in the species Epipactis purpurata Sm. and confirmed the spiral Fibonacci pattern as the dominant leaf arrangement. In addition, detailed analyses revealed the presence of atypical decussate phyllotaxis in this species, as well as demonstrated the ontogenetic formation of pseudowhorls. These findings confirm ontogenetic variability and plasticity in E. purpurata. Our results are discussed in the context of their significance in delimitations of complex taxa within the genus Epipactis.

  20. Love Matches and Arranged Marriages: A Chinese Replication.

    Science.gov (United States)

    Xiaohe, Xu; Whyte, Martin King

    1990-01-01

    Partially replicated Japanese study by examining transition from arranged to free-choice marriages in Chinese ever-married women (n=586). The results revealed that the role of parents had declined sharply, whereas young people more and more dominated the process of mate selection. However there was still little sign of a "dating culture" emerging.…

  1. Spatial Arrangement in Texture Discrimination and Texture Segregation

    Directory of Open Access Journals (Sweden)

    Kathleen Vancleef

    2013-02-01

    Full Text Available We investigated the role of spatial arrangement of texture elements in three psychophysical experiments on texture discrimination and texture segregation. In our stimuli, oriented Gabor elements formed an iso-oriented and a randomly oriented texture region. We manipulated (1 the orientation similarity in the iso-oriented region by adding orientation jitter to the orientation of each Gabor; (2 the spatial arrangement of the Gabors: quasi-random or regular; and (3 the shape of the edge between the two texture regions: straight or curved. In Experiment 1, participants discriminated an iso-oriented stimulus from a stimulus with only randomly oriented elements. Experiment 2 required texture segregation to judge the shape of the texture edge. Experiment 3 replicated Experiment 2 with Gabors of a smaller spatial extent in a denser arrangement. We found comparable performance levels with regular and quasi-random Gabor positions in the discrimination task but not in the segregation tasks. We conclude that spatial arrangement plays a role in a texture segregation task requiring shape discrimination of the texture edge but not in a texture discrimination task in which it is sufficient to discriminate an iso-oriented region from a completely random region.

  2. 40 CFR 265.37 - Arrangements with local authorities.

    Science.gov (United States)

    2010-07-01

    ... (4) Arrangements to familiarize local hospitals with the properties of hazardous waste handled at the.... 265.37 Section 265.37 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) INTERIM STATUS STANDARDS FOR OWNERS AND OPERATORS OF HAZARDOUS WASTE...

  3. BEPS Action 2: Neutralizing the Effects on Hybrid Mismatch Arrangements

    NARCIS (Netherlands)

    de Boer, R.; Marres, O.

    2015-01-01

    Curbing tax arbitrage is one of the main priorities of the Organization for Economic Cooperation and Development (OECD) (endorsed by the G20 and the G8) ever since the public debate on base erosion fully erupted. Neutralizing the effect of hybrid mismatch arrangements has become Action No. 2 of the

  4. Accountability after Structural Disaggregation: Comparing Agency Accountability Arrangements

    NARCIS (Netherlands)

    Overman, Sjors; Van Genugten, Marieke; Van Thiel, Sandra

    2015-01-01

    New accountability instruments – performance indicators, audits, and financial incentives – are expected to replace traditional accountability instruments in NPM reforms. We test this expectation by looking at the accountability arrangements of semi-autonomous agencies as a typical example of NPM re

  5. Interfacial re-arrangement in initial microbial adhesion to surfaces

    NARCIS (Netherlands)

    Busscher, Henk J.; Norde, Willem; Sharma, Prashant K.; van der Mei, Henny C.

    2010-01-01

    Upon initial microbial adhesion to a surface multiple events occur that include interfacial re-arrangements in the region between an adhering organism and a surface Application of physico-chemical mechanisms to explain microbial adhesion to surfaces requires better knowledge of the interfacial re ar

  6. 46 CFR 199.145 - Marine evacuation system launching arrangements.

    Science.gov (United States)

    2010-10-01

    ...; (2) So it is capable of individual release from its stowage rack; (3) In accordance with the... and if necessary, is capable of being adjusted to the position required for evacuation. (b) Stowage... and platform, when deployed; its stowage container; and its operational arrangement must not...

  7. 46 CFR 108.545 - Marine evacuation system launching arrangements.

    Science.gov (United States)

    2010-10-01

    ... capable of individual release from its stowage rack. (3) Each inflatable liferaft used in conjunction with...) Stowage. Each marine evacuation system must be stowed as follows: (1) There must not be any openings..., when deployed, its stowage container, and its operational arrangement must not interfere with...

  8. 46 CFR 133.145 - Marine evacuation system launching arrangements.

    Science.gov (United States)

    2010-10-01

    ... individual release from its stowage rack. (3) Each inflatable liferaft used in conjunction with the marine... evacuation. (b) Stowage. Each marine evacuation system must be stowed as follows: (1) There must not be any... deployed; its stowage container; and its operational arrangement must not interfere with the operation...

  9. A taxonomy of management challenges for developing shared services arrangements

    NARCIS (Netherlands)

    Knol, A.J.; Janssen, M.F.W.H.A.; Sol, H.G.

    2014-01-01

    Shared service centres (SSCs) are an organisational arrangement to deliver services. During SSC development organisations encounter a variety of challenges affecting its success or failure. Yet in this embryonic research field a systematic insight into management challenges is absent. Drawing on lit

  10. 26 CFR 1.881-3 - Conduit financing arrangements.

    Science.gov (United States)

    2010-04-01

    ... satisfaction of a repayment obligation is not an advance of money or other property. A financing arrangement... anticipated decline in the value of the property over its life. (2) Rate of tax. The rate at which tax is... the installment notes for FS. (ii) The C installment note now held by FS (as well as all of the...

  11. BEPS Action 2: Neutralizing the Effects on Hybrid Mismatch Arrangements

    NARCIS (Netherlands)

    de Boer, R.; Marres, O.

    2015-01-01

    Curbing tax arbitrage is one of the main priorities of the Organization for Economic Cooperation and Development (OECD) (endorsed by the G20 and the G8) ever since the public debate on base erosion fully erupted. Neutralizing the effect of hybrid mismatch arrangements has become Action No. 2 of the

  12. Comparative genome analysis of wheat blue dwarf phytoplasma, an obligate pathogen that causes wheat blue dwarf disease in China.

    Directory of Open Access Journals (Sweden)

    Wang Chen

    Full Text Available Wheat blue dwarf (WBD disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, de novo assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on

  13. Hexahedral mesh generation via the dual arrangement of surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, S.A.; Tautges, T.J. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    Given a general three-dimensional geometry with a prescribed quadrilateral surface mesh, the authors consider the problem of constructing a hexahedral mesh of the geometry whose boundary is exactly the prescribed surface mesh. Due to the specialized topology of hexahedra, this problem is more difficult than the analogous one for tetrahedra. Folklore has maintained that a surface mesh must have a constrained structure in order for there to exist a compatible hexahedral mesh. However, they have proof that a surface mesh need only satisfy mild parity conditions, depending on the topology of the three-dimensional geometry, for there to exist a compatible hexahedral mesh. The proof is based on the realization that a hexahedral mesh is dual to an arrangement of surfaces, and the quadrilateral surface mesh is dual to the arrangement of curves bounding these surfaces. The proof is constructive and they are currently developing an algorithm called Whisker Weaving (WW) that mirrors the proof steps. Given the bounding curves, WW builds the topological structure of an arrangement of surfaces having those curves as its boundary. WW progresses in an advancing front manner. Certain local rules are applied to avoid structures that lead to poor mesh quality. Also, after the arrangement is constructed, additional surfaces are inserted to separate features, so e.g., no two hexahedra share more than one quadrilateral face. The algorithm has generated meshes for certain non-trivial problems, but is currently unreliable. The authors are exploring strategies for consistently selecting which portion of the surface arrangement to advance based on the existence proof. This should lead us to a robust algorithm for arbitrary geometries and surface meshes.

  14. Community involvement

    Directory of Open Access Journals (Sweden)

    Editorial Office

    1979-09-01

    Full Text Available Community involvement is the main theme of Health Year. Governments have a responsibility for the health of their people, and in this country under the present 3-tier system of government, the responsibility for the rendering of health services is divided between central, provincial and local government. However, under our democratic system, all people have the right to, and it is indeed their duty, to participate individually and collectively in the planning and implementation of services to meet their health needs. Ultimately, through involvement of individuals, families and communities, greater self-reliance is achieved leading to greater responsibility being assumed by people for their own health.

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

    Science.gov (United States)

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

    2012-05-01

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

  16. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  17. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  18. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

    OpenAIRE

    Page, Justin T.; Huynh, Mark D; Zach S Liechty; Grupp, Kara; Stelly, David; Hulse, Amanda M; Ashrafi, Hamid; Van Deynze, Allen; Wendel, Jonathan F.; Udall, Joshua A.

    2013-01-01

    Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium ra...

  19. Effects of Magnetic Particles Entrance Arrange-ments on Mixing Efficiency of a Magnetic Bead Micromixer

    Institute of Scientific and Technical Information of China (English)

    Reza Kamali∗; Seyed Alireza Shekoohi; Alireza Binesh

    2014-01-01

    In this study, a computer code is developed to numerically investigate a magnetic bead micromixer under different conditions. The micromixer consists of a microchannel and numerous micro magnetic particles which enter the micromixer by fluid flows and are actuated by an alternating magnetic field normal to the main flow. An important feature of micromixer which is not considered before by researchers is the particle entrance arrangement into the micromixer. This parameter could effectively affect the micromixer efficiency. There are two general micro magnetic particle entrance arrangements in magnetic bead micromixers: determined position entrance and random position entrance. In the case of determined position entrances, micro magnetic particles enter the micromixer at specific positions of entrance cross section. However, in a random position entrance, particles enter the microchannel with no order. In this study mixing efficiencies of identical magnetic bead micromixers which only differ in particle entrance arrangement are numerically investigated and compared. The results reported in this paper illustrate that the prepared computer code can be one of the most powerful and beneficial tools for the magnetic bead micromixer performance analysis. In addition, the results show that some features of the magnetic bead micromixer are strongly affected by the entrance arrangement of the particles.

  20. Herbarium genomics

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  1. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Directory of Open Access Journals (Sweden)

    Wim Degrave

    1997-11-01

    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  2. From the double-helix to novel approaches to the sequencing of large genomes.

    Science.gov (United States)

    Szybalski, W

    1993-12-15

    Elucidation of the structure of DNA by Watson and Crick [Nature 171 (1953) 737-738] has led to many crucial molecular experiments, including studies on DNA replication, transcription, physical mapping, and most recently to serious attempts directed toward the sequencing of large genomes [Watson, Science 248 (1990) 44-49]. I am totally convinced of the great importance of the Human Genome Project, and toward achieving this goal I strongly favor 'top-down' approaches consisting of the physical mapping and preparation of contiguous 50-100-kb fragments directly from the genome, followed by their automated sequencing based on the rapid assembly of primers by hexamer ligation together with primer walking. Our 'top-down' procedures totally avoids conventional cloning, subcloning and random sequencing, which are the elements of the present 'bottom-up' procedures. Fragments of 50-100 kb are prepared in sufficient quantities either by in vitro excision with rare-cutting restriction systems (including Achilles' heel cleavage [AC] or the RecA-AC procedures of Koob et al. [Nucleic Acids Res. 20 (1992) 5831-5836]) or by in vivo excision and amplification using the yeast FRT/Flp system or the phage lambda att/Int system. Such fragments, when derived directly from the Escherichia coli genome, are arranged in consecutive order, so that 50 specially constructed strains of E. coli would supply 50 end-to-end arranged approx. 100-kb fragments, which will cover the entire approx. 5-Mb E. coli genome. For the 150-Mb Drosophila melanogaster genome, 1500 of such consecutive 100-kb fragments (supplied by 1500 strains) are required to cover the entire genome. The fragments will be sequenced by the SPEL-6 method involving hexamer ligation [Szybalski, Gene 90 (1990) 177-178; Fresenius J. Anal. Chem. 4 (1992) 343] and primer walking. The 18-mer primers are synthesized in only a few minutes from three contiguous hexamers annealed to the DNA strand to be sequenced when using an over 100-fold

  3. Quantum Integrable Model of an Arrangement of Hyperplanes

    Directory of Open Access Journals (Sweden)

    Alexander Varchenko

    2011-03-01

    Full Text Available The goal of this paper is to give a geometric construction of the Bethe algebra (of Hamiltonians of a Gaudin model associated to a simple Lie algebra. More precisely, in this paper a quantum integrable model is assigned to a weighted arrangement of affine hyperplanes. We show (under certain assumptions that the algebra of Hamiltonians of the model is isomorphic to the algebra of functions on the critical set of the corresponding master function. For a discriminantal arrangement we show (under certain assumptions that the symmetric part of the algebra of Hamiltonians is isomorphic to the Bethe algebra of the corresponding Gaudin model. It is expected that this correspondence holds in general (without the assumptions. As a byproduct of constructions we show that in a Gaudin model (associated to an arbitrary simple Lie algebra, the Bethe vector, corresponding to an isolated critical point of the master function, is nonzero.

  4. Experimental arrangement to measure dispersion in optical fiber devices

    Energy Technology Data Exchange (ETDEWEB)

    Armas Rivera, Ivan [Benemerita Universidad Autonoma de Puebla, Facultad de Ciencias de la Electronica (Mexico); Beltran Perez, Georgina; Castillo Mixcoatl, Juan; Munoz Aguirre, Severino [Benemerita Universidad Autonoma de Puebla, Facultad de Ciencias Fisico Matematicas (Mexico); Zaca Moran, Placido, E-mail: ivan_rr1@hotmail.com [Benemerita Universidad Autonoma de Puebla, Fisicoquimica de Materiales ICUAP (Mexico)

    2011-01-01

    Dispersion is a quite important parameter in systems based on optical fiber, especially in pulsed emission lasers, where the temporal width is affected by such parameter. Therefore, it is necessary to consider the dispersion provoked by each component in the cavity. There are various experimental interferometric arrangements to evaluate this parameter. Generally, these systems modify the wavelength to obtain information about the n({lambda}) dependency, which is contained in the interferogram phase. However, this makes the system quite slow and it requires tunable and narrow bandwidth laser sources. In the present work, results obtained from an arrangement based on Mach-Zehnder interferometer where one of the arms is the optical fiber under study, while the reference one is air, are presented. In order to determine the n({lambda}) dependency, a wide spectrum light source was used in the wavelength range of interest. The phase information was evaluated from the interferometric signal measured by an optical spectrum analyzer.

  5. Innovative Nuclear Power Plant Building Arrangement in Consideration of Decommissioning

    Directory of Open Access Journals (Sweden)

    Won-Jun Choi

    2017-04-01

    Full Text Available A new concept termed the Innovative Nuclear Power Plant Building Arrangement (INBA strategy is a new nuclear power plant building arrangement method which encompasses upfront consideration of more efficient decommissioning. Although existing decommissioning strategies such as immediate dismantling and differed dismantling has the advantage of either early site restoration or radioactive decommissioning waste reduction, the INBA strategy has the advantages of both strategies. In this research paper, the concept and the implementation method of the INBA strategy will be described. Two primary benefits will be further described: (1 early site restoration; and (2 radioactive waste reduction. Several other potential benefits will also be identified. For the estimation of economic benefit, the INBA strategy, with two primary benefits, will be compared with the immediate dismantling strategy. The effect of a short life cycle nuclear power plant in combination with the INBA strategy will be reviewed. Finally, some of the major impediments to the realization of this strategy will be discussed.

  6. Control arrangement for the actuation of hydraulic consumers

    Energy Technology Data Exchange (ETDEWEB)

    Kussel, W.; Dettmers, M.; Weirich, W.

    1988-11-09

    An arrangement for controlling the actuation of hydraulic consumers, by selectively connecting the consumers to hydraulic pressure and return lines; the control arrangement comprising a respective hydraulically operated directional control valve associated with each of the hydraulic consumers, a respective electro-magnetically operated pre-control valve associated with each of the hydraulic directional control valves, and further electro-magnetically operated directional control valve means associated with the pre-control valves, each of the hydraulic consumers being connectible to the hydraulic pressure or return lines via the associated hydraulically operated directional control valve which is actuatable by a hydraulic control line leading from the output of the associated pre-control valve, wherein the inputs of the pre-control valves are connected directly to the hydraulic return line and indirectly, via the further control valve means, to the hydraulic return line or to a hydraulic control pressure line.

  7. Reactive Scattering Wave Functions by Linear Combination of Arrangement Channels

    Institute of Scientific and Technical Information of China (English)

    邓从豪; 冯大诚; 蔡政亭

    1994-01-01

    The similarity and dissimilarity of reactive scattering wave functions and molecular orbitalby linear combination of atomic orbitals(LCAOMO)are examined.Based on the similarity a method is pro-posed to construct the reactive scattering wave functions by linear combination of arrangement channel wavefunctions(LCACSW).Based on the dissimilarity,it is shown that the combination coefficients can be deter-mined by solving s set of simultaneous algebraic equations.The elements of the reactive scattering matrix areshown to be related to the combination coefficients of open arrangement channels.The differential and totalreactive scattering cross-section derived by this method agrees completely with that derived by other meth-ods.

  8. On the topology of the world exchange arrangements web

    Science.gov (United States)

    Li, Xiang; Jin, Yu Ying; Chen, Guanrong

    2004-11-01

    Exchange arrangements among different countries over the world are foundations of the world economy, which generally stand behind the daily economic evolution. As the first study of the world exchange arrangements web (WEAW), we built a bipartite network with countries as one type of nodes and currencies as the other, and found it to have a prominent scale-free feature with a power-law degree distribution. In a further empirical study of the currency section of the WEAW, we calculated the clustering coefficients, average nearest-neighbors degree, and average shortest distance. As an essential economic network, the WEAW is found to be a correlated disassortative network with a hierarchical structure, possessing a more prominent scale-free feature than the world trade web (WTW).

  9. On the topology of the world exchange arrangements web

    CERN Document Server

    Chen, X L

    2004-01-01

    Exchange arrangements among different countries over the world are foundations of the world economy, which generally stand behind the daily economic evolution. As the first study of the world exchange arrangements web (WEAW), we built a bipartite network with countries as one type of nodes and currencies as the other, and found it to have a prominent scale-free feature with a power-law degree distribution. In a further empirical study of the currency section of the WEAW, we calculated the clustering coefficients, average nearest-neighbors degree, and average shortest distance. As an essential economic network, the WEAW is found to be a correlated disassortative network with a hierarchical structure, possessing a more prominent scale-free feature than the world trade web (WTW).

  10. A large scale cryopanel test arrangement for tritium pumping

    Energy Technology Data Exchange (ETDEWEB)

    Day, Chr. E-mail: christian.day@itp.fzk.de; Brennan, D.; Jensen, H.S.; Mack, A

    2003-09-01

    A cryosorption panel test arrangement will be installed in the cryogenic forevacuum system of the Active Gas Handling System (AGHS) at Joint European Torus (JET). The panel is of International Thermonuclear Experimental Reactor (ITER) relevant design in terms of geometry and dimension, coating and sorbent material. The central objective of this task is to study, for the first time in such an in-depth and parametric way, the interaction of tritium and tritiated gas mixtures with the panel, with respect to pumping performance, desorption characteristics and structural influences. This paper describes the motivation for this task and outlines the experimental aims and how they are planned to be achieved. It presents the actual status and gives a description of the test arrangement design. The paper demonstrates how the AGHS is used as a unique benchmark test bed for an ITER component to qualify ITER tritium technology.

  11. Arrangement scheme of a semi-parallel ventilation system

    Energy Technology Data Exchange (ETDEWEB)

    Konoplev, E.S.; Sharf, V.G.; Timukhin, S.A.

    1983-04-01

    This paper evaluates a version of the system with two parallel blowers. The system is used for blowing ventilation in coal and other mines. In the modified version the two blowers are not parallel but are inclined. Air channels which supply air to the blowers have a circular rather than square crosscut. Blower arrangement and shape of air channels are shown in two schemes. Comparative evaluations of the aerodynamic resistance of the half parallel blower system with two VOD 30 blowers show that resistance of the air channels which supply air to the blowers is reduced to 0.23. A calculation method for determining aerodynamic resistance of air channels in the systems of the semi-parallel blower system considering air channel shape, dimensions, arrangement and position of two blowers is presented. Examples of practical use of the method are discussed.

  12. Minimum cell connection and separation in line segment arrangements

    CERN Document Server

    Alt, Helmut; Giannopoulos, Panos; Knauer, Christian

    2011-01-01

    We study the complexity of the following cell connection and separation problems in segment arrangements. Given a set of straight-line segments in the plane and two points a and b: (i) compute the minimum number of segments one needs to remove so that there is a path connecting a to b that does not intersect any of the remaining segments; (ii) compute the minimum number of segments one needs to remove so that the arrangement induced by the remaining segments has a single cell; (iii) compute the minimum number of segments one needs to retain so that any path connecting a to b intersects some of the retained segments. We show that problems (i) and (ii) are NP-hard, while problem (iii) is polynomial-time solvable. We also discuss special polynomial-time and fixed-parameter tractable cases.

  13. Arrangement of peptidoglycan in the cell wall of Staphylococcus spp.

    OpenAIRE

    Amako, K.; Umeda, A; Murata, K

    1982-01-01

    The arrangement of peptidoglycan in the cell wall of Staphylococcus was observed with the newly developed freeze-fracture technique, using n-octanol instead of water as the freezing medium. The replica of the trichloroacetic acid-extracted cell wall (TCA-wall) showed two areas. One of them has a concentric circular structure, a characteristic surface structure of the staphylococcal cell wall, and the other showed an irregular and rough surface. The chemical analysis of the wall revealed that ...

  14. Arrangements, multiderivations, and adjoint quotient map of type ADE

    CERN Document Server

    Yoshinaga, Masahiko

    2010-01-01

    The first part of this paper is a survey on algebro-geometric aspects of sheaves of logarithmic vector fields of hyperplane arrangements. In the second part we prove that the relative de Rham cohomology (of degree two) of ADE-type adjoint quotient map is naturally isomorphic to the module of certain multiderivations. The isomorphism is obtained by the Gauss-Manin derivative of the Kostant-Kirillov form.

  15. Small-Firm Networks: hybrid arrangement or organizational form?

    OpenAIRE

    Verschoore,Jorge Renato; Balestrin,Alsones; Perucia,Alexandre

    2014-01-01

    In the field of organizations, one relevant question is whether or not to consider networks as organizational forms. On the one hand, Williamson (1985) says that networks are hybrid arrangements. On the other, authors like Powell (1990) argue that networks constitute themselves as organizational forms. Given this dilemma, the present article proposes the analysis of organizational characteristics of small-firm networks (SFN). To reach such objective, twelve SFNs in distinct stages of developm...

  16. Refrigeration arrangement and methods for reducing charge migration

    Science.gov (United States)

    Litch, Andrew D.; Wu, Guolian

    2017-04-11

    A refrigerator appliance including a refrigerant circuit between a condenser, an evaporator, and a compressor that includes two conduits and pressure reducing devices arranged in parallel between the evaporator and the condenser. The appliance also includes a valve system to direct refrigerant through one, both or none of the conduits and pressure reducing devices, and a heat exchanging member in thermal contact with either one pressure reducing device, or one conduit between the pressure reducing device and the valve system.

  17. Golden spirals as phyllotactic arrangements of optical patterns.

    Science.gov (United States)

    Haudin, F; Residori, S

    2013-02-01

    A nonlinear optical medium with nonlocal feedback is shown to have all the necessary ingredients to simulate a growthlike process that generates golden spirals and phyllotactic patterns. Elementary droplets of light are generated by the optical nonlinearity whereas the combination of rotation and translation in the feedback loop geometrically distributes them on spiraling patterns. The symmetry of the geometrical arrangements is described with the help of a simple replication algorithm.

  18. Implementation of an Arranged Preventive Consultation in Danish General Practice

    DEFF Research Database (Denmark)

    Junge, Anne Gram; Kirkegaard, Pia; Thomsen, Janus Laust

    Background: In 2006 an arranged preventive consultation (0106-service) was implemented in Danish general practice. The purpose of the consultation is an attempt to improve the systematic prevention of the main chronic lifestyle diseases. Aim: This study examines the GP's experiences with the arra...... interaction between the GP/nurse and the patient, and therefore the GPs/nurses can in some respects experience it as difficult to apply the theoretical guidelines of the new consultation to their daily work with the patients.......Background: In 2006 an arranged preventive consultation (0106-service) was implemented in Danish general practice. The purpose of the consultation is an attempt to improve the systematic prevention of the main chronic lifestyle diseases. Aim: This study examines the GP's experiences...... with the arranged preventive consultation with focus on facilitators and barriers in the implementation of the consultation. Material & Method: Semi-structured interviews with 10 GPs and nurses in general practice. Results & Conclusions: Economically lucrative services are not an isolated motivation for the GPs...

  19. Studies on optimal design and operation of integrated distillation arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, Atle Christer

    1997-12-31

    During the last decades, there has been growing concern in the chemical engineering environment over the task of developing more cost- and energy efficient process equipment. This thesis discusses measures for improving the end-use energy efficiency of separation systems. It emphasises a certain class of integrated distillation arrangements, in particular it considers means for direct coupling of distillation columns so as to use the underlying physics to facilitate more energy efficient separations. The numerical methods discussed are well suited to solve models of distillation columns. A tear and grid method is proposed that to some extent exploits the sparsity, since the number of tear variables required for solving a distillation model usually is rather small. The parameter continuation method described is well suited for ill-conditioned problems. The analysis of integrated columns is extended beyond the scope of numerical simulations by means of analytical results that applies in certain limiting cases. The consept of preferred separation, which is important for prefractionator arrangements, is considered. From this analysis is derived information that is important for the practical operation of such columns. Finally, the proposed numerical methods are used to optimize Petlyuk arrangements for separating ternary and quaternary mixtures. 166 refs., 130 figs., 20 tabs.

  20. Elastic properties of nematoid arrangements formed by amoeboid cells

    Science.gov (United States)

    Kemkemer, R.; Kling, D.; Kaufmann, D.; Gruler, H.

    2000-02-01

    In culture migrating and interacting amoeboid cells can form nematoid arrangements in analogy to a nematic liquid crystal phase. A nematoid arrangement is formed if the interaction has an apolar symmetry. Different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (=fat cells) etc., form a nematoid structure. Our hypothesis is that elastic properties of these nematoid structures can be described in analogy to that of classical nematic liquid crystals. The orientational elastic energy is derived and the orientational defects (disclination) of nematoid arrangements are investigated. The existence of half-numbered disclinations shows that the nematoid structure has an apolar symmetry. The density- and order parameter dependence of the orientational elastic constants and their absolute values are estimated. From the defect structure, one finds that the splay elastic constant is smaller than the bend elastic constant (melanocytes). The core of a disclination is either a cell free space or occupied by non oriented cells (isotropic state), by a cell with a different symmetry, or by another cell type.

  1. Intergenerational living arrangements in Myanmar and Thailand: a comparative analysis.

    Science.gov (United States)

    Knodel, John; Pothisiri, Wiraporn

    2015-03-01

    The present study compares living arrangements and related intergenerational support in Myanmar and Thailand based on recent national surveys of older persons in both countries and prior surveys in Thailand. The countries share relatively similar cultural contexts but differ radically in economic development. Substantially higher percentages of older persons in Myanmar currently coreside with their children and are considerably more likely to have non-coresident children living in the same locality. They are also less likely to live with a spouse and to have children living at a substantial distance. Older persons in Myanmar are much less likely to have phone contact with children living away and less likely to receive visits. Thai elders are considerably more likely to provide custodial care to grandchildren with absent parents and to live in skip generation households. Older Thais are also considerably more likely to receive substantial remittances from non-coresident children. The living arrangements of older age Thais in the past, however, more closely resembles the current situation in Myanmar. It appears that current differences are largely attributable to the more advanced Thai economic development through its associated impacts on migration, fertility and mortality. Contrasting political situations and government priorities also likely play a role. The results provide insights into the implications of development for older persons and suggest that if the recent course of political transformation and opening to the global economy continues in Myanmar, living arrangements there may well follow the trends in Thailand over past decades.

  2. Collaborative arrangements for Australian nurse practitioners: a policy analysis.

    Science.gov (United States)

    Cashin, Andrew

    2014-10-01

    In Australia in 2010, nurse practitioners (NPs) were granted legislated access to the Medical Benefits Scheme (MBS) and Pharmaceutical Benefits Scheme (PBS) as providers. These schemes are the federal schemes for third-party reimbursement for health care and medications. As a condition of access to the schemes, it was determined that collaborative arrangements needed to be in place as part of eligibility criteria for NPs. This article is the first published policy analysis of this determination. Published literature and available grey literature (including meeting minutes), and media content, was accessed and analyzed. The policy that was the National Health Collaborative arrangements for Nurse Practitioners Determination to amend the Australian National Health Act 1953 was a success. The policy led to NP access as providers to the MBS and PBS in Australia. Understanding the policy process as it relates to the determination of the need for collaborative arrangements demystifies the process and origins of the policy for NPs in Australia. Understanding the determination means NPs in Australia will not artificially reduce scope of practice based on recommendations from the medical lobby. Clear research direction is provided that may inform the next policy cycle. ©2014 American Association of Nurse Practitioners.

  3. A balanced t(5;17 (p15;q22-23 in chondroblastoma: frequency of the re-arrangement and analysis of the candidate genes

    Directory of Open Access Journals (Sweden)

    Wijers-Koster Pauline

    2009-11-01

    Full Text Available Abstract Background Chondroblastoma is a benign cartilaginous tumour of bone that predominantly affects the epiphysis of long bones in young males. No recurrent chromosomal re-arrangements have so far been observed. Methods: We identified an index case with a balanced translocation by Combined Binary Ratio-Fluorescent in situ Hybridisation (COBRA-FISH karyotyping followed by breakpoint FISH mapping and array-Comparative Genomic Hybridisation (aCGH. Candidate region re-arrangement and candidate gene expression were subsequently investigated by interphase FISH and immunohistochemistry in another 14 cases. Results A balanced t(5;17(p15;q22-23 was identified. In the index case, interphase FISH showed that the translocation was present only in mononucleated cells and was absent in the characteristic multinucleated giant cells. The t(5;17 translocation was not observed in the other cases studied. The breakpoint in 5p15 occurred close to the steroid reductase 5α1 (SRD5A1 gene. Expression of the protein was found in all cases tested. Similar expression was found for the sex steroid signalling-related molecules oestrogen receptor alpha and aromatase, while androgen receptors were only found in isolated cells in a few cases. The breakpoint in 17q22-23 was upstream of the carbonic anhydrase × (CA10 gene region and possibly involved gene-regulatory elements, which was indicated by the lack of CA10 protein expression in the index case. All other cases showed variable levels of CA10 expression, with low expression in three cases. Conclusion We report a novel t(5;17(p15;q22-23 translocation in chondroblastoma without involvement of any of the two chromosomal regions in other cases studied. Our results indicate that the characteristic multinucleated giant cells in chondroblastoma do not have the same clonal origin as the mononuclear population, as they do not harbour the same translocation. We therefore hypothesise that they might be either reactive or

  4. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  5. Components of Adenovirus Genome Packaging

    Science.gov (United States)

    Ahi, Yadvinder S.; Mittal, Suresh K.

    2016-01-01

    Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

  6. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  7. Cephalopod genomics

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  8. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  9. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

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

  10. Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position.

    Science.gov (United States)

    Eszterhas, Susan K; Bouhassira, Eric E; Martin, David I K; Fiering, Steven

    2002-01-01

    Transcriptional interference is the influence, generally suppressive, of one active transcriptional unit on another unit linked in cis. Its wide occurrence in experimental systems suggests that it may also influence transcription in many loci, but little is known about its precise nature or underlying mechanisms. Here we report a study of the interaction of two nearly identical transcription units juxtaposed in various arrangements. Each reporter gene in the constructs has its own promoter and enhancer and a strong polyadenylation signal. We used recombinase-mediated cassette exchange (RMCE) to insert the constructs into previously tagged genomic sites in cultured cells. This strategy also allows the constructs to be assessed in both orientations with respect to flanking chromatin. In each of the possible arrangements (tandem, divergent, and convergent), the presence of two genes strongly suppresses expression of both genes compared to that of an identical single gene at the same integration site. The suppression is most severe with the convergent arrangement and least severe in total with the divergent arrangement, while the tandem arrangement is most strongly influenced by the integration site and the genes' orientation within the site. These results suggest that transcriptional interference could underlie some position effects and contribute to the regulation of genes in complex loci.

  11. The diffeomorphic types of the complements of arrangements in CP3 Ⅱ

    Institute of Scientific and Technical Information of China (English)

    WANG ShaoBo; YAU Stephen S-T

    2008-01-01

    For any arrangement of hyperplanes in CP3,we introduce the soul of this arrangement.The soul,which is a pseudo-complex,is determined by the combinatorics of the arrangement of hyper- planes.In this paper,we give a sufficient combinatoric condition for two arrangements of hyperplanes to be diffeomorphic to each other.In particular we have found sufficient conditions on combinatorics for the arrangement of hyperplanes whose moduli space is connected.This generalizes our previous result on hyperplane point arrangements in CP3.

  12. The diffeomorphic types of the complements of arrangements in CP~3Ⅱ

    Institute of Scientific and Technical Information of China (English)

    YAU; Stephen; S-T

    2008-01-01

    For any arrangement of hyperplanes in CP~3,we introduce the soul of this arrangement. The soul,which is a pseudo-complex,is determined by the combinatorics of the arrangement of hyper- planes.In this paper,we give a sufficient combinatoric condition for two arrangements of hyperplanes to be diffeomorphic to each other.In particular we have found sufficient conditions on combinatorics for the arrangement of hyperplanes whose moduli space is connected.This generalizes our previous result on hyperplane point arrangements in CP~3.

  13. Zoned electrical heater arranged in spaced relationship from particulate filter

    Science.gov (United States)

    Gonze, Eugene V [Pinckney, MI

    2011-11-15

    A system comprises a particulate matter (PM) filter that comprises an upstream end for receiving exhaust gas and a downstream end. A zoned heater is arranged spaced from the upstream end and comprises N zones, where N is an integer greater than one, wherein each of the N zones comprises M sub-zones, where M is an integer greater than one. A control module selectively activates at least a selected one of the N zones to initiate regeneration in downstream portions of the PM filter from the one of the N zones and deactivates non-selected ones of the N zones.

  14. Engine Power Turbine and Propulsion Pod Arrangement Study

    Science.gov (United States)

    Robuck, Mark; Zhang, Yiyi

    2014-01-01

    A study has been conducted for NASA Glenn Research Center under contract NNC10BA05B, Task NNC11TA80T to identify beneficial arrangements of the turboshaft engine, transmissions and related systems within the propulsion pod nacelle of NASA's Large Civil Tilt-Rotor 2nd iteration (LCTR2) vehicle. Propulsion pod layouts were used to investigate potential advantages, disadvantages, as well as constraints of various arrangements assuming front or aft shafted engines. Results from previous NASA LCTR2 propulsion system studies and tasks performed by Boeing under NASA contracts are used as the basis for this study. This configuration consists of two Fixed Geometry Variable Speed Power Turbine Engines and related drive and rotor systems (per nacelle) arranged in tilting nacelles near the wing tip. Entry-into-service (EIS) 2035 technology is assumed for both the engine and drive systems. The variable speed rotor system changes from 100 percent speed for hover to 54 percent speed for cruise by the means of a two speed gearbox concept developed under previous NASA contracts. Propulsion and drive system configurations that resulted in minimum vehicle gross weight were identified in previous work and used here. Results reported in this study illustrate that a forward shafted engine has a slight weight benefit over an aft shafted engine for the LCTR2 vehicle. Although the aft shafted engines provide a more controlled and centered CG (between hover and cruise), the length of the long rotor shaft and complicated engine exhaust arrangement outweighed the potential benefits. A Multi-Disciplinary Analysis and Optimization (MDAO) approach for transmission sizing was also explored for this study. This tool offers quick analysis of gear loads, bearing lives, efficiencies, etc., through use of commercially available RomaxDESIGNER software. The goal was to create quick methods to explore various concept models. The output results from RomaxDESIGNER have been successfully linked to Boeing

  15. Make or buy: HMOs' contracting arrangements for mental health care.

    Science.gov (United States)

    Hodgkin, D; Horgan, C M; Garnick, D W

    1997-03-01

    Many health maintenance organizations (HMOs) are contracting with external vendors for mental health care, rather than maintaining an internal mental health department. We develop a framework for analyzing HMOs' contracting choices, rooted in transaction cost economics. Applying this framework, external contracting seems most likely to appeal to smaller, newer HMOs and those located in areas with multiple vendors. Pressure from value-oriented buyers may make it harder for HMOs to provide mental health internally, without costly reforms to their product. HMO contracting arrangements deserve further study, given their implications for cost and the quality of care.

  16. TrayGen: Arranging objects for exhibition and packaging

    KAUST Repository

    Yang, Yongliang

    2013-10-01

    We present a framework, called TrayGen, to generate tray designs for the exhibition and packaging of a collection of objects. Based on principles from shape perception and visual merchandising, we abstract a number of design guidelines on how to organize the objects on the tray for the exhibition of their individual features and mutual relationships. Our framework realizes these guidelines by analyzing geometric shapes of the objects and optimizing their arrangement. We demonstrate that the resultant tray designs not only save space, but also highlight the characteristic of each object and the inter-relations between objects. © 2013 The Eurographics Association and John Wiley & Sons Ltd.

  17. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  18. Cephalopod genomics

    DEFF Research Database (Denmark)

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

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  19. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  20. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    Directory of Open Access Journals (Sweden)

    Agustina Undabarrena

    2017-02-01

    Full Text Available Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes. Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes, oxidative stress (69 genes and antibiotic resistance (97 genes. This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2. Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  1. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    Science.gov (United States)

    Undabarrena, Agustina; Ugalde, Juan A.; Seeger, Michael

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment. PMID:28229018

  2. Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae).

    Science.gov (United States)

    Balakirev, Evgeniy S; Romanov, Nikolai S; Ayala, Francisco J

    2016-01-01

    The complete mitochondrial genomes were sequenced from the Northern and Southern Dolly Varden chars, Salvelinus malma and S. curilus. The genome sequences are 16,654 bp in size in both species, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The level of sequence divergence between S. malma and S. curilus inferred from the complete mitochondrial genomes is relatively low (1.88%) indicating recent divergence of the species and/or historical hybridization.

  3. Synthesis, characterization, and computational study of the supramolecular arrangement of a novel cinnamic acid derivative.

    Science.gov (United States)

    Oliveira, S S; Santin, L G; Almeida, L R; Malaspina, L A; Lariucci, C; Silva, J F; Fernandes, W B; Aquino, G L B; Gargano, R; Camargo, A J; Napolitano, H B

    2017-02-01

    In this work, we present the synthesis, characterization, and computational study of the supramolecular arrangement of a new cinnamic acid derivative: ethyl-(2E)-3-(4-hydroxy-3,5-dimethoxyphenyl)-prop-2-enoate (EHD). Single crystals of EHD were obtained using ethyl ether as solvent and a slow evaporation technique. Its crystallographic structure, derived from X-ray diffraction experiments, includes a disordered water molecule on the EHD supramolecular structure. This water molecule participates in four O-H···O hydrogen bonds, which are arranged as a centrosymmetric H-bond array with the water at the center. Electronic and structural properties of the isolated EHD molecule and of the EHD molecule in the presence of one water molecule were calculated at the B3LYP/6-311++G(2d,2p) level of theory. These calculations show that the HOMO-LUMO energy gap of EHD decreases upon the introduction of the water molecule, suggesting that EHD becomes a stronger electron acceptor. These results indicate that the water molecule helps to stabilize the crystal structure in this system containing unequal numbers of acceptor and donor atoms. The supramolecular synthon involving the disordered water molecule and the supramolecular features presented here provide new possibilities in the design of functional materials and should also help us to gain a deeper understanding of the processes by which molecules recognize biological targets.

  4. Benefit-Sharing Arrangements between Oil Companies and Indigenous People in Russian Northern Regions

    Directory of Open Access Journals (Sweden)

    Svetlana Tulaeva

    2017-07-01

    Full Text Available This research provides an insight into various modes of benefit-sharing agreements between oil and gas companies and indigenous people in Russia’s northern regions, e.g., paternalism, corporate social responsibility, and partnership. The paper examines factors that influence benefit-sharing arrangements, such as regional specifics, dependency on international investors, corporate policies, and the level of local community organization. It analyses which instruments of benefit-sharing are most favourable, and why, for indigenous communities. The authors conducted research in three regions of Russia (Nenets Autonomous Okrug; Khanty-Mansi Autonomous Okrug, and Sakhalin by using qualitative methodology that involved semi-structured interviews, participant observation, and document analysis. Theoretically, the paper builds on the concept of benefit-sharing arrangements combined with the social equity framework. We assessed each case study in terms of procedural and distributive equity in benefit-sharing. The paper demonstrates that the procedural equity is the highest in the partnership mode of benefit-sharing on the island of Sakhalin where companies implement globally-accepted standards recognized by investment banks. The cases in Nenets Autonomous Okrug and Khanti Mansi Autonomous Okrug represent a reset of Soviet practices on a market basis, but whereas the distributional equity may be sufficient, the procedural equity is low as decisions are made by the company in concord with regional authorities.

  5. The Antsy Social Network: Determinants of Nest Structure and Arrangement in Asian Weaver Ants.

    Science.gov (United States)

    Devarajan, Kadambari

    2016-01-01

    Asian weaver ants (Oecophylla smaragdina) are arboreal ants that are known to form mutualistic complexes with their host trees. They are eusocial ants that build elaborate nests in the canopy in tropical areas. A colony comprises of multiple nests, usually on multiple trees, and the boundaries of the colony may be difficult to identify. However, they provide the ideal model for studying group living in invertebrates since there are a definite number of nests for a given substrate, the tree. Here, we briefly examine the structure of the nests and the processes involved in the construction and maintenance of these nests. We have described the spatial arrangement of weaver ant nests on trees in two distinct tropical clusters, a few hundred kilometres apart in India. Measurements were made for 13 trees with a total of 71 nests in the two field sites. We have considered a host of biotic and abiotic factors that may be crucial in determining the location of the nesting site by Asian weaver ants. Our results indicate that tree characteristics and architecture followed by leaf features help determine nest location in Asian weaver ants. While environmental factors may not be as influential to nest arrangement, they seem to be important determinants of nest structure. The parameters that may be considered in establishing the nests could be crucial in picking the evolutionary drivers for colonial living in social organisms.

  6. Novel Arrangements for High Performance and Durable Dielectric Elastomer Actuation

    Directory of Open Access Journals (Sweden)

    Runan Zhang

    2016-07-01

    Full Text Available This paper advances the design of Rod Pre-strained Dielectric Elastomer Actuators (RP-DEAs in their capability to generate comparatively large static actuation forces with increased lifetime via optimized electrode arrangements. RP-DEAs utilize thin stiff rods to constrain the expansion of the elastomer and maintain the in-plane pre-strain in the rod longitudinal direction. The aim is to study both the force output and the durability of the RP-DEA. Initial design of the RP-DEA had poor durability, however, it generated significantly larger force compared with the conventional DEA due to the effects of pre-strain and rod constraints. The durability study identifies the in-electro-active-region (in-AR lead contact and the non-uniform deformation of the structure as causes of pre-mature failure of the RP-DEA. An optimized AR configuration is proposed to avoid actuating undesired areas in the structure. The results show that with the optimized AR, the RP-DEA can be effectively stabilized and survive operation at least four times longer than with a conventional electrode arrangement. Finally, a Finite Element simulation was also performed to demonstrate that such AR design and optimization can be guided by analyzing the DEA structure in the state of pre-activation.

  7. Exhaust hood for steam turbines-single-flow arrangement

    Institute of Scientific and Technical Information of China (English)

    Michal HOZNEDL; Ladislav TAJC; Jaroslav KREJCIK; Lukas BEDNAR; Kamil SEDLAK; Jiri LINHART

    2009-01-01

    In the past, increased attention was given to the development of an optimal shape for the inlet part of LP turbine casings in SKODA POWER. A double-flow design is typically used for high power output turbines. An optimized shape for the internal diffuser has been found,which transforms the kinetic energy of steam into increased pressure, thus effectively increasing the thermo-dynamic efficiency of the stage. Some conclusions have been drawn from laboratory experiments, others derived directly from on-site measurements at power plants. The conclusions from the development of double-flow turbines form the basis for the design of the single-flow turbine arrangement. Single-flow design is typically used for lower output turbines. There are still some limitations in applying this arrangement. The designer needs to resolve the bearing position and how to ensure access to them. Reinforcing the ribs and supports are used, therefore, to ensure the rigidity of the entire casing. The optimization of the single-flow diffuser shape is therefore the subject of the study presented below.

  8. Similar Sister Chromatid Arrangement in Mono- and Holocentric Plant Chromosomes.

    Science.gov (United States)

    Schubert, Veit; Zelkowski, Mateusz; Klemme, Sonja; Houben, Andreas

    2016-01-01

    Due to the X-shape formation at somatic metaphase, the arrangement of the sister chromatids is obvious in monocentric chromosomes. In contrast, the sister chromatids of holocentric chromosomes cannot be distinguished even at mitotic metaphase. To clarify their organization, we differentially labelled the sister chromatids of holocentric Luzula and monocentric rye chromosomes by incorporating the base analogue EdU during replication. Using super-resolution structured illumination microscopy (SIM) and 3D rendering, we found that holocentric sister chromatids attach to each other at their contact surfaces similar to those of monocentrics in prometaphase. We found that sister chromatid exchanges (SCEs) are distributed homogeneously along the whole holocentric chromosomes of Luzula, and that their occurrence is increased compared to monocentric rye chromosomes. The SCE frequency of supernumerary B chromosomes, present additionally to the essential A chromosome complement of rye, does not differ from that of A chromosomes. Based on these results, models of the sister chromatid arrangement in mono- and holocentric plant chromosomes are presented.

  9. Infant Sleeping Arrangements and Cultural Values among Contemporary Japanese Mothers

    Directory of Open Access Journals (Sweden)

    Mina eShimizu

    2014-08-01

    Full Text Available We examined infant sleeping arrangements and parenting ethnotheories of Japanese mothers in 2008 and 2009. Based on Greenfield's theory of social change and human development, we predicted that social change in Japan over the last decades (higher economic and education level, urbanization, complex technology, more women in the work force would lead to a decline in mother-infant cosleeping, compared with published findings concerning Japanese sleeping arrangements in the 1960s and 1980s. We also predicted that the practice of having babies sleep in their own beds and/or own rooms would be supported by ethnotheories stressing infant independence and other values adaptive in an urban, technologically sophisticated, relatively wealthy, and highly educated populace. Fifty-one Japanese mothers’ comments posted on Internet parenting forums were analyzed. Contrary to our hypothesis, cosleeping was as frequent among Japanese mothers in 2008-2009 as it had been in the 1960s and 1980s. However, analysis of the values of cosleeping mothers revealed frequent discrepancies between values and practices. In contrast, the minority of mothers whose babies slept alone in a separate room all expressed consonant ethnotheories. Our qualitative analysis indicates that it is not always easy for Japanese mothers to construct values for child rearing and gender roles that integrate traditional infant care practices with current sociodemographic conditions.

  10. Tetrahedral Arrangements of Perylene Bisimide Columns via Supramolecular Orientational Memory.

    Science.gov (United States)

    Sahoo, Dipankar; Peterca, Mihai; Aqad, Emad; Partridge, Benjamin E; Heiney, Paul A; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Percec, Virgil

    2017-01-24

    Chiral, shape, and liquid crystalline memory effects are well-known to produce commercial macroscopic materials with important applications as springs, sensors, displays, and memory devices. A supramolecular orientational memory effect that provides complex nanoscale arrangements was only recently reported. This supramolecular orientational memory was demonstrated to preserve the molecular orientation and packing within supramolecular units of a self-assembling cyclotriveratrylene crown at the nanoscale upon transition between its columnar hexagonal and Pm3̅n cubic periodic arrays. Here we report the discovery of supramolecular orientational memory in a dendronized perylene bisimide (G2-PBI) that self-assembles into tetrameric crowns and subsequently self-organizes into supramolecular columns and spheres. This supramolecular orientation memory upon transition between columnar hexagonal and body-centered cubic (BCC) mesophases preserves the 3-fold cubic [111] orientations rather than the 4-fold [100] axes, generating an unusual tetrahedral arrangement of supramolecular columns. These results indicate that the supramolecular orientational memory concept may be general for periodic arrays of self-assembling dendrons and dendrimers as well as for other periodic and quasiperiodic nanoscale organizations comprising supramolecular spheres, generated from other organized complex soft matter including block copolymers and surfactants.

  11. Numerical simulation of bionic foils in tandem arrangement

    Directory of Open Access Journals (Sweden)

    Kai Zhou

    2016-05-01

    Full Text Available Based on the backgrounds of underwater propulsors with high hydrodynamic performance, the article focuses on the flapping foils in tandem arrangement and tries to formulate the physical mode and mathematical model of flapping propulsion. Using the commercial software Fluent, the governing equations are discretized by the finite volume method, and dynamic mesh method is adopted to solve the moving boundaries. In order to verify validity and feasibility of the method, hydrodynamic performance of single flapping foil is analyzed. The present results of single flapping foil compare well with those in experimental researches. After that, numerical simulations of flapping foils in tandem arrangement are conducted to reveal the energy absorption mechanisms. By extracting performance parameters and characteristics of the flow field, the interaction between upstream foil and downstream foil is analyzed. The results indicate that the vortices shedding from upstream foil have a significant effect on the hydrodynamic performance of downstream foil, and the downstream foil can use energy from the flow field to improve the hydrodynamic performance. Therefore, the hydrodynamic performance of the system can be improved by adjusting the locations of foils and motion parameters.

  12. Factors affecting daughter cells' arrangement during the early bacterial divisions.

    Directory of Open Access Journals (Sweden)

    Pin-Tzu Su

    Full Text Available On agar plates, daughter cells of Escherichia coli mutually slide and align side-by-side in parallel during the first round of binary fission. This phenomenon has been previously attributed to an elastic material that restricts apparently separated bacteria from being in string. We hypothesize that the interaction between bacteria and the underneath substratum may affect the arrangement of the daughter bacteria. To test this hypothesis, bacterial division on hyaluronic acid (HA gel, as an alternative substratum, was examined. Consistent with our proposition, the HA gel differs from agar by suppressing the typical side-by-side alignments to a rare population. Examination of bacterial surface molecules that may contribute to the daughter cells' arrangement yielded an observation that, with disrupted lpp, the E. coli daughter cells increasingly formed non-typical patterns, i.e. neither sliding side-by-side in parallel nor forming elongated strings. Therefore, our results suggest strongly that the early cell patterning is affected by multiple interaction factors. With oscillatory optical tweezers, we further demonstrated that the interaction force decreased in bacteria without Lpp, a result substantiating our notion that the side-by-side sliding phenomenon directly reflects the strength of in-situ interaction between bacteria and substratum.

  13. Complete genome sequence of Anaerococcus prevotii type strain (PC1T)

    Energy Technology Data Exchange (ETDEWEB)

    LaButti, Kurt [U.S. Department of Energy, Joint Genome Institute; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Steenblock, Katja [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Tom [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

    2009-01-01

    Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family Peptostreptococcaceae . A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family Peptostreptococcaceae for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. 78 FR 31943 - Draft Guidance for Industry on Contract Manufacturing Arrangements for Drugs: Quality Agreements...

    Science.gov (United States)

    2013-05-28

    ... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry on Contract Manufacturing... guidance for industry entitled ``Contract Manufacturing Arrangements for Drugs: Quality Agreements.'' This... draft guidance for industry entitled ``Contract Manufacturing Arrangements for Drugs: Quality...

  15. Pseudomonas aeruginosa genomic structure and diversity

    Directory of Open Access Journals (Sweden)

    Jens eKlockgether

    2011-07-01

    Full Text Available The Pseudomonas aeruginosa genome (G + C content 65-67%, size 5.5 – 7 Mbp is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5 – 0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. 198 of the 231 SNPs were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.

  16. Genomic landscape of liposarcoma.

    Science.gov (United States)

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B; Said, Jonathan W; Mohith, S; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A; Silberman, Allan W; Forscher, Charles; Tyner, Jeffrey W; Ogawa, Seishi; Koeffler, H Phillip

    2015-12-15

    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.

  17. Jumbled Genomes: Missing Apicomplexan Synteny

    Science.gov (United States)

    DeBarry, Jeremy D.; Kissinger, Jessica C.

    2011-01-01

    Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes found on the same chromosome and in the same order within 25 kb up- and downstream of any orthologous genes. Conserved synteny between major lineages is limited to small regions in Plasmodium and Theileria/Babesia species, and within these conserved regions, there are a number of proteins putatively targeted to organelles. The observed overall lack of synteny is surprising considering the divergence times and the apparent absence of transposable elements (TEs) within any of the species examined. TEs are ubiquitous in all other groups of eukaryotes studied to date and have been shown to be involved in genomic rearrangements. It appears that there are different criteria governing genome evolution within the Apicomplexa relative to other well-studied unicellular and multicellular eukaryotes. PMID:21504890

  18. Lack of Involvement of Fenton Chemistry in Death of Methicillin-Resistant and Methicillin-Sensitive Strains of Staphylococcus aureus and Destruction of Their Genomes on Wet or Dry Copper Alloy Surfaces.

    Science.gov (United States)

    Warnes, Sarah L; Keevil, C William

    2016-01-29

    The pandemic of hospital-acquired infections caused by methicillin-resistant Staphylococcus aureus (MRSA) has declined, but the evolution of strains with enhanced virulence and toxins and the increase of community-associated infections are still a threat. In previous studies, 10(7) MRSA bacteria applied as simulated droplet contamination were killed on copper and brass surfaces within 90 min. However, contamination of surfaces is often via finger tips and dries rapidly, and it may be overlooked by cleaning regimes (unlike visible droplets). In this new study, a 5-log reduction of a hardy epidemic strain of MRSA (epidemic methicillin-resistant S. aureus 16 [EMRSA-16]) was observed following 10 min of contact with copper, and a 4-log reduction was observed on copper nickel and cartridge brass alloys in 15 min. A methicillin-sensitive S. aureus (MSSA) strain from an osteomyelitis patient was killed on copper surfaces in 15 min, and 4-log and 3-log reductions occurred within 20 min of contact with copper nickel and cartridge brass, respectively. Bacterial respiration was compromised on copper surfaces, and superoxide was generated as part of the killing mechanism. In addition, destruction of genomic DNA occurs on copper and brass surfaces, allaying concerns about horizontal gene transfer and copper resistance. Incorporation of copper alloy biocidal surfaces may help to reduce the spread of this dangerous pathogen. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. Lack of Involvement of Fenton Chemistry in Death of Methicillin-Resistant and Methicillin-Sensitive Strains of Staphylococcus aureus and Destruction of Their Genomes on Wet or Dry Copper Alloy Surfaces

    Science.gov (United States)

    2016-01-01

    The pandemic of hospital-acquired infections caused by methicillin-resistant Staphylococcus aureus (MRSA) has declined, but the evolution of strains with enhanced virulence and toxins and the increase of community-associated infections are still a threat. In previous studies, 107 MRSA bacteria applied as simulated droplet contamination were killed on copper and brass surfaces within 90 min. However, contamination of surfaces is often via finger tips and dries rapidly, and it may be overlooked by cleaning regimes (unlike visible droplets). In this new study, a 5-log reduction of a hardy epidemic strain of MRSA (epidemic methicillin-resistant S. aureus 16 [EMRSA-16]) was observed following 10 min of contact with copper, and a 4-log reduction was observed on copper nickel and cartridge brass alloys in 15 min. A methicillin-sensitive S. aureus (MSSA) strain from an osteomyelitis patient was killed on copper surfaces in 15 min, and 4-log and 3-log reductions occurred within 20 min of contact with copper nickel and cartridge brass, respectively. Bacterial respiration was compromised on copper surfaces, and superoxide was generated as part of the killing mechanism. In addition, destruction of genomic DNA occurs on copper and brass surfaces, allaying concerns about horizontal gene transfer and copper resistance. Incorporation of copper alloy biocidal surfaces may help to reduce the spread of this dangerous pathogen. PMID:26826226

  20. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

    Science.gov (United States)

    Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

    2000-12-15

    The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

  1. 29 CFR 794.117 - Effect of franchises and other arrangements.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Effect of franchises and other arrangements. 794.117... âindependently Owned and Controlled Local Enterpriseâ § 794.117 Effect of franchises and other arrangements. Whether a franchise or other contractual arrangement affects the status of the enterprise as...

  2. 46 CFR 167.20-17 - Bilge pumps, bilge piping and sounding arrangements.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Bilge pumps, bilge piping and sounding arrangements. 167... Ships § 167.20-17 Bilge pumps, bilge piping and sounding arrangements. The number, capacity, and arrangement of bilge pumps and bilge piping shall be in accordance with the requirements for cargo...

  3. 12 CFR 714.3 - Must you own the leased property in an indirect leasing arrangement?

    Science.gov (United States)

    2010-01-01

    ... leasing arrangement? 714.3 Section 714.3 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS LEASING § 714.3 Must you own the leased property in an indirect leasing arrangement? You do not have to own the leased property in an indirect leasing arrangement if: (a) You...

  4. The Life Course of Children Born to Unmarried Mothers: Childhood Living Arrangements and Young Adult Outcomes.

    Science.gov (United States)

    Aquilino, William S.

    1996-01-01

    Explored living arrangements among children born to unmarried mothers and the impact of childhood living arrangements on the young adult's life course. Analyses showed that living arrangement patterns after birth to a single mother influenced the likelihood of high school completion, post secondary education, and other conditions. (RJM)

  5. Designing efficient surveys: spatial arrangement of sample points for detection of invasive species

    Science.gov (United States)

    Ludek Berec; John M. Kean; Rebecca Epanchin-Niell; Andrew M. Liebhold; Robert G. Haight

    2015-01-01

    Effective surveillance is critical to managing biological invasions via early detection and eradication. The efficiency of surveillance systems may be affected by the spatial arrangement of sample locations. We investigate how the spatial arrangement of sample points, ranging from random to fixed grid arrangements, affects the probability of detecting a target...

  6. Gender and Ethnic Variation in Arranged Marriages in a Chinese City

    Science.gov (United States)

    Zang, Xiaowei

    2008-01-01

    Using a data set (N = 1,600) collected in the city of Urumchi in 2005, this article examines ethnic differences in arranged marriages in urban China. Data analysis shows a rapid decline in parental arrangement for both Uyghur Muslims and Han Chinese in Urumchi. Han Chinese are less likely than Uyghur Muslims to report arranged marriages, with main…

  7. 1 CFR 20.6 - Form, style, arrangement and apportionment of space.

    Science.gov (United States)

    2010-01-01

    ... 1 General Provisions 1 2010-01-01 2010-01-01 false Form, style, arrangement and apportionment of... Form, style, arrangement and apportionment of space. The form, style, and arrangement of agency... determined by the Director of the Federal Register. The U.S. Government Printing Office Style Manual is...

  8. Evolving Relationship Structures in Multi-sourcing Arrangements: The Case of Mission Critical Outsourcing

    Science.gov (United States)

    Heitlager, Ilja; Helms, Remko; Brinkkemper, Sjaak

    Information Technology Outsourcing practice and research mainly considers the outsourcing phenomenon as a generic fulfilment of the IT function by external parties. Inspired by the logic of commodity, core competencies and economies of scale; assets, existing departments and IT functions are transferred to external parties. Although the generic approach might work for desktop outsourcing, where standardisation is the dominant factor, it does not work for the management of mission critical applications. Managing mission critical applications requires a different approach where building relationships is critical. The relationships involve inter and intra organisational parties in a multi-sourcing arrangement, called an IT service chain, consisting of multiple (specialist) parties that have to collaborate closely to deliver high quality services.

  9. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  10. SOME COMMENTS ON THE SCHEME OF ARRANGEMENT AS AN AN "AFFECTED TRANSACTION" AS DEFINED IN THE COMPANIES ACT 71 OF 2008

    Directory of Open Access Journals (Sweden)

    Stephanie M Luiz

    2012-12-01

    Full Text Available A scheme of arrangement involving a regulated company and its shareholders is defined as an "affected transaction" in the Companies Act 71 of 2008. Although scheme of arrangements, which can be used to achieve a takeover of a company, are a common occurrence, the Act provides no definition of such schemes. The importance of knowing what actually constitutes a scheme of arrangement becomes apparent when it is noted that section 121 of the Actprovides that any person making an offer which if accepted would result in an affected transaction is obliged to comply with all the relevant reporting and approval requirements in the Act, as well as the Takeover Regulations, unless the Takeover Regulation Panel has granted an exemption. Giving effect to an affected transaction is prohibited, unless the Panel has issued a compliance certificate or granted an exemption. The article comments generally on the definition of a scheme of arrangement as an affected transaction, highlighting the elements of a scheme of arrangement. Specific consideration is given to transactions which include a re-acquisition by the company of its own previously issued securities and when such a re-acquisition on its own would be considered to be a scheme of arrangement and an affected transaction. Comment on the obligation to appoint an independent expert to report on the scheme and the relevance, if any, of the solvency and liquidity of the company embarking on a scheme of arrangement is included. Finally, consideration is given to the need to have a scheme of arrangement approved by a special resolution and the potential exclusion of certain voting rights. The article exposes a number of difficulties with the interpretation of the applicable provisions and suggests that these need to be revisited by the legislature for clarification.

  11. (Post-)genomics approaches in fungal research

    NARCIS (Netherlands)

    Aguilar-Pontes, María Victoria; de Vries, Ronald P; Zhou, M.; van den Brink, J.

    2014-01-01

    To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functio

  12. Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome.

    Science.gov (United States)

    Calcutt, M J; Schmidt, F J

    1992-01-01

    A 23-kb fragment of the Streptomyces coelicolor chromosome spanning the dnaA region has been isolated as a cosmid clone. Nucleotide sequence analysis of a 5-kb portion shows that the genes for the RNase P protein (rnpA), ribosomal protein L34 (rpmH), the replication initiator protein (dnaA), and the beta subunit of DNA polymerase III (dnaN) are present in the highly conserved gene arrangement found in all eubacterial genomes studied so far. The dnaA-dnaN intergenic region is approximately 1 kb and contains a cluster of at least 12 DnaA boxes with a consensus sequence of TTGTCCACA matching the consensus DnaA box in the phylogenetically related Micrococcus luteus. Two DnaA boxes precede the dnaA sequence. We propose that the chromosomal origin (oriC) of S. coelicolor lies between dnaA and dnaN. In related work, J. Zakrzewska-Czerwinska and H. Schrempf (J. Bacteriol. 174:2688-2693, 1992) have identified the homologous sequence from the closely-related Streptomyces lividans as capable of self-replication. PMID:1577691

  13. New arrangements in force in the field of transport

    CERN Multimedia

    Tom Wegelius

    2006-01-01

    Please take note of the following information concerning new arrangements in force in the field of transport: China: Regulations applying to wooden packaging materials as of 1st January 2006 As scheduled, China introduced standard ISPM No. 15 on 1st January 2006. This was officially confirmed in a letter from the Federal Minister for Consumer Protection, Food and Agriculture. Henceforth, China will apply the same conditions to the importation of wooden packaging materials as various other countries, including the United States, Mexico and Brazil. This means that items shipped to China in wooden packaging will no longer need to be accompanied by a certificate relating to the protection of plant species or other phytosanitary documents (such as heat treatment certificates). However, a guarantee that the wooden packaging complies with standard ISPM No. 15 will be required. Phase II of US regulations concerning wooden packaging material Phase II of regulations concerning the importation of wooden packaging ma...

  14. Neoliberalism and criticisms of earthquake insurance arrangements in New Zealand.

    Science.gov (United States)

    Hay, I

    1996-03-01

    Global collapse of the Fordist-Keynesian regime of accumulation and an attendant philosophical shift in New Zealand politics to neoliberalism have prompted criticisms of, and changes to, the Earthquake and War Damage Commission. Earthquake insurance arrangements made 50 years ago in an era of collectivist, welfarist political action are now set in an environment in which emphasis is given to competitive relations and individualism. Six specific criticisms of the Commission are identified, each of which is founded in the rhetoric and ideology of a neoliberal political project which has underpinned radical social and economic changes in New Zealand since the early 1980s. On the basis of those criticisms, and in terms of the Earthquake Commission Act 1993, the Commission has been restructured. The new Commission is withdrawing from its primary position as the nation's non-residential property hazards insurer and is restricting its coverage of residential properties.

  15. Multiple transnational household arrangements in the city of Cochabamba

    Directory of Open Access Journals (Sweden)

    Carmen Ledo García

    2014-09-01

    Full Text Available Evidence shows that over the last 15 years Bolivia and Cochabamba have experienced increased migration flows and that international emigration has become an important strategy for many households. The purpose of this article is to show intra-family solidarity, as well as how households respond to an absent parent in the Cochabamba urban area. The simultaneous interaction of six analytic dimensions is analysed: the socio-economic situation in the country of origin; the characteristics of migrants in the host country; maternal/paternal communication from a distance; the role of remittances; and political participation and role changes within the family remaining in the country of origin. The procedure of generalized canonical correlation analysis (GCCA allows us to demonstrate the multiple transnational maternity/paternity arrangements and the solidarity of the family networks in Cochabamba.

  16. Atomic arrangement and charge distribution in YBCO tilt grain boundaries

    Science.gov (United States)

    Bording, J. K.; Halley, J. W.; Zhu, Y.

    2005-03-01

    It is well known that the critical current, Jc, in high-Tc superconductors is reduced at grain boundaries. Recent high resolution holography experiments show the [100] tilt grain boundaries in YBa2Cu3O7-x to have an excess negative charge localized at the boundary dislocation core. Upon doping with Ca, this charge is reduced and the critical current increased. To shed light on this behavior at an atomic scale, we carried out Tight Binding (TB) calculations of these boundaries. Our TB scheme is charge self consistent to allow charge transfer typical for ionic materials. We present the arrangement of atoms and charge in YBCO tilt grain boundaries as determined by a combination of TB calculations, recent high resolution Scanning Transmission Electron Microscopy and Electron Energy Loss Spectroscopy measurements.

  17. Dementia prevalence, care arrangement, and access to care in Lebanon

    DEFF Research Database (Denmark)

    Phung, Thien Kieu Thi; Chaaya, Monique; Prince, Martin

    2017-01-01

    INTRODUCTION: In North Africa and the Middle East, studies about dementia prevalence are scarce. A pilot study was conducted in Lebanon to assess dementia prevalence, using the Arabic-validated 10/66 Dementia Research Group (DRG) diagnostic assessment for case ascertainment. The study also examined...... care arrangement and access to care. METHODS: A random sample of 502 persons older than 65 years and their informant were recruited from Beirut and Mount Lebanon governorates through multistage cluster sampling. RESULTS: The crude and age-standardized dementia prevalences were 7.4% and 9.......0%, respectively. People with dementia were mainly cared for by relatives at home. Access to formal care was very limited. DISCUSSION: Dementia prevalence in Lebanon ranks high within the global range of estimates. These first evidence-based data about disease burden and barriers to care serve to raise awareness...

  18. Licensing arrangements and the development of the solar energy industry

    Energy Technology Data Exchange (ETDEWEB)

    Green, M.

    1979-06-01

    The process by which technology and information related to technology are transferred within industry is explored. Property rights in technology are part of the broader field of intellectual property. The general contours of legal protection for knowledge are explored. The four basic forms of intellectual property - patents, trade secrets (or know-how), trademarks, and copyrights - are covered in varying degrees of depth, depending on their relative applicability to the development of the solar industry. Once this background has been established, the legal aspects of licensing are examined. A license is a legal arrangement whereby a party (licensor) who controls the right to use an idea, invention, etc. shares the right to use the particular intellectual property with someone else (licensee). The advantages and disadvantages of licensing are described from the point of view of potential licensees and licensors. Barriers to licensing are discussed.

  19. 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 My

  20. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  1. Innovation, market orientation and performance in the local embryonic productive arrangement of clothing in Londrina/PR

    Directory of Open Access Journals (Sweden)

    Fabiano Palhares Galão

    2009-01-01

    Full Text Available This research analyzes the impact on both the innovation and market orientation related to the companies’ performance of the local productive arrangement of clothing in Londrina. It identifies the rank of market orientation through the Markor scale, elaborated by Kohli, Jaworski and Kumar (1993 and the product innovation implementation, process and organizational innovations. The chosen method is the survey, involving a sample of 62 companies, and to proceed with the data analysis we use the coefficient of correlation of Pearson and the Clusters Analysis. The main results are: a the companies are highly market oriented; b the innovative behavior of the arrangement is low; c the launching of new products has been the most innovative practice used by the companies; d the market orientation and innovation contribute to the income growth and to the return of investment of the clothing industries in Londrina.

  2. Visualizing Similarity of Appearance by Arrangement of Cards.

    Science.gov (United States)

    Nakatsuji, Nao; Ihara, Hisayasu; Seno, Takeharu; Ito, Hiroshi

    2016-01-01

    This study proposes a novel method to extract the configuration of the psychological space by directly measuring subjects' similarity rating without computational work. Although multidimensional scaling (MDS) is well-known as a conventional method for extracting the psychological space, the method requires many pairwise evaluations. The times taken for evaluations increase in proportion to the square of the number of objects in MDS. The proposed method asks subjects to arrange cards on a poster sheet according to the degree of similarity of the objects. To compare the performance of the proposed method with the conventional one, we developed similarity maps of typefaces through the proposed method and through non-metric MDS. We calculated the trace correlation coefficient among all combinations of the configuration for both methods to evaluate the degree of similarity in the obtained configurations. The threshold value of trace correlation coefficient for statistically discriminating similar configuration was decided based on random data. The ratio of the trace correlation coefficient exceeding the threshold value was 62.0% so that the configurations of the typefaces obtained by the proposed method closely resembled those obtained by non-metric MDS. The required duration for the proposed method was approximately one third of the non-metric MDS's duration. In addition, all distances between objects in all the data for both methods were calculated. The frequency for the short distance in the proposed method was lower than that of the non-metric MDS so that a relatively small difference was likely to be emphasized among objects in the configuration by the proposed method. The card arrangement method we here propose, thus serves as a easier and time-saving tool to obtain psychological structures in the fields related to similarity of appearance.

  3. A theory for the arrangement of sensory organs in Drosophila

    Science.gov (United States)

    Zhu, Huifeng; Gunaratne, Preethi H.; Roman, Gregg W.; Gunaratne, Gemunu H.

    2010-03-01

    We study the arrangements of recurved bristles on the anterior wing margin of wild-type and mutant Drosophila. The epidermal or neural fate of a proneural cell depends on the concentrations of proteins of the achaete-scute complex. At puparium formation, concentrations of proteins are nearly identical in all cells of the anterior wing and each cell has the potential for neural fate. In wild-type flies, the action of regulatory networks drives the initial state to one where a bristle grows out of every fifth cell. Recent experiments have shown that the frequency of recurved bristles can be made to change by adjusting the mean concentrations of the zinc-finger transcription factor Senseless and the micro-RNA miR-9a. Specifically, mutant flies with reduced levels of miR-9a exhibit ectopic bristles, and those with lower levels of both miR-9a and Senseless show regular organization of recurved bristles, but with a lower periodicity of 4. We argue that these characteristics can be explained assuming an underlying Turing-type bifurcation whereby a periodic pattern spontaneously emerges from a uniform background. However, bristle patterns occur in a discrete array of cells, and are not mediated by diffusion. We argue that intracellular actions of transmembrane proteins such as Delta and Notch can play a role of diffusion in destabilizing the homogeneous state. In contrast to diffusion, intercellular actions can be activating or inhibiting; further, there can be lateral cross-species interactions. We introduce a phenomenological model to study bristle arrangements and make several model-independent predictions that can be tested in experiments. In our theory, miRNA-9a is one of the components of the underlying network and has no special regulatory role. The loss of periodicity in its absence is due to the transfer of the system to a bistable state.

  4. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

    Science.gov (United States)

    Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

    2016-01-01

    PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

  5. Horizontal arrangements: strategy for reducing the asymmetry information for dairy farmers in Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Marcel Moreira de Brito

    2015-11-01

    Full Text Available An empirical investigation was conducted to study whether dairy farmers involved in horizontal arrangements (HA have lower information asymmetry than those who do not participate in HA. Our assumption is that greater access to information results in fewer risky decisions in production systems. One hundred and twenty semi-structured questionnaires were applied to dairy farmers located in four different geographical regions in Paraná State, Brazil. Exploratory factor analysis was used to define factors related to information asymmetry in dairy agribusiness system (DAS and four factors were defined. In a second step, the 120 dairy farmers were split into two groups: the first one involved in HA and the second one not involved in HA. Mean test (t-student were performed to compare these groups between factors. Significant differences (P<0.05 were observed for factors related to transaction information and for general market information, and dairy farmers participating in HA achieved the greatest values. Finally, it can be concluded that dairy farmers who participate in HA have higher access to information, which can create an environment with lower information asymmetry and, consequently, be subject to lower risks than dairy farmers who do not participate in HA

  6. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Directory of Open Access Journals (Sweden)

    Nickerson Cheryl A

    2006-01-01

    Full Text Available Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305 and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not

  7. Study on pick arrangement of shearer drum based on load fluctuation

    Institute of Scientific and Technical Information of China (English)

    DU Chang-long; LIU Song-yong; CUI Xin-xia; LI Ti-jian

    2008-01-01

    According to the coal or rock cutting theory, a mechanical model and computing formula for a pick and the drum load fluctuation model were established in order to obtain relationships between pick arrangements and drum fluctuation loads, drum rotary speeds and haulage speeds. Based on a minimum load fluctuation, an optimal mathematical model was established for drum pick arrangements. The effects of pick arrangements (including punnett square, sequence, aberrance Ⅰ and Ⅱ) on the drum load fluctuation coefficient are discussed. The relationships between the pick arrangements of the drum with different start vanes and the cutting load fluctuation coefficient, the drum rotary speed and haulage speed were also studied. The results indicate that the punnett square arrangement has a smaller cutting load fluctuation coefficient than other forms of arrangement and the drum with the 4-start vanes has the smallest coefficient. The drum rotary speed and haulage speed are affected not only by pick arrangements, but also by the number of vanes.

  8. Comparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species.

    Science.gov (United States)

    Kim, Ji-Nu; Kim, Yeonbum; Jeong, Yujin; Roe, Jung-Hye; Kim, Byung-Gee; Cho, Byung-Kwan

    2015-10-01

    The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.

  9. A genome-wide screen identifies Salmonella Enteritidis lipopolysaccharide biosynthesis and the HtrA heat shock protein as crucial factors involved in egg white persistence at chicken body temperature.

    Science.gov (United States)

    Raspoet, R; Shearer, N; Appia-Ayme, C; Haesebrouck, F; Ducatelle, R; Thompson, A; Van Immerseel, F

    2014-05-01

    Eggs contaminated with Salmonella Enteritidis are an important source of human foodborne Salmonella infections. Salmonella Enteritidis is able to contaminate egg white during formation of the egg within the chicken oviduct, and it has developed strategies to withstand the antimicrobial properties of egg white to survive in this hostile environment. The mechanisms involved in the persistence of Salmonella Enteritidis in egg white are likely to be complex. To address this issue, a microarray-based transposon library screen was performed to identify genes necessary for survival of Salmonella Enteritidis in egg white at chicken body temperature. The majority of identified genes belonged to the lipopolysaccharide biosynthesis pathway. Additionally, we provide evidence that the serine protease/heat shock protein (HtrA) appears essential for the survival of Salmonella Enteritidis in egg white at chicken body temperature.

  10. Necessity of electromagnetic emission network arrangement in Georgia

    Science.gov (United States)

    Turazashvili, Ioseb; Kachakhidze, Nino; Machavariani, Kakhaber; Kachakhidze, Manana; Gogoberidze, Vitali; Khazaradze, Giorgi

    2015-04-01

    The field of the tectonic stress has the hierarchical structure. The most characteristic features connected with the regional tectonic elements are determined by the geologic - tectonic data. It is established that in the young folded areas like the Caucasus the field of tectonic stress is characterized by the sharp anisotropy with the predominance of the compression perpendicular to the trend of folding. Spatial location of the main positive and negative geotectonic morphostructures of the Caucasus shows the existence of the wavy tectonic movements in the region. They are caused by the horizontal compression, provoked evidently by advancement of the Arabian lithosphere plate to the North and its re-approach with the Euro-Asian plate. All these cause considerable deformation of the lithosphere of the Caucasian region and its breaking up in separate blocks. This, in its turn, causes the concentration of stress along the boundaries of the blocks and rising of earthquakes focuses there. According to the instrumental data starting from 1899 at about 40 large earthquakes were fixed in the Caucasus. The rate of risks associated with these hazards increases every year in Georgia due to the appearance of new complicated technological construction: oil and gas pipelines large dams and hydropower plants and others. Modern ground-based and satellite methods of viewing enables to reveal those multiple anomalous geophysical phenomena which become evident in the period preceding earthquake and are directly connected with the process of its preparation. Lately special attention is attributed to the electromagnetic emission fixed during large earthquake and has already been successfully detected in Japan, America and Europe. Unfortunately there is no electromagnetic emission detection network in Georgia yet. The presented abstract concerns arrange of EM emission net and begin implementation of this vital task by arrangement of the one relevant station on the fault near Tbilisi

  11. Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome.

    Science.gov (United States)

    Dermauw, Wannes; Vanholme, Bartel; Tirry, Luc; Van Leeuwen, Thomas

    2010-04-01

    In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) - which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms - the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.

  12. Current development and application of soybean genomics

    Institute of Scientific and Technical Information of China (English)

    Lingli HE; Jing ZHAO; Man ZHAO; Chaoying HE

    2011-01-01

    Soybean (Glycine max),an important domesticated species originated in China,constitutes a major source of edible oils and high-quality plant proteins worldwide.In spite of its complex genome as a consequence of an ancient tetraploidilization,platforms for map-based genomics,sequence-based genomics,comparative genomics and functional genomics have been well developed in the last decade,thus rich repertoires of genomic tools and resources are available,which have been influencing the soybean genetic improvement.Here we mainly review the progresses of soybean (including its wild relative Glycine soja) genomics and its impetus for soybean breeding,and raise the major biological questions needing to be addressed.Genetic maps,physical maps,QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine.Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes,which are instrumental to comparative genomics and functional genomics.Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process.Microarrays resources,mutagenesis and efficient transformation systems become essential components of soybean functional genomics.Furthermore,phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development,in response to abiotic stresses,functioning in plant-pathogenic microbe interactions,and controlling the oil and protein content of seed.These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.

  13. Arrangement at the nanoscale: Effect on magnetic particle hyperthermia

    Science.gov (United States)

    Myrovali, E.; Maniotis, N.; Makridis, A.; Terzopoulou, A.; Ntomprougkidis, V.; Simeonidis, K.; Sakellari, D.; Kalogirou, O.; Samaras, T.; Salikhov, R.; Spasova, M.; Farle, M.; Wiedwald, U.; Angelakeris, M.

    2016-11-01

    In this work, we present the arrangement of Fe3O4 magnetic nanoparticles into 3D linear chains and its effect on magnetic particle hyperthermia efficiency. The alignment has been performed under a 40 mT magnetic field in an agarose gel matrix. Two different sizes of magnetite nanoparticles, 10 and 40 nm, have been examined, exhibiting room temperature superparamagnetic and ferromagnetic behavior, in terms of DC magnetic field, respectively. The chain formation is experimentally visualized by scanning electron microscopy images. A molecular Dynamics anisotropic diffusion model that outlines the role of intrinsic particle properties and inter-particle distances on dipolar interactions has been used to simulate the chain formation process. The anisotropic character of the aligned samples is also reflected to ferromagnetic resonance and static magnetometry measurements. Compared to the non-aligned samples, magnetically aligned ones present enhanced heating efficiency increasing specific loss power value by a factor of two. Dipolar interactions are responsible for the chain formation of controllable density and thickness inducing shape anisotropy, which in turn enhances magnetic particle hyperthermia efficiency.

  14. Tailoring chiro-optical effects by helical nanowire arrangement.

    Science.gov (United States)

    Esposito, Marco; Tasco, Vittorianna; Todisco, Francesco; Benedetti, Alessio; Tarantini, Iolena; Cuscunà, Massimo; Dominici, Lorenzo; De Giorgi, Milena; Passaseo, Adriana

    2015-11-21

    In this work, we experimentally investigate the chiro-optical properties of 3D metallic helical systems at optical frequencies. Both single and triple-nanowire geometries have been studied. In particular, we found that in single-helical nanostructures, the enhancement of chiro-optical effects achievable by geometrical design is limited, especially with respect to the operation wavelength and the circular polarization conversion purity. Conversely, in the triple-helical nanowire configuration, the dominant interaction is the coupling among the intertwined coaxial helices which is driven by a symmetric spatial arrangement. Consequently, a general improvement in the g-factor, extinction ratio and signal-to-noise-ratio is achieved in a broad spectral range. Moreover, while in single-helical nanowires a mixed linear and circular birefringence results in an optical activity strongly dependent on the sample orientation and wavelength, in the triple-helical nanowire configuration, the obtained purely circular birefringence leads to a large optical activity up to 8°, independent of the sample angle, and extending in a broad band of 500 nm in the visible range. These results demonstrate a strong correlation between the configurational internal interactions and the chiral feature designation, which can be effectively exploited for nanoscale chiral device engineering.

  15. Influence of continuous mining arrangements on respirable dust exposures

    Science.gov (United States)

    Beck, T. W.; Organiscak, J. A.; Pollock, D. E.; Potts, J. D.; Reed, W. R.

    2017-01-01

    In underground continuous mining operations, ventilation, water sprays and machine-mounted flooded-bed scrubbers are the primary means of controlling respirable dust exposures at the working face. Changes in mining arrangements — such as face ventilation configuration, orientation of crosscuts mined in relation to the section ventilation and equipment operator positioning — can have impacts on the ability of dust controls to reduce occupational respirable dust exposures. This study reports and analyzes dust concentrations measured by the Pittsburgh Mining Research Division for remote-controlled continuous mining machine operators as well as haulage operators at 10 U.S. underground mines. The results of these respirable dust surveys show that continuous miner exposures varied little with depth of cut but are significantly higher with exhaust ventilation. Haulage operators experienced elevated concentrations with blowing face ventilation. Elevated dust concentrations were observed for both continuous miner operators and haulage operators when working in crosscuts driven into or counter to the section airflow. Individual cuts are highlighted to demonstrate instances of minimal and excessive dust exposures attributable to particular mining configurations. These findings form the basis for recommendations for lowering face worker respirable dust exposures. PMID:28529441

  16. Toward automated formation of microsphere arrangements using multiplexed optical tweezers

    Science.gov (United States)

    Rajasekaran, Keshav; Bollavaram, Manasa; Banerjee, Ashis G.

    2016-09-01

    Optical tweezers offer certain advantages such as multiplexing using a programmable spatial light modulator, flexibility in the choice of the manipulated object and the manipulation medium, precise control, easy object release, and minimal object damage. However, automated manipulation of multiple objects in parallel, which is essential for efficient and reliable formation of micro-scale assembly structures, poses a difficult challenge. There are two primary research issues in addressing this challenge. First, the presence of stochastic Langevin force giving rise to Brownian motion requires motion control for all the manipulated objects at fast rates of several Hz. Second, the object dynamics is non-linear and even difficult to represent analytically due to the interaction of multiple optical traps that are manipulating neighboring objects. As a result, automated controllers have not been realized for tens of objects, particularly with three dimensional motions with guaranteed collision avoidances. In this paper, we model the effect of interacting optical traps on microspheres with significant Brownian motions in stationary fluid media, and develop simplified state-space representations. These representations are used to design a model predictive controller to coordinate the motions of several spheres in real time. Preliminary experiments demonstrate the utility of the controller in automatically forming desired arrangements of varying configurations starting with randomly dispersed microspheres.

  17. Corn plant arrangement and its effect on silage quality

    Directory of Open Access Journals (Sweden)

    Fernando Reimann Skonieski

    2014-03-01

    Full Text Available This experiment was carried out to evaluate the effects of the row spacing between corn plants on silage quality. Different spacing between corn rows (40, 60, and 80 cm was used, but the population of plants was maintained around 65,000/ha in all treatments. Analysis of variance was carried out and means were compared by Tukey's test at 5% of probability. A reduction in row spacing provided better spatial distribution of plants, but did not alter morphological composition or dry matter production. The corn with most equidistant spatial distribution (lowest row spacing showed an increase in lignin concentration, neutral detergent fiber, and total carbohydrates, and showed a decrease in total digestible nutrients when compared with 80 cm row spacing. However, the organic digestibility matter was not affected by the treatments. The content and quality of protein were higher for 80 cm row spacing compared with the other levels; also, protein content was reduced as the spacing between rows became smaller. The only mineral affected was calcium, which had the lowest value at higher levels of spacing. Although differences were detected for many variables, the most appropriate spacing between rows should also take into account economic and practical aspects when choosing the best plant arrangement.

  18. Earth Observation Data Interoperability Arrangement with Ontology Registry

    Science.gov (United States)

    Nagai, M.; Ono, M.; Shibasaki, R.

    2012-08-01

    Standardization organizations are working for syntactic and schematic level of interoperability. At the same time, semantic interoperability must be considered as a heterogeneous condition and also very diversified with a large-volume data. The ontology registry has been developed and ontological information such as technical vocabularies for earth observation has been collected for data interoperability arrangement. This is a very challenging method for earth observation data interoperability because collaboration or cooperation with scientists of different disciplines is essential for common understanding. Multiple semantic MediaWikis are applied to register and update technical vocabularies as a part of the ontology registry, which promises to be a useful tool for users. In order to invite contributions from the user community, it is necessary to provide sophisticated and easy-to-use tools and systems, such as table-like editor, reverse dictionary, and graph representation for sustainable development and usage of ontological information. Registered ontologies supply the reference information required for earth observation data retrieval. We proposed data/metadata search with ontology such as technical vocabularies and visualization of relations among dataset to very large scale and various earth observation data.

  19. Optimal design of the satellite constellation arrangement reconfiguration process

    Science.gov (United States)

    Fakoor, Mahdi; Bakhtiari, Majid; Soleymani, Mahshid

    2016-08-01

    In this article, a novel approach is introduced for the satellite constellation reconfiguration based on Lambert's theorem. Some critical problems are raised in reconfiguration phase, such as overall fuel cost minimization, collision avoidance between the satellites on the final orbital pattern, and necessary maneuvers for the satellites in order to be deployed in the desired position on the target constellation. To implement the reconfiguration phase of the satellite constellation arrangement at minimal cost, the hybrid Invasive Weed Optimization/Particle Swarm Optimization (IWO/PSO) algorithm is used to design sub-optimal transfer orbits for the satellites existing in the constellation. Also, the dynamic model of the problem will be modeled in such a way that, optimal assignment of the satellites to the initial and target orbits and optimal orbital transfer are combined in one step. Finally, we claim that our presented idea i.e. coupled non-simultaneous flight of satellites from the initial orbital pattern will lead to minimal cost. The obtained results show that by employing the presented method, the cost of reconfiguration process is reduced obviously.

  20. Cooperating internationally. US/Japan Civil Industrial Technologies (CIT) Arrangement

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-12-01

    The Civil Industrial Technologies (CIT) Arrangement was signed in July 1994 between governments of the US and Japan. Areas of research range from scientific and technical databases and bioprocessing to precompetitive processing of functionally-gradient materials and ceramics. Papers presented in this symposium include studies on thin polymer films generated by vapor deposition polymerization, development of manufacturing technique of fusing 3D C/C composite materials, measurement and analysis for high performance computing systems, low-cost fabrication of ceramic components, bioprocessing, data exchange for mass spectral databases, development of high performance aluminum nitride ceramics, precompetitive processing of functionally-gradient materials, purity determination of organic reference materials, definitive methods traceable to SI unit, development of biocompatible artificial hard tissue materials, development of photoassisted catalysis technologies, surface analysis for catalysts by electron spectroscopy, development of ultra-solid lubricant with cluster diamond, precise determination of impurities in high-purity rare-earth metals, and highly accurate acceleration measurement system. 22 refs., 86 figs., 3 tabs.