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Sample records for repetitive dna final

  1. Haben repetitive DNA-Sequenzen biologische Funktionen?

    Science.gov (United States)

    John, Maliyakal E.; Knöchel, Walter

    1983-05-01

    By DNA reassociation kinetics it is known that the eucaryotic genome consists of non-repetitive DNA, middle-repetitive DNA and highly repetitive DNA. Whereas the majority of protein-coding genes is located on non-repetitive DNA, repetitive DNA forms a constitutive part of eucaryotic DNA and its amount in most cases equals or even substantially exceeds that of non-repetitive DNA. During the past years a large body of data on repetitive DNA has accumulated and these have prompted speculations ranging from specific roles in the regulation of gene expression to that of a selfish entity with inconsequential functions. The following article summarizes recent findings on structural, transcriptional and evolutionary aspects and, although by no means being proven, some possible biological functions are discussed.

  2. Transcription of repetitive DNA in Neurospora crassa

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    Dutta, S K; Chaudhuri, R K

    1975-01-01

    Repeated DNA sequences of Neurospora crassa were isolated and characterized. Approximately 10 to 12 percent of N. crassa DNA sequence were repeated, of which 7.3 percent were found to be transcribed in mid-log phase of mycelial growth as measured by DNA:RNA hybridization. It is suggested that part of repetitive DNA transcripts in N. crassa were mitochondrial and part were nuclear DNA. Most of the nuclear repeated DNAs, however, code for rRNA and tRNA in N. crassa. (auth)

  3. Transcription of tandemly repetitive DNA: functional roles.

    Science.gov (United States)

    Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco

    2015-09-01

    A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

  4. Directed PCR-free engineering of highly repetitive DNA sequences

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    Preissler Steffen

    2011-09-01

    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  5. Analysis of repetitive DNA in chromosomes by flow cytometry

    NARCIS (Netherlands)

    Brind'Amour, Julie; Lansdorp, Peter M.

    We developed a flow cytometry method, chromosome flow fluorescence in situ hybridization (FISH), called CFF, to analyze repetitive DNA in chromosomes using FISH with directly labeled peptide nucleic acid (PNA) probes. We used CFF to measure the abundance of interstitial telomeric sequences in

  6. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

    DEFF Research Database (Denmark)

    Svitashev, S.; Bryngelsson, T.; Vershinin, A.

    1994-01-01

    A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. In situ hybridization experiments showed dispersed organization of the sequences...

  7. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    OpenAIRE

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-01-01

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

  8. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    Science.gov (United States)

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-03-26

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

  9. Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus

    NARCIS (Netherlands)

    Foulongne-Oriol, M.; Murat, C.; Castanera, R.; Ramírez, L.; Sonnenberg, A.S.M.

    2013-01-01

    Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of

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

    Science.gov (United States)

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

    1988-09-12

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

  11. Impact of repetitive DNA on sex chromosome evolution in plants

    Czech Academy of Sciences Publication Activity Database

    Hobza, Roman; Kubát, Z.; Čegan, R.; Jesionek, W.; Vyskot, B.; Kejnovský, E.

    2015-01-01

    Roč. 23, č. 3 (2015), s. 561-570 ISSN 0967-3849 R&D Projects: GA ČR GBP501/12/G090; GA ČR GAP501/12/2220 Institutional support: RVO:61389030 Keywords : repetitive sequences * transposable elements * tandem repeats (satellites) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.590, year: 2015

  12. Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae

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    E. Coluccia

    2011-05-01

    Full Text Available Muraenidae is a species-rich family, with relationships among genera and species and taxonomy that have not been completely clarified. Few cytogenetic studies have been conducted on this family, and all of them showed the same diploid chromosome number (2n=42 but with conspicuous karyotypic variation among species. The Mediterranean moray eel Gymnothorax unicolor was previously cytogenetically studied using classical techniques that allowed the characterization of its karyotype structure and the constitutive heterochromatin and argyrophilic nucleolar organizer regions (Ag-NORs distribution pattern. In the present study, we describe two new repetitive elements (called GuMboI and GuDdeI obtained from restricted genomic DNA of G. unicolor that were characterized by Southern blot and physically localized by in situ hybridization on metaphase chromosomes. As they are highly repetitive DNA sequences, they map in heterochromatic regions. However, while GuDdeI was localized in the centromeric regions, the GuMboI fraction was distributed on some centromeres and was co-localized with the nucleolus organizer region (NOR. Comparative analysis with other Mediterranean species such as Muraena helena pointed out that these DNA fractions are species-specific and could potentially be used for species discrimination. As a new contribution to the karyotype of this species, we found that the major ribosomal genes are localized on acrocentric chromosome 9 and that the telomeres of each chromosome are composed of a tandem repeat derived from a poly-TTAGGG DNA sequence, as it occurs in most vertebrate species. The results obtained add new information useful in comparative genomics at the chromosomal level and contribute to the cytogenetic knowledge regarding this fish family, which has not been extensively studied.

  13. Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

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    Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

    1979-02-01

    Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

  14. Mammalian DNA Repair. Final Report

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    Wood, Richard D.

    2003-01-24

    The Gordon Research Conference (GRC) on Mammalian DNA Repair was held at Harbortown Resort, Ventura Beach, CA. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  15. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination

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    Hoang, Margaret L.; Tan, Frederick J.; Lai, David C.; Celniker, Sue E.; Hoskins, Roger A.; Dunham, Maitreya J.; Zheng, Yixian; Koshland, Douglas

    2010-08-27

    Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

  16. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

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    Margaret L Hoang

    2010-12-01

    Full Text Available Genome rearrangements often result from non-allelic homologous recombination (NAHR between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

  17. [Identification of a repetitive sequence element for DNA fingerprinting in Phytophthora sojae].

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    Yin, Lihua; Wang, Qinhu; Ning, Feng; Zhu, Xiaoying; Zuo, Yuhu; Shan, Weixing

    2010-04-01

    Establishment of DNA fingerprinting in Phytophthora sojae and an analysis of genetic relationship of Heilongjiang and Xinjiang populations. Bioinformatics tools were used to search repetitive sequences in P. sojae and Southern blot analysis was employed for DNA fingerprinting analysis of P. sojae populations from Heilongjiang and Xinjiang using the identified repetitive sequence. A moderately repetitive sequence was identified and designated as PS1227. Southern blot analysis indicated 34 distinct bands ranging in size from 1.5 kb-23 kb, of which 21 were polymorphic among 49 isolates examined. Analysis of single-zoospore progenies showed that the PS1227 fingerprint pattern was mitotically stable. DNA fingerprinting showed that the P. sojae isolates HP4002, SY6 and GJ0105 of Heilongjiang are genetically identical to DW303, 71228 and 71222 of Xinjiang, respectively. A moderately repetitive sequence designated PS1227 which will be useful for epidemiology and population biology studies of P. sojae was obtained, and a PS1227-based DNA fingerprinting analysis provided molecular evidence that P. sojae in Xinjiang was likely introduced from Heilongjiang.

  18. Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds

    Czech Academy of Sciences Publication Activity Database

    Křivánková, Anna; Kopecký, David; Stočes, Štěpán; Doležel, Jaroslav; Hřibová, Eva

    2017-01-01

    Roč. 151, č. 2 (2017), s. 96-105 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Fluorescence in situ hybridization * Karyotyping * Meadow fescue * Repetitive DNA * Tandem organized repeats Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.354, year: 2016

  19. Radiation-induced changes in DNA methylation of repetitive elements in the mouse heart

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    Koturbash, Igor, E-mail: ikoturbash@uams.edu [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Miousse, Isabelle R. [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Sridharan, Vijayalakshmi [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Nzabarushimana, Etienne; Skinner, Charles M. [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Melnyk, Stepan B.; Pavliv, Oleksandra [Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Hauer-Jensen, Martin [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Surgical Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205 (United States); Nelson, Gregory A. [Departments of Basic Sciences and Radiation Medicine, Loma Linda University, Loma Linda, CA 92354 (United States); Boerma, Marjan [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States)

    2016-05-15

    Highlights: • Radiation-induced dynamic changes in cardiac DNA methylation were detected. • Early LINE-1 hypomethylation was followed by hypermethylation at a later time-point. • Radiation affected one-carbon metabolism in the heart tissue. • Irradiation resulted in accumulation of satellite DNA mRNA transcripts. - Abstract: DNA methylation is a key epigenetic mechanism, needed for proper control over the expression of genetic information and silencing of repetitive elements. Exposure to ionizing radiation, aside from its strong genotoxic potential, may also affect the methylation of DNA, within the repetitive elements, in particular. In this study, we exposed C57BL/6J male mice to low absorbed mean doses of two types of space radiation—proton (0.1 Gy, 150 MeV, dose rate 0.53 ± 0.08 Gy/min), and heavy iron ions ({sup 56}Fe) (0.5 Gy, 600 MeV/n, dose rate 0.38 ± 0.06 Gy/min). Radiation-induced changes in cardiac DNA methylation associated with repetitive elements were detected. Specifically, modest hypomethylation of retrotransposon LINE-1 was observed at day 7 after irradiation with either protons or {sup 56}Fe. This was followed by LINE-1, and other retrotransposons, ERV2 and SINE B1, as well as major satellite DNA hypermethylation at day 90 after irradiation with {sup 56}Fe. These changes in DNA methylation were accompanied by alterations in the expression of DNA methylation machinery and affected the one-carbon metabolism pathway. Furthermore, loss of transposable elements expression was detected in the cardiac tissue at the 90-day time-point, paralleled by substantial accumulation of mRNA transcripts, associated with major satellites. Given that the one-carbon metabolism pathway can be modulated by dietary modifications, these findings suggest a potential strategy for the mitigation and, possibly, prevention of the negative effects exerted by ionizing radiation on the cardiovascular system. Additionally, we show that the methylation status and

  20. Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

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    Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

    2009-01-01

    The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

  1. Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Kejnovský, Eduard; Neumann, Pavel; Novák, Petr; Koblížková, Andrea; Vyskot, Boris

    2011-01-01

    Roč. 6, č. 11 (2011), e27335 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004; GA MŠk(CZ) LH11058; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP305/10/0930 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040702 Keywords : Plant genome * Sequencing-Based Analyses * Repetitive DNA * Silene latifolia Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

  2. B chromosome in the beetle Coprophanaeus cyanescens (Scarabaeidae: emphasis in the organization of repetitive DNA sequences

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    Gomes de Oliveira Sarah

    2012-11-01

    Full Text Available Abstract Background To contribute to the knowledge of coleopteran cytogenetics, especially with respect to the genomic content of B chromosomes, we analyzed the composition and organization of repetitive DNA sequences in the Coprophanaeus cyanescens karyotype. We used conventional staining and the application of fluorescence in situ hybridization (FISH mapping using as probes C0t-1 DNA fraction, the 18S and 5S rRNA genes, and the LOA-like non-LTR transposable element (TE. Results The conventional analysis detected 3 individuals (among 50 analyzed carrying one small metacentric and mitotically unstable B chromosome. The FISH analysis revealed a pericentromeric block of C0t-1 DNA in the B chromosome but no 18S or 5S rDNA clusters in this extra element. Using the LOA-like TE probe, the FISH analysis revealed large pericentromeric blocks in eight autosomal bivalents and in the B chromosome, and a pericentromeric block extending to the short arm in one autosomal pair. No positive hybridization signal was observed for the LOA-like element in the sex chromosomes. Conclusions The results indicate that the origin of the B chromosome is associated with the autosomal elements, as demonstrated by the hybridization with C0t-1 DNA and the LOA-like TE. The present study is the first report on the cytogenetic mapping of a TE in coleopteran chromosomes. These TEs could have been involved in the origin and evolution of the B chromosome in C. cyanescens.

  3. The fission yeast CENP-B protein Abp1 prevents pervasive transcription of repetitive DNA elements.

    Science.gov (United States)

    Daulny, Anne; Mejía-Ramírez, Eva; Reina, Oscar; Rosado-Lugo, Jesus; Aguilar-Arnal, Lorena; Auer, Herbert; Zaratiegui, Mikel; Azorin, Fernando

    2016-10-01

    It is well established that eukaryotic genomes are pervasively transcribed producing cryptic unstable transcripts (CUTs). However, the mechanisms regulating pervasive transcription are not well understood. Here, we report that the fission yeast CENP-B homolog Abp1 plays an important role in preventing pervasive transcription. We show that loss of abp1 results in the accumulation of CUTs, which are targeted for degradation by the exosome pathway. These CUTs originate from different types of genomic features, but the highest increase corresponds to Tf2 retrotransposons and rDNA repeats, where they map along the entire elements. In the absence of abp1, increased RNAPII-Ser5P occupancy is observed throughout the Tf2 coding region and, unexpectedly, RNAPII-Ser5P is enriched at rDNA repeats. Loss of abp1 also results in Tf2 derepression and increased nucleolus size. Altogether these results suggest that Abp1 prevents pervasive RNAPII transcription of repetitive DNA elements (i.e., Tf2 and rDNA repeats) from internal cryptic sites. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Human β satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA

    International Nuclear Information System (INIS)

    Waye, J.S.; Willard, H.F.

    1989-01-01

    The authors describe a class of human repetitive DNA, called β satellite, that, at a most fundamental level, exists as tandem arrays of diverged ∼68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. They have cloned, characterized, and determined the sequence of two β satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains that are marked by restriction fragment length polymorphisms. In total, β-satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes

  5. Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

    Science.gov (United States)

    Trofimova, Irina; Krasikova, Alla

    2016-12-01

    Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

  6. Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum

    Czech Academy of Sciences Publication Activity Database

    Renny-Byfield, S.; Kovařík, Aleš; Chester, M.; Nichols, R.A.; Macas, Jiří; Novák, Petr; Leitch, A.R.

    2012-01-01

    Roč. 7, č. 5 (2012), e36963 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP501/10/0208; GA MŠk OC10037 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z50510513 Keywords : chromosome evolution * repetitive DNA * allopolyploid Subject RIV: BO - Biophysics; EB - Genetics ; Molecular Biology (BC-A) Impact factor: 3.730, year: 2012

  7. S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

    Science.gov (United States)

    Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

    2016-02-01

    S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

  8. Gamma radiation-induced heritable mutations at repetitive DNA loci in out-bred mice

    International Nuclear Information System (INIS)

    Somers, C.M.; Sharma, R.; Quinn, J.S.; Boreham, D.R.

    2004-01-01

    Recent studies have shown that expanded-simple-tandem-repeat (ESTR) DNA loci are efficient genetic markers for detecting radiation-induced germ line mutations in mice. Dose responses following irradiation, however, have only been characterized in a small number of inbred mouse strains, and no studies have applied Esters to examine potential modifiers of radiation risk, such as adaptive response. We gamma-irradiated groups of male out-bred Swiss-Webster mice with single acute doses of 0.5 and 1.0 Gy, and compared germ line mutation rates at ESTR loci to a sham-irradiated control. To test for evidence of adaptive response we treated a third group with a total dose of 1.1 Gy that was fractionated into a 0.1 Gy adapting dose, followed by a challenge dose of 1.0 Gy 24 h later. Paternal mutation rates were significantly elevated above the control in the 0.5 Gy (2.8-fold) and 1.0 Gy (3.0-fold) groups, but were similar to each other despite the difference in radiation dose. The doubling dose for paternal mutation induction was 0.26 Gy (95% CI = 0.14-0.51 Gy). Males adapted with a 0.1 Gy dose prior to a 1.0 Gy challenge dose had mutation rates that were not significantly elevated above the control, and were 43% reduced compared to those receiving single doses. We conclude that pre-meiotic male germ cells in out-bred Swiss-Webster mice are sensitive to ESTR mutations induced by acute doses of ionizing radiation, but mutation induction may become saturated at a lower dose than in some strains of inbred mice. Reduced mutation rates in the adapted group provide intriguing evidence for suppression of ESTR mutations in the male germline through adaptive response. Repetitive DNA markers may be useful tools for exploration of biological factors affecting the probability of heritable mutations caused by low-dose ionizing radiation exposure. The biological significance of ESTR mutations in terms of radiation risk assessment, however, is still undetermined

  9. Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus.

    Science.gov (United States)

    Pita, Sebastián; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Sánchez, Antonio; Panzera, Francisco; Lorite, Pedro

    2018-04-24

    Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as "kissing bugs" (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2 n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.

  10. Repetitive stress leads to impaired cognitive function that is associated with DNA hypomethylation, reduced BDNF and a dysregulated HPA axis.

    Science.gov (United States)

    Makhathini, Khayelihle B; Abboussi, Oualid; Stein, Dan J; Mabandla, Musa V; Daniels, William M U

    2017-08-01

    Exposure to repetitive stress has a negative influence on cognitive-affective functioning, with growing evidence that these effects may be mediated by a dysregulated hypothalamic-pituitary-adrenal (HPA) axis, abnormal neurotrophic factor levels and its subsequent impact on hippocampal function. However, there are few data about the effect of repetitive stressors on epigenetic changes in the hippocampus. In the present study, we examine how repetitive restrain stress (RRS) affects cognitive-affective functioning, HPA axis regulation, brain-derived neurotrophic factor (BDNF) levels, and global hippocampal DNA methylation. RRS was induced in rats by restraining the animals for 6h per day for 28 days. The novel object recognition test (NORT) was used to assess cognitive functioning and the open field test (OFT) was performed to assess anxiety-like behavior during the last week of stress. Hippocampal BDNF levels, glucocorticoid (GR) and mineralocorticoid (MR) receptor mRNA were assessed using real-time PCR and confirmed with Western blot, while ELISAs were used to determine plasma corticosterone levels and the global methylation status of the hippocampus. Animals exposed to repetitive stress demonstrated significant alterations in the NORT and OFT, had significantly increased plasma corticosterone and significantly decreased hippocampal BDNF concentrations. The expression levels of GR and MR mRNA and protein levels of these genes were significantly decreased in the stressed group compared to control animals. The global DNA methylation of the hippocampal genome of stressed animals was also significantly decreased compared to controls. The data here are consistent with previous work emphasizing the role of the HPA axis and neurotrophic factors in mediating cognitive-affective changes after exposure to repetitive stressors. Our findings, however, extend the literature by indicating that epigenetic alterations in the hippocampal genome may also play an important role in the

  11. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

    Science.gov (United States)

    Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

    2009-07-23

    Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

  12. The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

    Directory of Open Access Journals (Sweden)

    Lee Robert W

    2009-03-01

    Full Text Available Abstract Background The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA and plastid DNA (ptDNA sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence. Results We sequenced 30 and 420 kilobases (kb of the mitochondrial and plastid genomes of V. carteri, respectively – resulting in partial assemblies of these genomes. The mitochondrial genome is the most bloated green-algal mtDNA observed to date: ~61% of the sequence is noncoding, most of which is comprised of short palindromic repeats spread throughout the intergenic and intronic regions. The plastid genome is the largest (>420 kb and most expanded (>80% noncoding ptDNA sequence yet discovered, with a myriad of palindromic repeats in the noncoding regions, which have a similar size and secondary structure to those of the mtDNA. We found that 15 kb (~0.01% of the nuclear genome are homologous to the palindromic elements of the mtDNA, and 50 kb (~0.05% are homologous to those of the ptDNA. Conclusion Selfish elements in the form of short palindromic repeats have propagated in the V. carteri mtDNA and ptDNA, resulting in the distension of these genomes. Copies of these same repeats are also found in a small fraction of the nucDNA, but appear to be inert in this

  13. The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

    Directory of Open Access Journals (Sweden)

    Armen Sanosyan

    Full Text Available Viral load monitoring and early Epstein-Barr virus (EBV DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples.Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux. Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples.BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002. BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12. Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays.Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

  14. The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

    Science.gov (United States)

    Sanosyan, Armen; Fayd'herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

    2017-01-01

    Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

  15. Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the basis of poisson statistics.

    Science.gov (United States)

    De Spiegelaere, Ward; Malatinkova, Eva; Lynch, Lindsay; Van Nieuwerburgh, Filip; Messiaen, Peter; O'Doherty, Una; Vandekerckhove, Linos

    2014-06-01

    Quantification of integrated proviral HIV DNA by repetitive-sampling Alu-HIV PCR is a candidate virological tool to monitor the HIV reservoir in patients. However, the experimental procedures and data analysis of the assay are complex and hinder its widespread use. Here, we provide an improved and simplified data analysis method by adopting binomial and Poisson statistics. A modified analysis method on the basis of Poisson statistics was used to analyze the binomial data of positive and negative reactions from a 42-replicate Alu-HIV PCR by use of dilutions of an integration standard and on samples of 57 HIV-infected patients. Results were compared with the quantitative output of the previously described Alu-HIV PCR method. Poisson-based quantification of the Alu-HIV PCR was linearly correlated with the standard dilution series, indicating that absolute quantification with the Poisson method is a valid alternative for data analysis of repetitive-sampling Alu-HIV PCR data. Quantitative outputs of patient samples assessed by the Poisson method correlated with the previously described Alu-HIV PCR analysis, indicating that this method is a valid alternative for quantifying integrated HIV DNA. Poisson-based analysis of the Alu-HIV PCR data enables absolute quantification without the need of a standard dilution curve. Implementation of the CI estimation permits improved qualitative analysis of the data and provides a statistical basis for the required minimal number of technical replicates. © 2014 The American Association for Clinical Chemistry.

  16. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Science.gov (United States)

    Piednoël, Mathieu; Aberer, Andre J.; Schneeweiss, Gerald M.; Macas, Jiri; Novak, Petr; Gundlach, Heidrun; Temsch, Eva M.; Renner, Susanne S.

    2013-01-01

    We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. PMID:22723303

  17. Conformational Diversity of Single-Stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases

    Czech Academy of Sciences Publication Activity Database

    Charnavets, Tatsiana; Nunvář, Jaroslav; Nečasová, Iva; Voelker, J.; Breslauer, K.J.; Schneider, Bohdan

    2015-01-01

    Roč. 103, č. 10 (2015), s. 585-596 ISSN 0006-3525 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109; GA ČR GAP305/12/1801; GA MŠk(CZ) EE2.3.30.0020 Institutional support: RVO:86652036 Keywords : bacterial repetitive extragenic palindromes (REP) * circular dichroism spectroscopy * REP associated tyrosine transposases (RAYTs) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.248, year: 2015

  18. Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter

    Science.gov (United States)

    Maumus, Florian; Quesneville, Hadi

    2014-01-01

    Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and non-annotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the A. thaliana repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant. PMID:24709859

  19. By-product formation in repetitive PCR amplification of DNA libraries during SELEX.

    Science.gov (United States)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.

  20. Repetitive DNA Reeling by the Cascade-Cas3 Complex in Nucleotide Unwinding Steps

    NARCIS (Netherlands)

    Loeff, Luuk; Brouns, Stan J.J.; Joo, Chirlmin

    2018-01-01

    CRISPR-Cas provides RNA-guided adaptive immunity against invading genetic elements. Interference in type I systems relies on the RNA-guided Cascade complex for target DNA recognition and the Cas3 helicase/nuclease protein for target degradation. Even though the biochemistry of CRISPR interference

  1. Condensin suppresses recombination and regulates double-strand break processing at the repetitive ribosomal DNA array to ensure proper chromosome segregation during meiosis in budding yeast

    Science.gov (United States)

    Li, Ping; Jin, Hui; Yu, Hong-Guo

    2014-01-01

    During meiosis, homologues are linked by crossover, which is required for bipolar chromosome orientation before chromosome segregation at anaphase I. The repetitive ribosomal DNA (rDNA) array, however, undergoes little or no meiotic recombination. Hyperrecombination can cause chromosome missegregation and rDNA copy number instability. We report here that condensin, a conserved protein complex required for chromosome organization, regulates double-strand break (DSB) formation and repair at the rDNA gene cluster during meiosis in budding yeast. Condensin is highly enriched at the rDNA region during prophase I, released at the prophase I/metaphase I transition, and reassociates with rDNA before anaphase I onset. We show that condensin plays a dual role in maintaining rDNA stability: it suppresses the formation of Spo11-mediated rDNA breaks, and it promotes DSB processing to ensure proper chromosome segregation. Condensin is unnecessary for the export of rDNA breaks outside the nucleolus but required for timely repair of meiotic DSBs. Our work reveals that condensin coordinates meiotic recombination with chromosome segregation at the repetitive rDNA sequence, thereby maintaining genome integrity. PMID:25103240

  2. By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX

    DEFF Research Database (Denmark)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recogniz......The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target......-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments....... Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation...

  3. Homologous subfamilies of human alphoid repetitive DNA on different nucleolus organizing chromosomes

    International Nuclear Information System (INIS)

    Joergensen, A.L.; Bostock, C.J.; Bak, A.L.

    1987-01-01

    The organization of alphoid repeated sequences on human nucleolus-organizing (NOR) chromosomes 13, 21, and 22 has been investigated. Analysis of hybridization of alphoid DNA probes to Southern transfers of restriction enzyme-digested DNA fragments from hybrid cells containing single human chromosomes shows that chromosomes 13 and 21 share one subfamily of alphoid repeats, whereas a different subfamily may be held in common by chromosomes 13 and 22. The sequences of cloned 680-base-pair EcoRI fragments of the alphoid DNA from chromosomes 13 and 21 show that the basic unit of this subfamily is indistinguishable on each chromosome. The sequence of cloned 1020-base-pair Xba I fragments from chromosome 22 is related to, but distinguishable from, that of the 680-base-pair EcoRI alphoid subfamily of chromosomes 13 and 21. These results suggest that, at some point after they originated and were homogenized, different subfamilies of alphoid sequences must have exchanged between chromosomes 13 and 21 and separately between chromosomes 13 and 22

  4. 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.

  5. DNA Fingerprinting of Lactobacillus crispatus Strain CTV-05 by Repetitive Element Sequence-Based PCR Analysis in a Pilot Study of Vaginal Colonization

    OpenAIRE

    Antonio, May A. D.; Hillier, Sharon L.

    2003-01-01

    Lactobacillus crispatus is one of the predominant hydrogen peroxide (H2O2)-producing species found in the vagina and is under development as a probiotic for the treatment of bacterial vaginosis. In this study, we assessed whether DNA fingerprinting by repetitive element sequence-based PCR (rep-PCR) can be used to distinguish the capsule strain of L. crispatus (CTV-05) from other endogenous strains as well as other species of vaginal lactobacilli. Vaginal and rectal lactobacilli were identifie...

  6. Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides.

    Science.gov (United States)

    Nakata, A; Yoshimura, A; Kuro-o, M; Obara, Y

    2005-01-01

    The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.

  7. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  8. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Science.gov (United States)

    Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

    2015-01-01

    The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  9. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Directory of Open Access Journals (Sweden)

    Jiří Macas

    Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  10. Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    Science.gov (United States)

    Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

    2010-01-01

    Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. PMID:20047966

  11. Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.

    Science.gov (United States)

    Mason, Christopher E; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M; Kallen, Roland G; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B

    2010-04-01

    Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.

  12. Molecular mechanisms in radiation damage to DNA: Final report

    International Nuclear Information System (INIS)

    Osman, R.

    1996-01-01

    The objectives of this work were to elucidate the molecular mechanisms that were responsible for radiation-induced DNA damage. The studies were based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA

  13. DNA Methylation Status of the Interspersed Repetitive Sequences for LINE-1, Alu, HERV-E, and HERV-K in Trabeculectomy Specimens from Glaucoma Eyes

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    Sunee Chansangpetch

    2018-01-01

    Full Text Available Background/Aims. Epigenetic mechanisms via DNA methylation may be related to glaucoma pathogenesis. This study aimed to determine the global DNA methylation level of the trabeculectomy specimens among patients with different types of glaucoma and normal subjects. Methods. Trabeculectomy sections from 16 primary open-angle glaucoma (POAG, 12 primary angle-closure glaucoma (PACG, 16 secondary glaucoma patients, and 10 normal controls were assessed for DNA methylation using combined-bisulfite restriction analysis. The percentage of global methylation level of the interspersed repetitive sequences for LINE-1, Alu, HERV-E, and HERV-K were compared between the 4 groups. Results. There were no significant differences in the methylation for LINE-1 and HERV-E between patients and normal controls. For the Alu marker, the methylation was significantly lower in all types of glaucoma patients compared to controls (POAG 52.19% versus control 52.83%, p=0.021; PACG 51.50% versus control, p=0.005; secondary glaucoma 51.95% versus control, p=0.014, whereas the methylation level of HERV-K was statistically higher in POAG patients compared to controls (POAG 49.22% versus control 48.09%, p=0.017. Conclusions. The trabeculectomy sections had relative DNA hypomethylation of Alu in all glaucoma subtypes and relative DNA hypermethylation of HERV-K in POAG patients. These methylation changes may lead to the fibrotic phenotype in the trabecular meshwork.

  14. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

    Science.gov (United States)

    Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

    2017-01-01

    High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713

  15. Repair of damaged DNA in vivo: Final technical report

    International Nuclear Information System (INIS)

    Hanawalt, P.C.

    1987-09-01

    This contract was initiated in 1962 with the US Atomic Energy Commission to carry out basic research on the effects of radiation on the process of DNA replication in bacteria. Within the first contract year we discovered repair replication at the same time that Setlow and Carrier discovered pyrimidine dimer excision. These discoveries led to the elucidation of the process of excision-repair, one of the most important mechanisms by which living systems, including humans, respond to structural damage in their genetic material. We improved methodology for distinguishing repair replication from semiconservative replication and instructed others in these techniques. Painter then was the first to demonstrate repair replication in ultraviolet irradiated human cells. He, in turn, instructed James Cleaver who discovered that skin fibroblasts from patients with xeroderma pigmentosum were defective in excision-repair. People with this genetic defect are extremely sensitive to sunlight and they develop carcinomas and melanomas of the skin with high frequency. The existence of this hereditary disease attests to the importance of DNA repair in man. We certainly could not survive in the normal ultraviolet flux from the sun if our DNA were not continuously monitored for damage and repaired. Other hereditary diseases such as ataxia telangiectasia, Cockayne's syndrome, Blooms syndrome and Fanconi's anemia also involve deficiencies in DNA damage processing. The field of DNA repair has developed rapidly as we have learned that most environmental chemical carcinogens as well as radiation produce repairable damage in DNA. 251 refs

  16. GENETIC DIVERSITY OF TYPHA LATIFOLIA (TYPHACEAE) AND THE IMPACT OF POLLUTANTS EXAMINED WITH TANDEM-REPETITIVE DNA PROBES

    Science.gov (United States)

    Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated "core" sequences (GACA, GATA, and GCAC). The principal objectives of this investigation w...

  17. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    Science.gov (United States)

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Navrátilová Alice

    2007-11-01

    Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

  19. Vertically integrated analysis of human DNA. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Olson, M.

    1997-10-01

    This project has been oriented toward improving the vertical integration of the sequential steps associated with the large-scale analysis of human DNA. The central focus has been on an approach to the preparation of {open_quotes}sequence-ready{close_quotes} maps, which is referred to as multiple-complete-digest (MCD) mapping, primarily directed at cosmid clones. MCD mapping relies on simple experimental steps, supported by advanced image-analysis and map-assembly software, to produce extremely accurate restriction-site and clone-overlap maps. We believe that MCD mapping is one of the few high-resolution mapping systems that has the potential for high-level automation. Successful automation of this process would be a landmark event in genome analysis. Once other higher organisms, paving the way for cost-effective sequencing of these genomes. Critically, MCD mapping has the potential to provide built-in quality control for sequencing accuracy and to make possible a highly integrated end product even if there are large numbers of discontinuities in the actual sequence.

  20. Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

    Science.gov (United States)

    Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

    2003-09-01

    Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

  1. Novel porcine repetitive elements

    Directory of Open Access Journals (Sweden)

    Nonneman Dan J

    2006-12-01

    Full Text Available Abstract Background Repetitive elements comprise ~45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals. Results We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI. These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute, covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats. Conclusion The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

  2. Differential chromosomal organization between Saguinus midas and Saguinus bicolor with accumulation of differences the repetitive sequence DNA.

    Science.gov (United States)

    Serfaty, Dayane Martins Barbosa; Carvalho, Natália Dayane Moura; Gross, Maria Claudia; Gordo, Marcelo; Schneider, Carlos Henrique

    2017-10-01

    Saguinus is the largest and most complex genus of the subfamily Callitrichinae, with 23 species distributed from the south of Central America to the north of South America with Saguinus midas having the largest geographical distribution while Saguinus bicolor has a very restricted one, affected by the population expansion in the state of Amazonas. Considering the phylogenetic proximity of the two species along with evidence on the existence of hybrids between them, as well as cytogenetic studies on Saguinus describing a conserved karyotypic macrostructure, we carried out a physical mapping of DNA repeated sequences in the mitotic chromosome of both species, since these sequences are less susceptible to evolutionary pressure and possibly perform an important function in speciation. Both species presented 2n = 46 chromosomes; in S. midas, chromosome Y is the smallest. Multiple ribosomal sites occur in both species, but chromosome pairs three and four may be regarded as markers that differ the species when subjected to G banding and distribution of retroelement LINE 1, suggesting that it may be cytogenetic marker in which it can contribute to identification of first generation hybrids in contact zone. Saguinus bicolor also presented differences in the LINE 1 distribution pattern for sexual chromosome X in individuals from different urban fragments, probably due to geographical isolation. In this context, cytogenetic analyses reveal a differential genomic organization pattern between species S. midas and S. bicolor, in addition to indicating that individuals from different urban fragments have been accumulating differences because of the isolation between them.

  3. A repetitive DNA element regulates expression of the Helicobacter pylori sialic acid binding adhesin by a rheostat-like mechanism.

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    Anna Åberg

    2014-07-01

    Full Text Available During persistent infection, optimal expression of bacterial factors is required to match the ever-changing host environment. The gastric pathogen Helicobacter pylori has a large set of simple sequence repeats (SSR, which constitute contingency loci. Through a slipped strand mispairing mechanism, the SSRs generate heterogeneous populations that facilitate adaptation. Here, we present a model that explains, in molecular terms, how an intergenically located T-tract, via slipped strand mispairing, operates with a rheostat-like function, to fine-tune activity of the promoter that drives expression of the sialic acid binding adhesin, SabA. Using T-tract variants, in an isogenic strain background, we show that the length of the T-tract generates multiphasic output from the sabA promoter. Consequently, this alters the H. pylori binding to sialyl-Lewis x receptors on gastric mucosa. Fragment length analysis of post-infection isolated clones shows that the T-tract length is a highly variable feature in H. pylori. This mirrors the host-pathogen interplay, where the bacterium generates a set of clones from which the best-fit phenotypes are selected in the host. In silico and functional in vitro analyzes revealed that the length of the T-tract affects the local DNA structure and thereby binding of the RNA polymerase, through shifting of the axial alignment between the core promoter and UP-like elements. We identified additional genes in H. pylori, with T- or A-tracts positioned similar to that of sabA, and show that variations in the tract length likewise acted as rheostats to modulate cognate promoter output. Thus, we propose that this generally applicable mechanism, mediated by promoter-proximal SSRs, provides an alternative mechanism for transcriptional regulation in bacteria, such as H. pylori, which possesses a limited repertoire of classical trans-acting regulatory factors.

  4. Use of a repetitive DNA probe to type clinical and environmental isolates of Aspergillus flavus from a cluster of cutaneous infections in a neonatal intensive care unit.

    Science.gov (United States)

    James, M J; Lasker, B A; McNeil, M M; Shelton, M; Warnock, D W; Reiss, E

    2000-10-01

    Aspergillus flavus is second to A. fumigatus as a cause of invasive aspergillosis, but no standard method exists for molecular typing of strains from human sources. A repetitive DNA sequence cloned from A. flavus and subcloned into a pUC19 vector, pAF28, was used to type 18 isolates from diverse clinical, environmental, and geographic sources. The restriction fragment length polymorphisms generated with EcoRI- or PstI-digested genomic DNA and probed with digoxigenin-labeled pAF28 revealed complete concordance between patterns. Eighteen distinct fingerprints were observed. The probe was used to investigate two cases of cutaneous A. flavus infection in low-birth-weight infants in a neonatal intensive care unit (NICU). Both infants were transported by the same ambulance and crew to the NICU on the same day. A. flavus strains of the same genotype were isolated from both infants, from a roll of tape used to fasten their umbilical catheters, from a canvas bag used to store the tape in the ambulance, and from the tape tray in the ambulance isolette. These cases highlight the need to consider exposures in critically ill neonates that might occur during their transport to the NICU and for stringent infection control practices. The hybridization profiles of strains from a second cluster of invasive A. flavus infections in two pediatric hematology-oncology patients revealed a genotype common to strains from a definite case patient and a health care worker. A probable case patient was infected with a strain with a genotype different from that of the strain from the definite case patient but highly related to that of an environmental isolate. The high degree of discrimination and reproducibility obtained with the pAF28 probe underscores its utility for typing clinical and environmental isolates of A. flavus.

  5. Repetitive Stress Injuries

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Repetitive Stress Injuries KidsHealth / For Teens / Repetitive Stress Injuries What's ... t had any problems since. What Are Repetitive Stress Injuries? Repetitive stress injuries (RSIs) are injuries that ...

  6. Chromosomal distribution of pTa-535, pTa-86, pTa-713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L.) and spelt (Triticum spelta L.).

    Science.gov (United States)

    Goriewa-Duba, Klaudia; Duba, Adrian; Kwiatek, Michał; Wiśniewska, Halina; Wachowska, Urszula; Wiwart, Marian

    2018-01-01

    Fluorescent in situ hybridization (FISH) relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines), to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids. The FISH procedure was carried out with four DNA clones, pTa-86, pTa-535, pTa-713 and 35S rDNA used as probes. The observed polymorphisms between the investigated lines of common wheat, spelt and their hybrids was relatively low. However, differences were observed in the distribution of repetitive sequences on chromosomes 4A, 6A, 1B and 6B in selected hybrid genomes. The polymorphisms observed in common wheat and spelt hybrids carry valuable information for wheat breeders. The results of our study are also a valuable source of knowledge about genome organization and diversification in common wheat, spelt and their hybrids. The relevant information is essential for common wheat breeders, and it can contribute to breeding programs aimed at biodiversity preservation.

  7. Chromosomal distribution of pTa-535, pTa-86, pTa-713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L. and spelt (Triticum spelta L..

    Directory of Open Access Journals (Sweden)

    Klaudia Goriewa-Duba

    Full Text Available Fluorescent in situ hybridization (FISH relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines, to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids. The FISH procedure was carried out with four DNA clones, pTa-86, pTa-535, pTa-713 and 35S rDNA used as probes. The observed polymorphisms between the investigated lines of common wheat, spelt and their hybrids was relatively low. However, differences were observed in the distribution of repetitive sequences on chromosomes 4A, 6A, 1B and 6B in selected hybrid genomes. The polymorphisms observed in common wheat and spelt hybrids carry valuable information for wheat breeders. The results of our study are also a valuable source of knowledge about genome organization and diversification in common wheat, spelt and their hybrids. The relevant information is essential for common wheat breeders, and it can contribute to breeding programs aimed at biodiversity preservation.

  8. Repetition and the Concept of Repetition

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    Arne Grøn

    2013-11-01

    Full Text Available This paper offers a description of the meaning of the category of repetition. Firstly, it is pointed out that Constantin uses repetition as a concept that means the creation of epochs; the passing from Greece to Modernity is accomplished distinguishing between recollection, a concept that looks back to the past, and repetition, a concept that looks forward to future. Secondly, it is showed that the category of repetition, as a religious category, relates with what Climacus calls “ethic despair” and with what Vigilius calls “second ethics”; it is through repetition that it can be understood that sin finds its place in ethics and these shows the tension between it and dogmatics. And thirdly, it is showed that the descovery of the new category of repetition is a rediscovery of what Kierkegaard calls category of spirit; repetition has for its object the individuality, and coming to be oneself is what Kierkegaard undertands as liberty. At the end of the paper it is questioned if the category of repetition is inconsistent with the book Repetition.

  9. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    Science.gov (United States)

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  10. Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

    Science.gov (United States)

    Barionovi, D; Giorgi, S; Stoeger, A R; Ruppitsch, W; Scortichini, M

    2006-05-01

    The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic

  11. A fully automated 384 capillary array for DNA sequencer. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qingbo; Kane, T

    2003-03-20

    Phase I SpectruMedix has successfully developed an automatic 96-capillary array DNA prototype based on the multiplexed capillary electrophoresis system originated from Ames Laboratory-USDOE, Iowa State University. With computer control of all steps involved in a 96-capillary array running cycle, the prototype instrument (the SCE9600) is now capable of sequencing 450 base pairs (bp) per capillary, or 48,000 bp per instrument run within 2 hrs. Phase II of this grant involved the advancement of the core 96 capillary technologies, as well as designing a high density 384 capillary prototype. True commercialization of the 96 capillary instrument involved finalization of the gel matrix, streamlining the instrument hardware, creating a more reliable capillary cartridge, and further advancement of the data processing software. Together these silos of technology create a truly commercializable product (the SCE9610) capable of meeting the operation needs of the sequencing centers.

  12. Variation in extragenic repetitive DNA sequences in Pseudomonas syringae and potential use of modified REP primers in the identification of closely related isolates

    Directory of Open Access Journals (Sweden)

    Elif Çepni

    2012-01-01

    Full Text Available In this study, Pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific PCR and their genetic diversity was assessed by repetitive extragenic palindromic (REP-PCR. Reverse universal primers for REP-PCR were designed by using the bases of A, T, G or C at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. Binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in eight isolates of P. savastanoi pv. savastanoi and two isolates of P. syringae pv. tomato. The use of four different bases in the primer sequences did not affect the PCR reproducibility and was very efficient in revealing intra-pathovar diversity, particularly in P. savastanoi pv. savastanoi. At the pathovar level, the primer BOX1AR yielded shared fragments, in addition to five bands that discriminated among the pathovars P. syringae pv. phaseolicola, P. savastanoi pv. savastanoi and P. syringae pv. tomato. REP-PCR with a modified primer containing C produced identical bands among the isolates in a pathovar but separated three pathovars more distinctly than four other primers. Although REP-and BOX-PCRs have been successfully used in the molecular identification of Pseudomonas isolates from Turkish flora, a PCR based on inter-enterobacterial repetitive intergenic concensus (ERIC sequences failed to produce clear banding patterns in this study.

  13. Feature-based motion control for near-repetitive structures

    NARCIS (Netherlands)

    Best, de J.J.T.H.

    2011-01-01

    In many manufacturing processes, production steps are carried out on repetitive structures which consist of identical features placed in a repetitive pattern. In the production of these repetitive structures one or more consecutive steps are carried out on the features to create the final product.

  14. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Neumann, Pavel; Navrátilová, Alice

    2007-01-01

    Roč. 8, č. 1 (2007), s. 427 ISSN 1471-2164 R&D Projects: GA AV ČR IAA500960702; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : DNA * Pisum sativum L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.180, year: 2007

  15. Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes.

    Directory of Open Access Journals (Sweden)

    Octavio M Palacios-Gimenez

    Full Text Available A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂ = 29,X0 (Gryllus assimilis and 2n = 9, neo-X1X2Y (Eneoptera surinamensis. The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the

  16. Identification and molecular epidemiology of dermatophyte isolates by repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system in Turkey.

    Science.gov (United States)

    Koc, A Nedret; Atalay, Mustafa A; Inci, Melek; Sariguzel, Fatma M; Sav, Hafize

    2017-05-01

    Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux). The genotyping of dermatophyte isolates from different patients was determined by rep-PCR. In the identification of dermatophyte isolates, agreement between rep-PCR and conventional methods was 87.8 % ( 36 of 41). The dermatophyte strains belonged to four clones (A -D) which were determined by the use of rep-PCR. The dermatophyte strains in Clone B, D showed identical patterns with respect to the region. In conclusion, rep-PCR appears to be useful for evaluation of the identification and clonal relationships between Trichophyton rubrum species complex and Trichophyton mentagrophytes species complex isolates. The similarity and diversity of these isolates may be assessed according to different regions by rep-PCR. © 2017 Blackwell Verlag GmbH.

  17. Final Report: The DNA Files: Unraveling the mysteries of genetics, January 1, 1998-March 31, 1999

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Bari

    1999-05-01

    The DNA Files is an award-winning radio documentary series on genetics created by SoundVision Productions. The DNA Files was hosted by John Hockenberry and was presented in documentary and discussion format. The programs covered a range of topics from prenatal and predictive gene testing, gene therapy, and commercialization of genetic information to new evolutionary genetic evidence, transgenic vegetables and use of DNA in forensics.

  18. Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

    Directory of Open Access Journals (Sweden)

    Natalia Borowska-Zuchowska

    2016-10-01

    Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

  19. Repetition code of 15 qubits

    Science.gov (United States)

    Wootton, James R.; Loss, Daniel

    2018-05-01

    The repetition code is an important primitive for the techniques of quantum error correction. Here we implement repetition codes of at most 15 qubits on the 16 qubit ibmqx3 device. Each experiment is run for a single round of syndrome measurements, achieved using the standard quantum technique of using ancilla qubits and controlled operations. The size of the final syndrome is small enough to allow for lookup table decoding using experimentally obtained data. The results show strong evidence that the logical error rate decays exponentially with code distance, as is expected and required for the development of fault-tolerant quantum computers. The results also give insight into the nature of noise in the device.

  20. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon.

    Science.gov (United States)

    Gomes Júnior, Renan Gabriel; Schneider, Carlos Henrique; de Lira, Thatianna; Carvalho, Natália Dayane Moura; Feldberg, Eliana; da Silva, Maria Nazareth Ferreira; Gross, Maria Claudia

    2016-01-01

    Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui , Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui . The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.

  1. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae: comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Renan Gabriel Gomes Junior

    2016-09-01

    Full Text Available Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939, O. bicolor (Tomes, 1860 and O. rutilus (Anthony, 1921. COI sequence analysis grouped O. auyantepui, O. bicolor and O. rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for O. auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while O. bicolor exhibited 2n=80/NFa=142 and O. rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in O. auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.

  2. Repetition and Translation Shifts

    Directory of Open Access Journals (Sweden)

    Simon Zupan

    2006-06-01

    Full Text Available Repetition manifests itself in different ways and at different levels of the text. The first basic type of repetition involves complete recurrences; in which a particular textual feature repeats in its entirety. The second type involves partial recurrences; in which the second repetition of the same textual feature includes certain modifications to the first occurrence. In the article; repetitive patterns in Edgar Allan Poe’s short story “The Fall of the House of Usher” and its Slovene translation; “Konec Usherjeve hiše”; are compared. The author examines different kinds of repetitive patterns. Repetitions are compared at both the micro- and macrostructural levels. As detailed analyses have shown; considerable microstructural translation shifts occur in certain types of repetitive patterns. Since these are not only occasional; sporadic phenomena; but are of a relatively high frequency; they reduce the translated text’s potential for achieving some of the gothic effects. The macrostructural textual property particularly affected by these shifts is the narrator’s experience as described by the narrative; which suffers a reduction in intensity.

  3. Mechanisms for radiation damage in DNA. Final report, June 1, 1986--August 31, 1996

    International Nuclear Information System (INIS)

    Sevilla, M.D.

    1996-08-01

    Over the last 10 years significant advances have been made impacting the understanding of radiation damage to DNA. The principal objective of this work was the elucidation of the fundamental mechanisms of radiation damage to DNA through the direct and indirect effects. Recently the work concentrated on the direct effect of radiation damage on DNA. The objective was to elucidate the ultimate radiation chemical damage to DNA arising from the direct effect. In this effort the focus was on the application of three techniques. ESR spectroscopic measurement of initial radicals formed in DNA and its hydration layer at low temperatures. Ab initio molecular orbital calculations were employed to give highly accurate theoretical predictions of early events such as electron and hole localization sites which serve to test and to clarify the experimental observations. HPLC and GC-mass spectroscopic assays of DNA base products formation provide the ultimate chemical outcome of the initial radiation events. The bridge between the early ion radical species and the non-radical products is made in ESR studies which follow the chemistry of the early species as they react with water and or other DNA bases. The use of these techniques has resulted in a new and fundamental understanding of the radiation damage to DNA on a molecular scale. From this work, a working model for DNA damage from the initial ionization event to the eventual formation of molecular base damage products and strand breaks has been formulated. Results over the past several years which have led to the formulation of this model are described

  4. Development of DNA Pillar Chip Final Report CRADA No. TSB-2035-01

    Energy Technology Data Exchange (ETDEWEB)

    Ness, K. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Long, G. W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-10-16

    This was a collaborative effort between The Regents of the University of California, Lawrence Livermore National Laboratory (LLNL) and Tetracore, to demonstrate a proof of principal device for the capture and controlled release of DNA moving within a flow stream.

  5. Regulation of chloroplast number and DNA synthesis in higher plants. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Mullet, J.E.

    1995-11-10

    The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

  6. Repetitive Questioning Exasperates Caregivers

    Directory of Open Access Journals (Sweden)

    R. C. Hamdy MD

    2018-01-01

    Full Text Available Repetitive questioning is due to an impaired episodic memory and is a frequent, often presenting, problem in patients with Alzheimer’s disease (amnestic type. It is due to the patients’ difficulties learning new information, retaining it, and recalling it, and is often aggravated by a poor attention span and easy distractibility. A number of factors may trigger and maintain repetitive questioning. Caregivers should try to identify and address these triggers. In the case discussion presented, it is due to the patient’s concerns about her and her family’s safety triggered by watching a particularly violent movie aired on TV. What went wrong in the patient/caregiver interaction and how it could have been avoided or averted are explored. Also reviewed are the impact of repetitive questioning, the challenges it raises for caregivers, and some effective intervention strategies that may be useful to diffuse the angst that caregivers experience with repetitive questioning.

  7. Characterization of ionizing radiation damage in DNA. Final report, February 1, 1977--September 30, 1977

    International Nuclear Information System (INIS)

    Hawkins, R.B.

    1977-01-01

    An experimental method for the measurement of covalent DNA-protein cross-links in bacteriophage T7 based on phenol-water countercurrent distribution has been developed and a statistical model for quantitative interpretation of these measurements has been devised. It has been found that DNA-protein cross links accumulate linearly with dose in response to exposure to 60 Co gamma radiation at a rate .05 to .20 times the rate of accumulation of double strand breaks if phage are exposed in highly protective medium (tryptone broth). It has been found that fast neutrons also induce DNA-protein cross-linkage. Furthermore, cross-link and double strand break lesions induced by neutrons occur in multiple clusters in randomly chosen phage, in contrast to those induced by gamma radiation, which occur singly in randomly chosen phage. It also appears that neutrons induce double strand breaks in the phage with an efficiency 50 times that of gamma rays. It was found that protein-DNA cross-links occur 30 times more frequently per lethal lesion after exposure to gamma rays than after exposure to ultraviolet light. Investigations of the occurrence of double strand breaks, protein-DNA cross-links and other DNA lesions in eucaryotic cells currently being pursued are also described

  8. 1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report

    International Nuclear Information System (INIS)

    NONE

    1999-01-01

    This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair

  9. 1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-02-12

    This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair.

  10. [Studies on the repair of damaged DNA in bacteriophage, bacterial and mammalian systems]: Final report

    International Nuclear Information System (INIS)

    Friedberg, E.C.

    1987-08-01

    This study sought to exploit the use of uv radiation as a source of genomic damage. We explored the molecular mechanism of the repair of DNA damage at a number of different levels of biological organization, by investigating bacteriophage, bacterial, yeast and mammalian cells. Not only have observations obtained in one biological system suggested specific experimental approaches in others, but we have also learned that some biochemical pathways for DNA repair are unique to specific organisms. Our studies are summarized in terms of 4 major areas of research activity that span the past 16 years. 86 refs

  11. Sequencing of megabase plus DNA by hybridization: Method development ENT. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-01-31

    Sequencing by hybridization (SBH) is the only sequencing method based on the experimental determination of the content of oligonucleotide sequences. The data acquisition relies on the natural process of base pairing. It is possible to determine the content of complementary oligosequences in the target DNA by the process of hybridization with oligonucleotide probes of known sequences.

  12. Document retrieval on repetitive string collections.

    Science.gov (United States)

    Gagie, Travis; Hartikainen, Aleksi; Karhu, Kalle; Kärkkäinen, Juha; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

    2017-01-01

    Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their repetitiveness, which can reduce their space usage by orders of magnitude. We study the problem of indexing repetitive string collections in order to perform efficient document retrieval operations on them. Document retrieval problems are routinely solved by search engines on large natural language collections, but the techniques are less developed on generic string collections. The case of repetitive string collections is even less understood, and there are very few existing solutions. We develop two novel ideas, interleaved LCPs and precomputed document lists , that yield highly compressed indexes solving the problem of document listing (find all the documents where a string appears), top- k document retrieval (find the k documents where a string appears most often), and document counting (count the number of documents where a string appears). We also show that a classical data structure supporting the latter query becomes highly compressible on repetitive data. Finally, we show how the tools we developed can be combined to solve ranked conjunctive and disjunctive multi-term queries under the simple [Formula: see text] model of relevance. We thoroughly evaluate the resulting techniques in various real-life repetitiveness scenarios, and recommend the best choices for each case.

  13. Radioactively labelled DNA probes for crop improvement. Proceedings of a final research co-ordination meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-11-01

    With the advent of DNA molecular marker technology in the 1980s plant breeding had a new and powerful tool with which to increase its efficacy. Such markers are abundant and directly reveal information about the genotype and therefore are more useful than simple phenotypic markers. In plant breeding applications, molecular markers reveal information about variability and genetic relationships, and enable genetic mapping, which greatly assists the breeder in selection of parents and progeny, as well as in management of breeding strategies. Furthermore, molecular markers linked to phenotypic traits permit very early selection of superior progenies from breeding populations, therefore significantly reducing the need for field testing and greatly increasing efficiency of plant breeding programmes. For this to occur the oligonucleotide probes for labelling genetic markers and/or the primers for polymerase chain reactions to amplify genetic markers needed to be also accessible to scientists in developing Member States. In addition, technical information, training and troubleshooting were needed to support the utilization of DNA markers. In the early 1990s there was a dramatic increase in requests for access to this technology. This co-ordinated research project (CRP) facilitated the transfer of molecular marker technology, in terms of both material and information, from advanced laboratories to assist breeding programmes in developing countries. Two other CRPs were conducted concurrently in order to assist developing Member States to utilise molecular markers - Application of DNA Based Marker Mutations for Improvement of Cereals and other Sexually Reproduced Crop Plants, and Use of Novel DNA Fingerprinting Techniques for the Detection and Characterisation of Genetic Variation in Vegetatively Propagated Crops (IAEA-TECDOC-1010 and IAEA-TECDOC-1047, respectively). The present CRP built upon the success of the former projects by ensuring the availability of probes

  14. Radioactively labelled DNA probes for crop improvement. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    2001-11-01

    With the advent of DNA molecular marker technology in the 1980s plant breeding had a new and powerful tool with which to increase its efficacy. Such markers are abundant and directly reveal information about the genotype and therefore are more useful than simple phenotypic markers. In plant breeding applications, molecular markers reveal information about variability and genetic relationships, and enable genetic mapping, which greatly assists the breeder in selection of parents and progeny, as well as in management of breeding strategies. Furthermore, molecular markers linked to phenotypic traits permit very early selection of superior progenies from breeding populations, therefore significantly reducing the need for field testing and greatly increasing efficiency of plant breeding programmes. For this to occur the oligonucleotide probes for labelling genetic markers and/or the primers for polymerase chain reactions to amplify genetic markers needed to be also accessible to scientists in developing Member States. In addition, technical information, training and troubleshooting were needed to support the utilization of DNA markers. In the early 1990s there was a dramatic increase in requests for access to this technology. This co-ordinated research project (CRP) facilitated the transfer of molecular marker technology, in terms of both material and information, from advanced laboratories to assist breeding programmes in developing countries. Two other CRPs were conducted concurrently in order to assist developing Member States to utilise molecular markers - Application of DNA Based Marker Mutations for Improvement of Cereals and other Sexually Reproduced Crop Plants, and Use of Novel DNA Fingerprinting Techniques for the Detection and Characterisation of Genetic Variation in Vegetatively Propagated Crops (IAEA-TECDOC-1010 and IAEA-TECDOC-1047, respectively). The present CRP built upon the success of the former projects by ensuring the availability of probes

  15. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Directory of Open Access Journals (Sweden)

    Amanda Malvessi Cattani

    Full Text Available Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  16. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

    Science.gov (United States)

    Cattani, Amanda Malvessi; Siqueira, Franciele Maboni; Guedes, Rafael Lucas Muniz; Schrank, Irene Silveira

    2016-01-01

    Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

  17. Repetitive Questioning II

    Directory of Open Access Journals (Sweden)

    R. C. Hamdy MD

    2018-02-01

    Full Text Available Repetitive questioning is a major problem for caregivers, particularly taxing if they are unable to recognize and understand the reasons why their loved one keeps asking the same question over and over again. Caregivers may be tempted to believe that the patient does not even try to remember the answer given or is just getting obnoxious. This is incorrect. Repetitive questioning is due to the underlying disease: The patient’s short term memory is impaired and he is unable to register, encode, retain and retrieve the answer. If he is concerned about a particular topic, he will keep asking the same question over and over again. To the patient each time she asks the question, it is as if she asked it for the first time. Just answering repetitive questioning by providing repeatedly the same answer is not sufficient. Caregivers should try to identify the underlying cause for this repetitive questioning. In an earlier case study, the patient was concerned about her and her family’s safety and kept asking whether the doors are locked. In this present case study, the patient does not know how to handle the awkward situation he finds himself in. He just does not know what to do. He is not able to adjust to the new unexpected situation. So he repeatedly wants to reassure himself that he is not intruding by asking the same question over and over again. We discuss how the patient’s son-in-law could have avoided this situation and averted the catastrophic ending.

  18. Repetition or Reconfiguration

    DEFF Research Database (Denmark)

    Andersen, Kristina Vaarst

    , the cognitive quality of knowledge held by individual professionals is the key microfoundation for project level performance. This paper empirically tests effects of project participants with and without knowledge diversity for project level performance for projects aiming for varying degrees of repetition...... and reconfiguration. The results indicate that project performance benefits form contributions from individuals holding diverse knowledge only when projects aim for high differentiation levels. This positive association is not just moderated, it may even be reversed in the case of professionals participating in low...

  19. MIMICRY, DIFFERENCE AND REPETITION

    Directory of Open Access Journals (Sweden)

    Marcelo Mendes de Souza

    2008-07-01

    Full Text Available This article addresses Homi K. Bhabha’s concept of mimicry in a broader context, other than that of cultural studies and post-colonial studies, bringing together other concepts, such as that of Gilles Deleuze in Difference and repetition, among other texts, and other names, such as Silviano Santiago, Jorge Luís Borges, Franz Kafka and Giorgio Agamben. As a partial conclusion, the article intends to oppose Bhabha’s freudian-marxist view to Five propositions on Psychoanalysis (1973, Gilles Deleuze’s text about Psychoanalysis published right after his book The Anti-Oedipus.

  20. Repair of DNA treated with γ-irradiation and chemical carcinogens. Final report, June 1, 1981-May 31, 1984

    International Nuclear Information System (INIS)

    Goldthwait, D.A.

    1984-01-01

    Work done in the past three years has been on DNA repair, on genetic transposition and on the effect of carcinogens on alu sequence transcription. DNA repair work was completed on β-propiolactone DNA adducts, on procaryotic and eucaryotic enzymes capable of removal of 3-methyladenine from DNA, and on in vitro repair of neucleosomal core particle DNA and chromatin DNA. Attempts were made to isolate a human transposable element through the isolation of double stranded RNA and probing of a human library. Experiments were also done to determine whether carcinogens altered the expression of alu sequences in human DNA

  1. Chromosomal Mapping of Repetitive DNAs in the Grasshopper Abracris flavolineata Reveal Possible Ancestry of the B Chromosome and H3 Histone Spreading

    Science.gov (United States)

    Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Cabral-de-Mello, Diogo Cavalcanti

    2013-01-01

    Supernumerary chromosomes (B chromosomes) occur in approximately 15% of eukaryote species. Although these chromosomes have been extensively studied, knowledge concerning their specific molecular composition is lacking in most cases. The accumulation of repetitive DNAs is one remarkable characteristic of B chromosomes, and the occurrence of distinct types of multigene families, satellite DNAs and some transposable elements have been reported. Here, we describe the organization of repetitive DNAs in the A complement and B chromosome system in the grasshopper species Abracris flavolineata using classical cytogenetic techniques and FISH analysis using probes for five multigene families, telomeric repeats and repetitive C0t-1 DNA fractions. The 18S rRNA and H3 histone multigene families are highly variable and well distributed in A. flavolineata chromosomes, which contrasts with the conservation of U snRNA genes and less variable distribution of 5S rDNA sequences. The H3 histone gene was an extensively distributed with clusters occurring in all chromosomes. Repetitive DNAs were concentrated in C-positive regions, including the pericentromeric region and small chromosomal arms, with some occurrence in C-negative regions, but abundance was low in the B chromosome. Finally, the first demonstration of the U2 snRNA gene in B chromosomes in A. flavolineata may shed light on its possible origin. These results provide new information regarding chromosomal variability for repetitive DNAs in grasshoppers and the specific molecular composition of B chromosomes. PMID:23826099

  2. Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish

    Directory of Open Access Journals (Sweden)

    Maria L. Terencio

    2015-08-01

    Full Text Available The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions – thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841 and Semaprochilodus taeniurus (Valenciennes, 1817 and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (S. insignis, S. taeniurus, and Prochilodus lineatus (Valenciennes, 1836 by cross-FISH using Cot-1 DNA (renaturation kinetics probes. We found that the repetitive fractions of the genomes of S. insignis and S. taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of P. lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of S. insignis and S. taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the S. insignis and S. taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the P. lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.

  3. Role of Cell Cycle Regulation and MLH1, A Key DNA Mismatch Repair Protein, In Adaptive Survival Responses. Final Report; FINAL

    International Nuclear Information System (INIS)

    David A. Boothman

    1999-01-01

    Due to several interesting findings on both adaptive survival responses (ASRs) and DNA mismatch repair (MMR), this grant was separated into two discrete Specific Aim sets (each with their own discrete hypotheses). The described experiments were simultaneously performed

  4. PCR amplification of repetitive sequences as a possible approach in relative species quantification

    DEFF Research Database (Denmark)

    Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

    2012-01-01

    Abstract Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification...... of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species...... to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control....

  5. Ionizing radiation-induced DNA damage and its repair in human cells. Final performance report, July 1992 - June 1995

    International Nuclear Information System (INIS)

    Dizdaroglu, M.

    1995-01-01

    The studies of DNA damage in living cells in vitro and in vivo were continued. A variety of systems including cultured mammalian cells, animals, and human tissues were used to conduct these studies. In addition, enzymatic repair of DNA base damage was studied using several DNA glycosylases. To this end, substrate specificities of these enzymes were examined in terms of a large number of base lesions in DNA. In the first phase of the studies, the author sought to introduce improvements to his methodologies for measurement of DNA damage using the technique of gas chromatography/mass spectrometry (GC/MS). In particular, the quantitative measurement of DNA base damage and DNA-protein crosslinks was improved by incorporation of isotope-dilution mass spectrometry into the methodologies. This is one of the most accurate techniques for quantification of organic compounds. Having improved the measurement technique, studies of DNA damage in living cells and DNA repair by repair enzymes were pursued. This report provides a summary of these studies with references to the original work

  6. Emotional response to musical repetition.

    Science.gov (United States)

    Livingstone, Steven R; Palmer, Caroline; Schubert, Emery

    2012-06-01

    Two experiments examined the effects of repetition on listeners' emotional response to music. Listeners heard recordings of orchestral music that contained a large section repeated twice. The music had a symmetric phrase structure (same-length phrases) in Experiment 1 and an asymmetric phrase structure (different-length phrases) in Experiment 2, hypothesized to alter the predictability of sensitivity to musical repetition. Continuous measures of arousal and valence were compared across music that contained identical repetition, variation (related), or contrasting (unrelated) structure. Listeners' emotional arousal ratings differed most for contrasting music, moderately for variations, and least for repeating musical segments. A computational model for the detection of repeated musical segments was applied to the listeners' emotional responses. The model detected the locations of phrase boundaries from the emotional responses better than from performed tempo or physical intensity in both experiments. These findings indicate the importance of repetition in listeners' emotional response to music and in the perceptual segmentation of musical structure.

  7. High repetition rate intense ion beam source

    International Nuclear Information System (INIS)

    Hammer, D.A.; Glidden, S.C.; Noonan, B.

    1992-01-01

    This final report describes a ≤ 150kV, 40kA, 100ns high repetition rate pulsed power system and intense ion beam source which is now in operation at Cornell University. Operation of the Magnetically-controlled Anode Plasma (MAP) ion diode at > 100Hz (burst mode for up to 10 pulse bursts) provides an initial look at repetition rate limitations of both the ion diode and beam diagnostics. The pulsed power systems are capable of ≥ 1kHz operation (up to 10 pulse bursts), but ion diode operation was limited to ∼100Hz because of diagnostic limitations. By varying MAP diode operating parameters, ion beams can be extracted at a few 10s of keV or at up to 150keV, the corresponding accelerating gap impedance ranging from about 1Ω to about 10Ω. The ability to make hundreds of test pulses per day at an average repetition rate of about 2 pulses per minute permits statistical analysis of diode operation as a function of various parameters. Most diode components have now survived more than 10 4 pulses, and the design and construction of the various pulsed power components of the MAP diode which have enabled us to reach this point are discussed. A high speed data acquisition system and companion analysis software capable of acquiring pulse data at 1ms intervals (in bursts of up to 10 pulses) and processing it in ≤ min is described

  8. In vitro enzymatic studies on the nature and repair of x-ray-induced damages in DNA. Final report

    International Nuclear Information System (INIS)

    Wallace, S.S.

    1981-03-01

    An enzyme has been purified some 4000 fold from Escherichia coli which recognizes alkali stable base damages in x-irradiated DNA. The enzyme has broad specificity incising: DNA damaged by OsO 4 which produces thymine glycols, DNA treated with heat and acid which produces apurinic sites, and DNA uv-irradiated with high fluences which produces a variety of damages including the above. These activities co-chromatograph through Fraction VII the most purified form; however, the optimum reaction parameters differ among the various substrates suggesting the presence of more than one active site. Similar studies have been done with Saccharomyces cerevisiae. Several apurinic activities have been elucidated in this organism, one of which, Endonuclease E, has been purified over 1000 fold. Endonuclease E has been characterized with respect to various reaction parameters as well as by gel electrophoresis. Both the E. coli and yeast enzymes have been used to quantify DNA damage. Apurinic PM2 DNA and OsO 4 -treated PM2 DNA have also been used in a transfection system to estimate the inactivation efficiencies of AP sites and thymine glycols. AP sites have a relatively high inactivation efficiency and contribute about 15% to the inactivation of x-irradiated PM2 phage while thymine glycols contribute significantly less

  9. Role of Cell Cycle Regulation and MLH1, A Key DNA Mismatch Repair Protein, In Adaptive Survival Responses. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David A. Boothman

    1999-08-11

    Due to several interesting findings on both adaptive survival responses (ASRs) and DNA mismatch repair (MMR), this grant was separated into two discrete Specific Aim sets (each with their own discrete hypotheses). The described experiments were simultaneously performed.

  10. Carcinogen-DNA interaction study by base sequence footprinting. Final report, July 1, 1983-June 30, 1986

    International Nuclear Information System (INIS)

    Bases, R.

    1986-01-01

    Our previous studies on acetylaminofluorene (AAF) modified DNA demonstrated three kinds of structural changes in DNA of defined base sequence. For example, adduct formation by N-Aco-AAF was found at each guanine. We studied the interaction of IgG specific for AAF guanosine in an in vitro system using AAF modified phi X-174 rf DNA. We had expected to find protection against DNAase I digestion. Instead, when the DNA was immunobound to an inert matrix via the IgG, DNAase I digestion was enhanced 20 fold without changing the base sequence pattern of digestion. DNAase I hypersensitive sites are a necessary but not a sufficient condition for transcription. Moreover, some hypersensitive sites are stably propagated, independent of the continued presence of the inducer. Stability of these hypersensitive sites in the absence of their inducer suggests that they can be propagated. It appeared likely that distortion of DNA by a carcinogen adduct such as AAF, and the interaction of this modified DNA with a specific protein such as IgG or cellular proteins might inappropriately enhance the transcription of specific genes. That hypothesis will be tested; surprisingly, little is known about the early action of carcinogens on expression of specific genes. 34 refs., 2 figs., 1 tab

  11. Repetition and lag effects in movement recognition.

    Science.gov (United States)

    Hall, C R; Buckolz, E

    1982-03-01

    Whether repetition and lag improve the recognition of movement patterns was investigated. Recognition memory was tested for one repetition, two-repetitions massed, and two-repetitions distributed with movement patterns at lags of 3, 5, 7, and 13. Recognition performance was examined both immediately afterwards and following a 48 hour delay. Both repetition and lag effects failed to be demonstrated, providing some support for the claim that memory is unaffected by repetition at a constant level of processing (Craik & Lockhart, 1972). There was, as expected, a significant decrease in recognition memory following the retention interval, but this appeared unrelated to repetition or lag.

  12. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  13. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences; FINAL

    International Nuclear Information System (INIS)

    Robb, Frank T.

    2001-01-01

    The major objective of this research was to provide appropriate sequences and assemble a DNA array of oligonucleotides to be used for rapid profiling of microbial populations from polluted areas and other areas of interest. The sequences to be assigned to the DNA array were chosen from cloned genomic DNA taken from groundwater sites having well characterized pollutant histories at Hanford Nuclear Plant and Lawrence Livermore Site 300. Glass-slide arrays were made and tested; and a new multiplexed, bead-based method was developed that uses nucleic acid hybridization on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences. The test data revealed considerable strain variation between sample sites showing a striking distribution of sequences. It also suggests that diversity varies greatly with bioremediation, and that there are many bacterial intergenic spacer region sequences that can indicate its effects. The bead method exhibited superior sequence discrimination and has features for easier and more accurate measurement

  14. Base sequence effects on DNA replication influenced by bulky adducts. Final report, March 1, 1995--February 28, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Geacintov, N.E.

    1997-05-31

    Polycyclic aromatic hydrocarbons (PAH) are environmental pollutants that are present in air, food, and water. While PAH compounds are chemically inert and are sparingly soluble in aqueous solutions, in living cells they are metabolized to a variety of oxygenated derivatives, including the high mutagenic and tumorigenic diol epoxide derivatives. The diol epoxides of the sterically hindered fjord region compound benzo[c]phenanthrene (B[c]PhDE) are among the most powerful tumorigenic compounds in animal model test systems. In this project, site-specifically modified oligonucleotides containing single B[c]PhDE-N{sup 6}-dA lesions derived from the reactions of the 1S,2R,3R,4S and 1R,2S,3S,4R diol epoxides of B[c]PhDE with dA residues were synthesized. The replication of DNA catalyzed by a prokaryotic DNA polymerase (the exonuclease-free Klenow fragment E. Coli Po1 I) in the vicinity of the lesion at base-specific sites on B[c]PhDE-modified template strands was investigated in detail. The Michaelis-Menten parameters for the insertion of single deoxynucleotide triphosphates into growing DNA (primer) strands using the modified dA* and the bases just before and after the dA* residue as templates, depend markedly on the stereochemistry of the B[c]PhDE-modified dA residues. These observations provide novel insights into the mechanisms by which bulky PAH-DNA adducts affect normal DNA replication.

  15. Global Repetition Influences Contextual Cueing

    Science.gov (United States)

    Zang, Xuelian; Zinchenko, Artyom; Jia, Lina; Li, Hong

    2018-01-01

    Our visual system has a striking ability to improve visual search based on the learning of repeated ambient regularities, an effect named contextual cueing. Whereas most of the previous studies investigated contextual cueing effect with the same number of repeated and non-repeated search displays per block, the current study focused on whether a global repetition frequency formed by different presentation ratios between the repeated and non-repeated configurations influence contextual cueing effect. Specifically, the number of repeated and non-repeated displays presented in each block was manipulated: 12:12, 20:4, 4:20, and 4:4 in Experiments 1–4, respectively. The results revealed a significant contextual cueing effect when the global repetition frequency is high (≥1:1 ratio) in Experiments 1, 2, and 4, given that processing of repeated displays was expedited relative to non-repeated displays. Nevertheless, the contextual cueing effect reduced to a non-significant level when the repetition frequency reduced to 4:20 in Experiment 3. These results suggested that the presentation frequency of repeated relative to the non-repeated displays could influence the strength of contextual cueing. In other words, global repetition statistics could be a crucial factor to mediate contextual cueing effect. PMID:29636716

  16. Repetitive elements in parasitic protozoa

    Directory of Open Access Journals (Sweden)

    Clayton Christine

    2010-05-01

    Full Text Available Abstract A recent paper published in BMC Genomics suggests that retrotransposition may be active in the human gut parasite Entamoeba histolytica. This adds to our knowledge of the various types of repetitive elements in parasitic protists and the potential influence of such elements on pathogenicity. See research article http://www.biomedcentral.com/1471-2164/11/321

  17. Typing of Ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromic-polymerase chain reaction DNA fingerprinting and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.

    Science.gov (United States)

    Quirino, Angela; Pulcrano, Giovanna; Rametti, Linda; Puccio, Rossana; Marascio, Nadia; Catania, Maria Rosaria; Matera, Giovanni; Liberto, Maria Carla; Focà, Alfredo

    2014-03-22

    Ochrobactrum anthropi (O. anthropi), is a non-fermenting gram-negative bacillus usually found in the environment. Nevertheless, during the past decade it has been identified as pathogenic to immunocompromised patients. In this study, we assessed the usefulness of the automated repetitive extragenic palindromic-polymerase chain reaction (rep-PCR-based DiversiLab™ system, bioMèrieux, France) and of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF MS) for typing of twentythree O. anthropi clinical isolates that we found over a four-months period (from April 2011 to August 2011) in bacteriemic patients admitted in the same operative unit of our hospital. Pulsed-field gel electrophoresis (PFGE), commonly accepted as the gold standard technique for typing, was also used. Analysis was carried out using the Pearson correlation coefficient to determine the distance matrice and the unweighted pair group method with arithmetic mean (UPGMA) to generate dendogram. Rep-PCR analysis identified four different patterns: three that clustered together with 97% or more pattern similarity, and one whose members showed < 95% pattern similarity. Interestingly, strains isolated later (from 11/06/2011 to 24/08/2011) displayed a pattern with 99% similarity. MALDI-TOF MS evaluation clustered the twentythree strains of O. anthropi into a single group containing four distinct subgroups, each comprising the majority of strains clustering below 5 distance levels, indicating a high similarity between the isolates. Our results indicate that these isolates are clonally-related and the methods used afforded a valuable contribution to the epidemiology, prevention and control of the infections caused by this pathogen.

  18. The repetition effect in building and construction works

    DEFF Research Database (Denmark)

    Gottlieb, Stefan Christoffer; Haugbølle, Kim

    are then applied on the Public Transport Authorities' main account structure of units and costs, and a method for assessing the possibilities of achieving effects of repetition for each account is described. Finally, the report summarises the core conditions necessary to take into consideration in relation......This report summarises the results from the work undertaken for the Public Transport Authority on the effect of learning and repetition in building and construction works. The results are applied by the Public Transport Authority in a new budgeting model, while the agency investigates...

  19. Computer-Related Repetitive Stress Injuries

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Computer-Related Repetitive Stress Injuries KidsHealth / For Parents / Computer-Related Repetitive Stress Injuries What's in this article? ...

  20. Repetitive learning control of continuous chaotic systems

    International Nuclear Information System (INIS)

    Chen Maoyin; Shang Yun; Zhou Donghua

    2004-01-01

    Combining a shift method and the repetitive learning strategy, a repetitive learning controller is proposed to stabilize unstable periodic orbits (UPOs) within chaotic attractors in the sense of least mean square. If nonlinear parts in chaotic systems satisfy Lipschitz condition, the proposed controller can be simplified into a simple proportional repetitive learning controller

  1. Analysis and Design of a Fiber-optic Probe for DNA Sensors Final Report CRADA No. TSB-1147-95

    Energy Technology Data Exchange (ETDEWEB)

    Molau, Nicole [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vail, Curtis [Accu.Photonics, Inc., Ann Arbor, MI (United States)

    2018-01-24

    In 1995, a challenge in the field of genetics dealt with the acquisition of efficient DNA sequencing techniques for reading the 3 billion base-pairs that comprised the human genome. AccuPhotonics, Inc. proposed to develop and manufacture a state-of-the-art near-field scanning optical microscopy (NSOM) fiber-optic probe that was expected to increase probe efficiency by two orders of magnitude over the existing state-of-the-art and to improve resolution to 10Å. The detailed design calculation and optimization of electrical properties of the fiber-optic probe tip geometry would be performed at LLNL, using existing finite-difference time-domain (FDTD) electromagnetic (EM) codes.

  2. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres

  3. GRAIL-genQuest: A comprehensive computational system for DNA sequence analysis. Final report, DOE SBIR Phase II

    Energy Technology Data Exchange (ETDEWEB)

    Manning, Ruth Ann

    1999-01-05

    Recent advances in DNA sequencing and genome mapping technologies are making it possible, for the first time in history, to find genes in plants and animals and to elucidate their function. This means that diagnostics and therapeutics can be developed for human diseases such as cancer, obesity, hypertension, and cardiovascular problems. Crop and animal strains can be developed that are hardier, resistant to diseases, and produce higher yields. The challenge is to develop tools that will find the nucleotides in the DNA of a living organism that comprise a particular gene. In the human genome alone it is estimated that only about 51% of the approximately 3 billion pairs of nucleotides code for some 100,000 human genes. In this search for nucleotides within a genome which are active in the actual coding of proteins, efficient tools to locate and identify their function can be of significant value to mankind. Software tools such as ApoCom GRAIL{trademark} have assisted in this search. It can be used to analyze genome information, to identify exons (coding regions) and to construct gene models. Using a neural network approach, this software can ''learn'' sequence patterns and refine its ability to recognize a pattern as it is exposed to more and more examples of it. Since 1992 versions of GRAIL{trademark} have been publicly available over the Internet from Oak Ridge National Laboratory. Because of the potential for security and patent compromise, these Internet versions are not available to many researchers in pharmaceutical and biotechnology companies who cannot send proprietary sequences past their data-secure firewalls. ApoCom is making available commercial versions of the GRAIL{trademark} software to run self-contained over local area networks. As part of the commercialization effort, ApoCom has developed a new Java{trademark}-based graphical user interface, the ApoCom Client Tool for Genomics (ACTG){trademark}. Two products, ApoCom GRAIL

  4. Repetitively pulsed material testing facility

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    A continuously operated, 1 pps, dense-plasma-focus device capable of delivering a minimum of 10 15 neutrons per pulse for material testing purposes is described. Moderate scaling from existing results is sufficient to provide 2 x 10 13 n/cm 2 .s to a suitable target. The average power consumption, which has become a major issue as a result of the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. A novel approach to the capacitor bank and switch design allowing repetitive operation is discussed. (U.S.)

  5. Repetitively pulsed material testing facility

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R.; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    A continuously operated, 1 pps, dense-plasma-focus device capable of delivering a minimum of 10 15 neutrons per pulse for material testing purposes is described. Moderate scaling from existing results is sufficient to provide 2 x 10 13 n/cm 2 . s to a suitable target. The average power consumption, which has become a major issue as a result of the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. A novel approach to the capacitor bank and switch design allowing repetitive operation is discussed

  6. Application of DNA based marker mutations for improvement of cereals and other sexually reproduced crop plants. Proceedings of a final research co-ordination meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

    The Co-ordinated Research Programme (CRP) on the Application of DNA Based Marker Mutations for Improvement of Cereals and Other Sexually Reproduced Crop Plants represents the first of three CRPs dealing with the application of molecular markers to mutations and plant breeding and was implemented between 1992 and 1996. A second companion CRP entitled Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops devoted to the application of molecular markers in vegetatively propagated crops species was implemented between 1993 and 1997. One positive consequence of these two CRPs has been the implementation of a third CRP entitled Radioactively Labeled DNA Probes for Crop Improvement, which began in 1995 and aims to provide enabling technologies, in the form of probes and primers, to laboratories in developing countries. The rapid development of molecular marker technologies has also resulted in a dramatic increase in request from developing Member States for technical co-operation projects utilizing molecular markers to improve local varieties for biotic and abiotic stresses and other traits of relevance. With the intensified use of induced mutations in genetic studies, it will be important to continue the important work of understanding induced mutations at the molecular level. Evidence of the progress made in implementing molecular marker technologies in laboratories around the world is presented in this publication, which contains the results presented by the participants at the fourth and final Research Co-ordination Meeting of the CRP held in Vienna, 4-8 November 1996. The FAO and IAEA wish to express their sincere appreciation to the participants of the meeting for their work during the project period resulting in the summary and scientific reports presented in this publication. Refs, figs, tabs.

  7. Application of DNA based marker mutations for improvement of cereals and other sexually reproduced crop plants. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    1998-03-01

    The Co-ordinated Research Programme (CRP) on the Application of DNA Based Marker Mutations for Improvement of Cereals and Other Sexually Reproduced Crop Plants represents the first of three CRPs dealing with the application of molecular markers to mutations and plant breeding and was implemented between 1992 and 1996. A second companion CRP entitled Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops devoted to the application of molecular markers in vegetatively propagated crops species was implemented between 1993 and 1997. One positive consequence of these two CRPs has been the implementation of a third CRP entitled Radioactively Labeled DNA Probes for Crop Improvement, which began in 1995 and aims to provide enabling technologies, in the form of probes and primers, to laboratories in developing countries. The rapid development of molecular marker technologies has also resulted in a dramatic increase in request from developing Member States for technical co-operation projects utilizing molecular markers to improve local varieties for biotic and abiotic stresses and other traits of relevance. With the intensified use of induced mutations in genetic studies, it will be important to continue the important work of understanding induced mutations at the molecular level. Evidence of the progress made in implementing molecular marker technologies in laboratories around the world is presented in this publication, which contains the results presented by the participants at the fourth and final Research Co-ordination Meeting of the CRP held in Vienna, 4-8 November 1996. The FAO and IAEA wish to express their sincere appreciation to the participants of the meeting for their work during the project period resulting in the summary and scientific reports presented in this publication

  8. Repetitive trauma and nerve compression.

    Science.gov (United States)

    Carragee, E J; Hentz, V R

    1988-01-01

    Repetitive movement of the upper extremity, whether recreational or occupational, may result in various neuropathies, the prototype of which is the median nerve neuropathic in the carpal canal. The pathophysiology of this process is incompletely understood but likely involves both mechanical and ischemic features. Experimentally increased pressures within the carpal canal produced reproducible progressive neuropathy. Changes in vibratory (threshold-type) sensibility appears to be more sensitive than two-point (innervation density-type) sensibility. The specific occupational etiologies of carpal neuropathy are obscured by methodologic and sociological difficulties, but clearly some occupations have high incidences of CTS. History and physical examination are usually sufficient for the diagnosis, but diagnostic assistance when required is available through electrophysiological testing, CT scanning, and possibly MRI. Each of these tests has limitations in both sensitivity and specificity. Treatment by usual conservative means should be combined with rest from possible provocative activities. Surgical release of the carpal canal is helpful in patients failing conservative therapy. Occupational modifications are important in both treatment and prevention of median neuropathy due to repetitive trauma.

  9. A repetitive probe for FISH analysis of bovine interphase nuclei

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond

    2000-03-01

    Full Text Available Abstract The purpose of this study was to generate repetitive DNA sequence probes for the analysis of interphase nuclei by fluorescent in situ hybridisation (FISH. Such probes are useful for the diagnosis of chromosomal abnormalities in bovine preimplanted embryos. Of the seven probes (E1A, E4A, Ba, H1A, W18, W22, W5 that were generated and partially sequenced, five corresponded to previously described Bos taurus repetitive DNA (E1A, E4A, Ba, W18, W5, one probe (W22 shared no homology with other DNA sequences and one (H1A displayed a significant homology with Rattus norvegicus mRNA for secretin receptor transmembrane domain 3. Fluorescent in situ hybridisation was performed on metaphase bovine fibroblast cells and showed that five of the seven probes hybridised most centromeres (E1A, E4A, Ba, W18, W22, one labelled the arms of all chromosomes (W5 and the H1A probe was specific to three chromosomes (ch14, ch20, and ch25. Moreover, FISH with H1A resulted in interpretable signals on interphase nuclei in 88% of the cases, while the other probes yielded only dispersed overlapping signals.

  10. Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

    Science.gov (United States)

    Biltueva, Larisa S; Prokopov, Dimitry Y; Makunin, Alexey I; Komissarov, Alexey S; Kudryavtseva, Anna V; Lemskaya, Natalya A; Vorobieva, Nadezhda V; Serdyukova, Natalia A; Romanenko, Svetlana A; Gladkikh, Olga L; Graphodatsky, Alexander S; Trifonov, Vladimir A

    2017-01-01

    Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order. © 2017 S. Karger AG, Basel.

  11. A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

    Science.gov (United States)

    Shriberg, Lawrence D.; Lohmeier, Heather L.; Campbell, Thomas F.; Dollaghan, Christine A.; Green, Jordan R.; Moore, Christopher A.

    2009-01-01

    Purpose: Conceptual and methodological confounds occur when non(sense) word repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. In this article, the authors (a) describe a nonword repetition task, the Syllable Repetition Task…

  12. The Developmental Trajectory of Nonword Repetition

    Science.gov (United States)

    Chiat, Shula

    2006-01-01

    In line with the original presentation of nonword repetition as a measure of phonological short-term memory (Gathercole & Baddeley, 1989), the theoretical account Gathercole (2006) puts forward in her Keynote Article focuses on phonological storage as the key capacity common to nonword repetition and vocabulary acquisition. However, evidence that…

  13. Grade Repetition in Queensland State Prep Classes

    Science.gov (United States)

    Anderson, Robyn

    2012-01-01

    The current study considers grade repetition rates in the early years of schooling in Queensland state schools with specific focus on the pre-schooling year, Prep. In particular, it provides empirical evidence of grade repetition in Queensland state schools along with groups of students who are more often repeated. At the same time, much of the…

  14. REPETITIVE STRENGTH AMONG STUDENTS OF AGE 14

    Directory of Open Access Journals (Sweden)

    Besim Halilaj

    2014-06-01

    Full Text Available The study involved 82 male students of the primary school “Qamil Ilazi” in Kaçanik-Kosovo.Four movement tests, which test the repetitive strength, were conducted: 1. Pull-up, 2. Sit-Up, 3. Back extension, 4. Push-up.The main goal of this study was to verify the actual motor status, respectively the component of the repetitive strength among students of age 14 of masculine gender. In addition to verifying the actual motor status, another objective was to verify the relationship between the variables employed.Basic statistical parameters show a distribution which is not significantly different from the normal distribution, yielded highly correlative values among the repetitive strength tests. Space factorization resulted in extracting two latent squares defined as repetitive strength of arms factor, and repetitive strength of body factor.

  15. Microbial expression of proteins containing long repetitive Arg-Gly-Asp cell adhesive motifs created by overlap elongation PCR

    International Nuclear Information System (INIS)

    Kurihara, Hiroyuki; Shinkai, Masashige; Nagamune, Teruyuki

    2004-01-01

    We developed a novel method for creating repetitive DNA libraries using overlap elongation PCR, and prepared a DNA library encoding repetitive Arg-Gly-Asp (RGD) cell adhesive motifs. We obtained various length DNAs encoding repetitive RGD from a short monomer DNA (18 bp) after a thermal cyclic reaction without a DNA template for amplification, and isolated DNAs encoding 2, 21, and 43 repeats of the RGD motif. We cloned these DNAs into a protein expression vector and overexpressed them as thioredoxin fusion proteins: RGD2, RGD21, and RGD43, respectively. The solubility of RGD43 in water was low and it formed a fibrous precipitate in water. Scanning electron microscopy revealed that RGD43 formed a branched 3D-network structure in the solid state. To evaluate the function of the cell adhesive motifs in RGD43, mouse fibroblast cells were cultivated on the RGD43 scaffold. The fibroblast cells adhered to the RGD43 scaffold and extended long filopodia

  16. Repetitive elements dynamics in cell identity programming, maintenance and disease

    KAUST Repository

    Bodega, Beatrice

    2014-12-01

    The days of \\'junk DNA\\' seem to be over. The rapid progress of genomics technologies has been unveiling unexpected mechanisms by which repetitive DNA and in particular transposable elements (TEs) have evolved, becoming key issues in understanding genome structure and function. Indeed, rather than \\'parasites\\', recent findings strongly suggest that TEs may have a positive function by contributing to tissue specific transcriptional programs, in particular as enhancer-like elements and/or modules for regulation of higher order chromatin structure. Further, it appears that during development and aging genomes experience several waves of TEs activation, and this contributes to individual genome shaping during lifetime. Interestingly, TEs activity is major target of epigenomic regulation. These findings are shedding new light on the genome-phenotype relationship and set the premises to help to explain complex disease manifestation, as consequence of TEs activity deregulation.

  17. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Macas, Jiří

    2010-01-01

    Roč. 11, č. 1 (2010), s. 378-389 ISSN 1471-2105 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : repetitive DNA * plant genome * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.028, year: 2010

  18. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

    Science.gov (United States)

    Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J

    2011-09-01

    The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

  19. Refining borders of genome-rearrangements including repetitions

    Directory of Open Access Journals (Sweden)

    JA Arjona-Medina

    2016-10-01

    Full Text Available Abstract Background DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR, the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. Methods and results We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. Conclusion The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements.

  20. Subjective duration distortions mirror neural repetition suppression.

    Science.gov (United States)

    Pariyadath, Vani; Eagleman, David M

    2012-01-01

    Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression. Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli) followed by a line presented at a different orientation (oddball stimulus). We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials. Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  1. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  2. A longitudinal investigation of perfectionism and repetitive negative thinking in perinatal depression.

    Science.gov (United States)

    Egan, Sarah J; Kane, Robert T; Winton, Karen; Eliot, Catherine; McEvoy, Peter M

    2017-10-01

    Repetitive negative thinking and perfectionism have both been proposed as processes that are related to depressive symptoms. The purpose of this study was to investigate concurrent and prospective relationships between antenatal and postnatal depression, perfectionism, and repetitive negative thinking. A longitudinal design was used and 71 women were followed from their third trimester of pregnancy to six weeks post birth. A structural equation model was tested with antenatal perfectionism predicting antenatal repetitive negative thinking, perfectionism predicting postnatal depression, and antenatal repetitive negative thinking predicting antenatal and postnatal depression. The final model provided an adequate fit to the data but the pathway from antenatal repetitive negative thinking to postnatal depression was not significant. The findings provide support for the role of perfectionism and repetitive negative thinking in the onset and maintenance of perinatal symptoms of depression. It is suggested that future research investigates the efficacy of targeting repetitive negative thinking and perfectionism in pregnancy to examine if this can reduce perinatal depression. Copyright © 2017. Published by Elsevier Ltd.

  3. Repetitive Bibliographical Information in Relational Databases.

    Science.gov (United States)

    Brooks, Terrence A.

    1988-01-01

    Proposes a solution to the problem of loading repetitive bibliographic information in a microcomputer-based relational database management system. The alternative design described is based on a representational redundancy design and normalization theory. (12 references) (Author/CLB)

  4. Use of novel DNA fingerprinting techniques for the detection and characterization of genetic variation in vegetatively propagated crops. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    1998-10-01

    Vegetative propagated crops, such as banana and platain, sweet potato, yam, sugarcane and cassava, represent important sources of food in the developing countries. Although some of these crops may produce seeds, they must for practical purposes be propagated vegetatively. As normal plant breeding strategies based on genetic hybridization are of limited value or not applicable to such crops, it is necessary to assess the genetic diversity already existing in these crops and to design breeding strategies accordingly. If the existing genetic variation is shown to be too narrow for breeding purposes, one promising possibility for the introduction of genetic variability is the use of mutations induced by radiation or chemical mutagens. This CRP focused on: the detection of genetic diversity induced by mutagenic treatment or in vitro culture; the development of crop-specific markers; and increasing co-operation between molecular biologists in advanced laboratories and plant breeders and molecular biologists in the developing countries. The success of this CRP is evidenced by the introduction and application of new molecular methods by laboratories in developing countries, specially for the analysis of local crop genetic diversity. These exciting preliminary results show the potential for applications in crop improvement but much work remains to be done. Many of the vegetatively propagated species are ''orphan crops'', under-investigated on the international level. The development of new uses of transgenesis for the development of edible vaccines should not be overlooked. The challenge that remains is in the application of these new tools for practical end-user oriented improvements in vegetatively propagated crops. The present publication summarizes the third and final Research Co-ordination Meeting on the Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops

  5. Use of novel DNA fingerprinting techniques for the detection and characterization of genetic variation in vegetatively propagated crops. Proceedings of a final research co-ordination meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-10-01

    Vegetative propagated crops, such as banana and platain, sweet potato, yam, sugarcane and cassava, represent important sources of food in the developing countries. Although some of these crops may produce seeds, they must for practical purposes be propagated vegetatively. As normal plant breeding strategies based on genetic hybridization are of limited value or not applicable to such crops, it is necessary to assess the genetic diversity already existing in these crops and to design breeding strategies accordingly. If the existing genetic variation is shown to be too narrow for breeding purposes, one promising possibility for the introduction of genetic variability is the use of mutations induced by radiation or chemical mutagens. This CRP focused on: the detection of genetic diversity induced by mutagenic treatment or in vitro culture; the development of crop-specific markers; and increasing co-operation between molecular biologists in advanced laboratories and plant breeders and molecular biologists in the developing countries. The success of this CRP is evidenced by the introduction and application of new molecular methods by laboratories in developing countries, specially for the analysis of local crop genetic diversity. These exciting preliminary results show the potential for applications in crop improvement but much work remains to be done. Many of the vegetatively propagated species are ``orphan crops``, under-investigated on the international level. The development of new uses of transgenesis for the development of edible vaccines should not be overlooked. The challenge that remains is in the application of these new tools for practical end-user oriented improvements in vegetatively propagated crops. The present publication summarizes the third and final Research Co-ordination Meeting on the Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops Refs, figs, tabs

  6. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

    Science.gov (United States)

    Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

    2016-06-01

    Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

  7. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome

    International Nuclear Information System (INIS)

    Economou, E.P.; Bergen, A.W.; Warren, A.C.; Antonarakis, S.E.

    1990-01-01

    To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, the authors hypothesize that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. Analysis of the 3' ends of three specific Alu sequences showed two occurrences, one in the adenosine deaminase gene and other in the β-globin pseudogene, were polymorphic. This novel class of polymorphism, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome

  8. Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients.

    Science.gov (United States)

    Prudencio, Mercedes; Gonzales, Patrick K; Cook, Casey N; Gendron, Tania F; Daughrity, Lillian M; Song, Yuping; Ebbert, Mark T W; van Blitterswijk, Marka; Zhang, Yong-Jie; Jansen-West, Karen; Baker, Matthew C; DeTure, Michael; Rademakers, Rosa; Boylan, Kevin B; Dickson, Dennis W; Petrucelli, Leonard; Link, Christopher D

    2017-09-01

    Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analysed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls. Transcripts from multiple classes and subclasses of repetitive elements (LINEs, endogenous retroviruses, DNA transposons, simple repeats, etc.) were significantly increased in the frontal cortex of C9orf72 ALS patients. A large collection of patient samples, representing both C9orf72 positive and negative ALS, ALS/FTLD, and FTLD cases, was used to validate the levels of several repetitive element transcripts. These analyses confirmed that repetitive element expression was significantly increased in C9orf72-positive compared to C9orf72-negative or control cases. While previous studies suggest an important link between TDP-43 and repetitive element biology, our data indicate that TDP-43 pathology alone is insufficient to account for the observed changes in repetitive elements in ALS/FTLD. Instead, we found that repetitive element expression positively correlated with RNA polymerase II activity in postmortem brain, and pharmacologic modulation of RNA polymerase II activity altered repetitive element expression in vitro. We conclude that increased RNA polymerase II activity in ALS/FTLD may lead to increased repetitive element transcript expression, a novel pathological feature of ALS/FTLD. © The Author 2017. Published by Oxford University Press.

  9. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  10. Subjective duration distortions mirror neural repetition suppression.

    Directory of Open Access Journals (Sweden)

    Vani Pariyadath

    Full Text Available Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression.Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli followed by a line presented at a different orientation (oddball stimulus. We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials.Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  11. Independent and additive repetition priming of motion direction and color in visual search.

    Science.gov (United States)

    Kristjánsson, Arni

    2009-03-01

    Priming of visual search for Gabor patch stimuli, varying in color and local drift direction, was investigated. The task relevance of each feature varied between the different experimental conditions compared. When the target defining dimension was color, a large effect of color repetition was seen as well as a smaller effect of the repetition of motion direction. The opposite priming pattern was seen when motion direction defined the target--the effect of motion direction repetition was this time larger than for color repetition. Finally, when neither was task relevant, and the target defining dimension was the spatial frequency of the Gabor patch, priming was seen for repetition of both color and motion direction, but the effects were smaller than in the previous two conditions. These results show that features do not necessarily have to be task relevant for priming to occur. There is little interaction between priming following repetition of color and motion, these two features show independent and additive priming effects, most likely reflecting that the two features are processed at separate processing sites in the nervous system, consistent with previous findings from neuropsychology & neurophysiology. The implications of the findings for theoretical accounts of priming in visual search are discussed.

  12. An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Netzel, T.L.

    1997-03-01

    The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.

  13. Formation and repair of physically and chemically induced DNA damage in human cells. Final report, September 1, 1976-November 30, 1978

    International Nuclear Information System (INIS)

    Cerutti, P.A.

    1979-01-01

    The major topic was the study of the formation and repair of DNA damage by energy related physical and chemical agents in cultured human cells. Two pathways of damage production were distinguished: (1) indirect action, i.e., attack of DNA by active oxygen species which are formed by the reaction of the primary agent with a non-DNA target; and (2) direct action, i.e., reaction of the primary agent or a chemical derivative of the primary agent with DNA usually resulting in the formation of a covalent adduct. Near-ultraviolet light and ionizing radiation were studied as agents which operate at least in part via indirect action and benzo(a)pyrene as chemical carcinogen operating mostly by direct action. The formation of monomeric thymine damage of the 5,6-dihydroxy-dihydrothymine type by γ-rays and ultraviolet light was investigated. Indirect action of near-ultraviolet light is also responsible for the induction of DNA single strand breaks. Their formation and repair following exposure to 313 nm light was studied in skin fibroblasts from patients with the hereditary disease Xeroderma pigmentosum (XP). Excision repair of γ-ray induced 5,6-dihydroxy-dihydrothymine type lesions was studied in fibroblasts from Ataxia telangiectasia (AT) patients. The formation and repair of covalent purine adducts was studied in actively metabolizing rodent and human cells following treatment with the procarcinogen benzo(a)pyrene and with the ultimate metabolite benzo(a)pyrene-diol-epoxide I

  14. An effective repetitive training schedule to achieve skill proficiency using a novel robotic virtual reality simulator.

    Science.gov (United States)

    Kang, Sung Gu; Ryu, Byung Ju; Yang, Kyung Sook; Ko, Young Hwii; Cho, Seok; Kang, Seok Ho; Patel, Vipul R; Cheon, Jun

    2015-01-01

    A robotic virtual reality simulator (Mimic dV-Trainer) can be a useful training method for the da Vinci surgical system. Herein, we investigate several repetitive training schedules and determine which is the most effective. A total of 30 medical students were enrolled and were divided into 3 groups according to the training schedule. Group 1 performed the task 1 hour daily for 4 consecutive days, group II performed the task on once per week for 1 hour for 4 consecutive weeks, and group III performed the task for 4 consecutive hours in 1 day. The effects of training were investigated by analyzing the number of repetitions and the time required to complete the "Tube 2" simulation task when the learning curve plateau was reached. The point at which participants reached a stable score was evaluated using the cumulative sum control graph. The average time to complete the task at the learning curve plateau was 150.3 seconds in group I, 171.9 seconds in group II, and 188.5 seconds in group III. The number of task repetitions required to reach the learning curve plateau was 45 repetitions in group I, 36 repetitions in group II, and 39 repetitions in group III. Therefore, there was continuous improvement in the time required to perform the task after 40 repetitions in group I only. There was a significant correlation between improvement in each trial interval and attempt, and the correlation coefficient (0.924) in group I was higher than that in group II (0.899) and group III (0.838). Daily 1-hour practice sessions performed for 4 consecutive days resulted in the best final score, continuous score improvement, and effective training while minimizing fatigue. This repetition schedule can be used for effectively training novices in future. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  15. Satellite DNA: An Evolving Topic.

    Science.gov (United States)

    Garrido-Ramos, Manuel A

    2017-09-18

    Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

  16. Decreased microvascular cerebral blood flow assessed by diffuse correlation spectroscopy after repetitive concussions in mice.

    Science.gov (United States)

    Buckley, Erin M; Miller, Benjamin F; Golinski, Julianne M; Sadeghian, Homa; McAllister, Lauren M; Vangel, Mark; Ayata, Cenk; Meehan, William P; Franceschini, Maria Angela; Whalen, Michael J

    2015-12-01

    Repetitive concussions are associated with long-term cognitive dysfunction that can be attenuated by increasing the time intervals between concussions; however, biomarkers of the safest rest interval between injuries remain undefined. We hypothesize that deranged cerebral blood flow (CBF) is a candidate biomarker for vulnerability to repetitive concussions. Using a mouse model of human concussion, we examined the effect of single and repetitive concussions on cognition and on an index of CBF (CBFi) measured with diffuse correlation spectroscopy. After a single mild concussion, CBFi was reduced by 35±4% at 4 hours (Pconcussions spaced 1 day apart, CBFi was also reduced from preinjury levels 4 hours after each concussion but had returned to preinjury levels by 72 hours after the final concussion. Interestingly, in this repetitive concussion model, lower CBFi values measured both preinjury and 4 hours after the third concussion were associated with worse performance on the Morris water maze assessed 72 hours after the final concussion. We conclude that low CBFi measured either before or early on in the evolution of injury caused by repetitive concussions could be a useful predictor of cognitive outcome.

  17. Storytelling and Repetitive Narratives for Design Empathy

    DEFF Research Database (Denmark)

    Fritsch, Jonas; Judice, Andrea; Soini, Katja

    2007-01-01

    study. In this paper, we show how we attained an empathic understanding through storytelling and aroused empathy to others using repetitive narratives in an experimental presentation bringing forth factual, reflective and experiential aspects of the user information. Taking as a starting point our...

  18. Universal data compression and repetition times

    NARCIS (Netherlands)

    Willems, Frans M J

    1989-01-01

    A new universal data compression algorithm is described. This algorithm encodes L source symbols at a time. For the class of binary stationary sources, its rate does not exceed [formula omitted] [formula omitted] bits per source symbol. In our analysis, a property of repetition times turns out to be

  19. Matriculation Research Report: Course Repetition Data & Analysis.

    Science.gov (United States)

    Gerda, Joe

    Due to concerns that its policy on class repetition was not promoting student success, California's College of the Canyons (CoC) undertook a project to analyze student course-taking patterns and make recommendations to modify the policy. Existing college policy did not follow Section 58161 of the State Educational Code that allows colleges to…

  20. Reducing Repetitive Speech: Effects of Strategy Instruction.

    Science.gov (United States)

    Dipipi, Caroline M.; Jitendra, Asha K.; Miller, Judith A.

    2001-01-01

    This article describes an intervention with an 18-year-old young woman with mild mental retardation and a seizure disorder, which focused on her repetitive echolalic verbalizations. The intervention included time delay, differential reinforcement of other behaviors, and self-monitoring. Overall, the intervention was successful in facilitating…

  1. Neurobehavioural Correlates of Abnormal Repetitive Behaviour

    Directory of Open Access Journals (Sweden)

    R. A. Ford

    1991-01-01

    Full Text Available Conditions in which echolalia and echopraxia occur are reviewed, followed by an attempt to elicit possible mechanisms of these phenomena. A brief description of stereotypical and perseverative behaviour and obsessional phenomena is given. It is suggested that abnormal repetitive behaviour may occur partly as a result of central dopaminergic dysfunction.

  2. Verbal Repetitions and Echolalia in Alzheimer's Discourse

    Science.gov (United States)

    Da Cruz, Fernanda Miranda

    2010-01-01

    This article reports on an investigation of echolalic repetition in Alzheimer's disease (AD). A qualitative analysis of data from spontaneous conversations with MHI, a woman with AD, is presented. The data come from the DALI Corpus, a corpus of spontaneous conversations involving subjects with AD. This study argues that echolalic effects can be…

  3. Bystanders' Reactions to Witnessing Repetitive Abuse Experiences

    Science.gov (United States)

    Janson, Gregory R.; Carney, JoLynn V.; Hazler, Richard J.; Oh, Insoo

    2009-01-01

    The Impact of Event Scale-Revised (D. S. Weiss & C. R. Marmar, 1997) was used to obtain self-reported trauma levels from 587 young adults recalling childhood or adolescence experiences as witnesses to common forms of repetitive abuse defined as bullying. Mean participant scores were in a range suggesting potential need for clinical assessment…

  4. New tool to assemble repetitive regions using next-generation sequencing data

    Science.gov (United States)

    Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz

    2017-08-01

    The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

  5. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  6. Indices of methylation in sperm DNA from fertile men differ between distinct geographical regions

    DEFF Research Database (Denmark)

    Consales, C; Leter, G; Bonde, Jens Peter

    2014-01-01

    STUDY QUESTION: Which are the main determinants, if any, of sperm DNA methylation levels? SUMMARY ANSWER: Geographical region resulted associated with the sperm methylation status assessed on genome-wide repetitive sequences. WHAT IS KNOWN ALREADY: DNA methylation level, assessed on repetitive se...

  7. Prediction of the Maximum Number of Repetitions and Repetitions in Reserve From Barbell Velocity.

    Science.gov (United States)

    García-Ramos, Amador; Torrejón, Alejandro; Feriche, Belén; Morales-Artacho, Antonio J; Pérez-Castilla, Alejandro; Padial, Paulino; Haff, Guy Gregory

    2018-03-01

    To provide 2 general equations to estimate the maximum possible number of repetitions (XRM) from the mean velocity (MV) of the barbell and the MV associated with a given number of repetitions in reserve, as well as to determine the between-sessions reliability of the MV associated with each XRM. After determination of the bench-press 1-repetition maximum (1RM; 1.15 ± 0.21 kg/kg body mass), 21 men (age 23.0 ± 2.7 y, body mass 72.7 ± 8.3 kg, body height 1.77 ± 0.07 m) completed 4 sets of as many repetitions as possible against relative loads of 60%1RM, 70%1RM, 80%1RM, and 90%1RM over 2 separate sessions. The different loads were tested in a randomized order with 10 min of rest between them. All repetitions were performed at the maximum intended velocity. Both the general equation to predict the XRM from the fastest MV of the set (CV = 15.8-18.5%) and the general equation to predict MV associated with a given number of repetitions in reserve (CV = 14.6-28.8%) failed to provide data with acceptable between-subjects variability. However, a strong relationship (median r 2  = .984) and acceptable reliability (CV  .85) were observed between the fastest MV of the set and the XRM when considering individual data. These results indicate that generalized group equations are not acceptable methods for estimating the XRM-MV relationship or the number of repetitions in reserve. When attempting to estimate the XRM-MV relationship, one must use individualized relationships to objectively estimate the exact number of repetitions that can be performed in a training set.

  8. If you negate, you may forget: negated repetitions impair memory compared with affirmative repetitions.

    Science.gov (United States)

    Mayo, Ruth; Schul, Yaacov; Rosenthal, Meytal

    2014-08-01

    One of the most robust laws of memory is that repeated activation improves memory. Our study shows that the nature of repetition matters. Specifically, although both negated repetition and affirmative repetition improve memory compared with no repetition, negated repetition hinders memory compared with affirmative repetition. After showing participants different entities, we asked them about features of these entities, leading to either "yes" or "no" responses. Our findings show that correctly negating an incorrect feature of an entity elicits an active forgetting effect compared with correctly affirming its true features. For example, after seeing someone drink a glass of white wine, answering "no" to "was it red wine?" may lead one to greater memory loss of the individual drinking wine at all compared with answering "yes" to "was it white wine?" We find this negation-induced forgetting effect in 4 experiments that differ in (a) the meaning given for the negation, (b) the type of stimuli (visual or verbal), and (c) the memory measure (recognition or free recall). We discuss possible underlying mechanisms and offer theoretical and applied implications of the negation-induced forgetting effect in relation to other known inhibition effects. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  9. The development of a repetition-load scheme for the eccentric-only bench press exercise.

    Science.gov (United States)

    Moir, Gavin L; Erny, Kyle F; Davis, Shala E; Guers, John J; Witmer, Chad A

    2013-01-01

    The purpose of the present study was to develop a repetition-load scheme for the eccentric-only bench press exercise. Nine resistance trained men (age: 21.6 ± 1.0 years; 1-repetition maximum [RM] bench press: 137.7 ± 30.4 kg) attended four testing sessions during a four week period. During the first session each subject's 1-RM bench press load utilizing the stretch-shortening cycle was determined. During the remaining sessions they performed eccentric-only repetitions to failure using supra-maximal loads equivalent to 110%, 120% and 130% of their 1-RM value with a constant cadence (30 reps·min(-1)). Force plates and a three dimensional motion analysis system were used during these final three sessions in order to evaluate kinematic and kinetic variables. More repetitions were completed during the 110% 1-RM condition compared to the 130% 1-RM condition (p=0.01). Mean total work (p=0.046) as well as vertical force (p=0.049), vertical work (p=0.017), and vertical power output (p=0.05) were significantly greater during the 130% 1-RM condition compared to the 110% 1-RM condition. A linear function was fitted to the number of repetitions completed under each load condition that allowed the determination of the maximum number of repetitions that could be completed under other supra-maximal loads. This linear function predicted an eccentric-only 1-RM in the bench press with a load equivalent to 164.8% 1-RM, producing a load of 227.0 ± 50.0 kg. The repetition-load scheme presented here should provide a starting point for researchers to investigate the kinematic, kinetic and metabolic responses to eccentric-only bench press workouts.

  10. High power, repetitive stacked Blumlein pulse generators

    Energy Technology Data Exchange (ETDEWEB)

    Davanloo, F; Borovina, D L; Korioth, J L; Krause, R K; Collins, C B [Univ. of Texas at Dallas, Richardson, TX (United States). Center for Quantum Electronics; Agee, F J [US Air Force Phillips Lab., Kirtland AFB, NM (United States); Kingsley, L E [US Army CECOM, Ft. Monmouth, NJ (United States)

    1997-12-31

    The repetitive stacked Blumlein pulse power generators developed at the University of Texas at Dallas consist of several triaxial Blumleins stacked in series at one end. The lines are charged in parallel and synchronously commuted with a single switch at the other end. In this way, relatively low charging voltages are multiplied to give a high discharge voltage across an arbitrary load. Extensive characterization of these novel pulsers have been performed over the past few years. Results indicate that they are capable of producing high power waveforms with rise times and repetition rates in the range of 0.5-50 ns and 1-300 Hz, respectively, using a conventional thyratron, spark gap, or photoconductive switch. The progress in the development and use of stacked Blumlein pulse generators is reviewed. The technology and the characteristics of these novel pulsers driving flash x-ray diodes are discussed. (author). 4 figs., 5 refs.

  11. Physiological responses to four hours of low-level repetitive work

    DEFF Research Database (Denmark)

    Garde, A Helene; Hansen, Åse Marie; Jensen, Bente R

    2003-01-01

    OBJECTIVES: The study investigated physiological responses to 4 hours of standardized low-level repetitive work. It was hypothesized that accumulative effects not observed after 1 hour could be found after 4 hours of repetitive work. METHODS: Ten healthy women performed intermittent (5 seconds + 5...... muscle activity during a mental reference task with low exerted force indicated attention-related muscle activity. Finally, it was indicated that repetitive work including high demands for attention is performed at the expense of the precision of the exerted force....... seconds) handgrip contractions at 10% of the maximal voluntary contraction combined with mental demands for concentration and attention. Muscle activity in the working forearm muscles, cardiovascular responses, and concentrations of biomarkers in biological fluids were recorded along with exerted force...

  12. Incremental learning of perceptual and conceptual representations and the puzzle of neural repetition suppression.

    Science.gov (United States)

    Gotts, Stephen J

    2016-08-01

    Incremental learning models of long-term perceptual and conceptual knowledge hold that neural representations are gradually acquired over many individual experiences via Hebbian-like activity-dependent synaptic plasticity across cortical connections of the brain. In such models, variation in task relevance of information, anatomic constraints, and the statistics of sensory inputs and motor outputs lead to qualitative alterations in the nature of representations that are acquired. Here, the proposal that behavioral repetition priming and neural repetition suppression effects are empirical markers of incremental learning in the cortex is discussed, and research results that both support and challenge this position are reviewed. Discussion is focused on a recent fMRI-adaptation study from our laboratory that shows decoupling of experience-dependent changes in neural tuning, priming, and repetition suppression, with representational changes that appear to work counter to the explicit task demands. Finally, critical experiments that may help to clarify and resolve current challenges are outlined.

  13. Primary power supply of repetitive pulsed intense current accelerator charged by capacitance of energy store

    International Nuclear Information System (INIS)

    Chen Jun; Yang Jianhua; Shu Ting; Zhang Jiande; Zhou Xiang; Wen Jianchun

    2008-01-01

    The primary power supply of repetitive pulsed intense current accelerator charged by capacitance of energy store is studied. The principle of primary power supply circuit and its time diagram of switches are presented. The circuit is analyzed and some expressions are got, especially, the usable voltage scope of capacitance of energy store, and the correlation between the parameters of circuit and time delay, which is between the turn-on of the charging circuit of capacitance of energy store and the circuit of recuperation. The time delay of 256 x 256 lookup table is made with the instruction of theory and the simulation of the actual parameters of circuits. The table is used by the control program to control the repetitive operating of the actual pulsed intense current accelerator. Finally, some conclusions of the primary power supply of repetitive pulsed intense current accelerator charged by capacitance of energy store are got. (authors)

  14. A repetitive elements perspective in Polycomb epigenetics.

    Directory of Open Access Journals (Sweden)

    Valentina eCasa

    2012-10-01

    Full Text Available Repetitive elements comprise over two-thirds of the human genome. For a long time, these elements have received little attention since they were considered non functional. On the contrary, recent evidence indicates that they play central roles in genome integrity, gene expression and disease. Indeed, repeats display meiotic instability associated with disease and are located within common fragile sites, which are hotspots of chromosome rearrangements in tumors. Moreover, a variety of diseases have been associated with aberrant transcription of repetitive elements. Overall this indicates that appropriate regulation of repetitive elements’ activity is fundamental.Polycomb group (PcG proteins are epigenetic regulators that are essential for the normal development of multicellular organisms. Mammalian PcG proteins are involved in fundamental processes, such as cellular memory, cell proliferation, genomic imprinting, X-inactivation, and cancer development. PcG proteins can convey their activity through long-distance interactions also on different chromosomes. This indicates that the 3D organization of PcG proteins contributes significantly to their function. However, it is still unclear how these complex mechanisms are orchestrated and which role PcG proteins play in the multi-level organization of gene regulation. Intriguingly, the greatest proportion of Polycomb-mediated chromatin modifications is located in genomic repeats and it has been suggested that they could provide a binding platform for Polycomb proteins.Here, these lines of evidence are woven together to discuss how repetitive elements could contribute to chromatin organization in the 3D nuclear space.

  15. Modeling repetitive motions using structured light.

    Science.gov (United States)

    Xu, Yi; Aliaga, Daniel G

    2010-01-01

    Obtaining models of dynamic 3D objects is an important part of content generation for computer graphics. Numerous methods have been extended from static scenarios to model dynamic scenes. If the states or poses of the dynamic object repeat often during a sequence (but not necessarily periodically), we call such a repetitive motion. There are many objects, such as toys, machines, and humans, undergoing repetitive motions. Our key observation is that when a motion-state repeats, we can sample the scene under the same motion state again but using a different set of parameters; thus, providing more information of each motion state. This enables robustly acquiring dense 3D information difficult for objects with repetitive motions using only simple hardware. After the motion sequence, we group temporally disjoint observations of the same motion state together and produce a smooth space-time reconstruction of the scene. Effectively, the dynamic scene modeling problem is converted to a series of static scene reconstructions, which are easier to tackle. The varying sampling parameters can be, for example, structured-light patterns, illumination directions, and viewpoints resulting in different modeling techniques. Based on this observation, we present an image-based motion-state framework and demonstrate our paradigm using either a synchronized or an unsynchronized structured-light acquisition method.

  16. Lingual Kinematics during Rapid Syllable Repetition in Parkinson's Disease

    Science.gov (United States)

    Wong, Min Ney; Murdoch, Bruce E.; Whelan, Brooke-Mai

    2012-01-01

    Background: Rapid syllable repetition tasks are commonly used in the assessment of motor speech disorders. However, little is known about the articulatory kinematics during rapid syllable repetition in individuals with Parkinson's disease (PD). Aims: To investigate and compare lingual kinematics during rapid syllable repetition in dysarthric…

  17. Grade Repetition and Primary School Dropout in Uganda

    Science.gov (United States)

    Kabay, Sarah

    2016-01-01

    Research on education in low-income countries rarely focuses on grade repetition. When addressed, repetition is typically presented along with early school dropout as the "wasting" of educational resources. Simplifying grade repetition in this way often fails to recognize significant methodological concerns and also overlooks the unique…

  18. Identification and chromosome mapping of repetitive elements in the Astyanax scabripinnis (Teleostei: Characidae) species complex.

    Science.gov (United States)

    Barbosa, Patrícia; de Oliveira, Luiz Antonio; Pucci, Marcela Baer; Santos, Mateus Henrique; Moreira-Filho, Orlando; Vicari, Marcelo Ricardo; Nogaroto, Viviane; de Almeida, Mara Cristina; Artoni, Roberto Ferreira

    2015-02-01

    Most part of the eukaryotic genome is composed of repeated sequences or multiple copies of DNA, which were considered as "junk DNA", and may be associated to the heterochromatin. In this study, three populations of Astyanax aff. scabripinnis from Brazilian rivers of Guaratinguetá and Pindamonhangaba (São Paulo) and a population from Maringá (Paraná) were analyzed concerning the localization of the nucleolar organizer regions (Ag-NORs), the As51 satellite DNA, the 18S ribosomal DNA (rDNA), and the 5S rDNA. Repeated sequences were also isolated and identified by the Cot - 1 method, which indicated similarity (90%) with the LINE UnaL2 retrotransposon. The fluorescence in situ hybridization (FISH) showed the retrotransposon dispersed and more concentrated markers in centromeric and telomeric chromosomal regions. These sequences were co-localized and interspaced with 18S and 5S rDNA and As51, confirmed by fiber-FISH essay. The B chromosome found in these populations pointed to a conspicuous hybridization with LINE probe, which is also co-located in As51 sequences. The NORs were active at unique sites of a homologous pair in the three populations. There were no evidences that transposable elements and repetitive DNA had influence in the transcriptional regulation of ribosomal genes in our analyses.

  19. A new protocol for extraction of C 0 t-1 DNA from rice | Yan | African ...

    African Journals Online (AJOL)

    C0t-1 DNA, enriched for repetitive DNA sequences, has been proved to be valuable in the studies of plant species differentiation and genome evolution. A new protocol to steadily obtain the aimed range of DNA fragments has been developed by shearing the genomic DNA with the digest system containing DNase ...

  20. Modulation of repetitive genes in the parent forms of heterozygous corn hybrids

    International Nuclear Information System (INIS)

    Gilyazetdinov, S.Ya.; Zimnitskii, A.N.; Yakhin, I.A.; Bikbaeva, E.S.

    1987-01-01

    The number of copies of the genes of high-molecular-weight rRNA, 5 S r RNA, and certain other families of repetitive sequences of DNA in the genome of different forms of corn is not coordinated but is stably inherited in the same strains. The authors present the results of their investigations into the repetition of the genes of tRNA, 5 S rRNA, histones, and the controlling element Ds of corn for the highly heterozygous hybrid Slava (VIR 44 x VIR 38), the medium-heterozygous hybrid Svetoch (VIR 40 x VIR 43), the low heterozygous hybrid Iskra (VIR 26 x VIR 27), and their parent strains. The relative content of these sequences was studied by the molecular hybridization of DNA immobilized on nitrocellulose filters with [ 125 I]tRNA labeled in vitro, 5 S rRNA, histone DNA of Drosophila, and the Ds-element of corn. The DNA preparations were isolated from the zones of the meristem (1.5-2mm), elongation (4-5mm), differentiation of the roots (3 cm), of 3-4 day seedlings, and from isolated embryos of 4 h and 24 h seedlings. The DNA of the embryos immobilized on the filters was preliminarily incubated with unlabeled high-molecular-weight rRNA in the experiments with tRNA and 5 S rRNA, while when histone DNA and the Ds element of corn were used in the hybridization reaction, it was preliminary incubated with plasmid DNA

  1. Imbalance between abstract and concrete repetitive thinking modes in schizophrenia.

    Science.gov (United States)

    Maurage, Pierre; Philippot, Pierre; Grynberg, Delphine; Leleux, Dominique; Delatte, Benoît; Mangelinckx, Camille; Belge, Jan-Baptist; Constant, Eric

    2017-10-01

    Repetitive thoughts can be divided in two modes: abstract/analytic (decontextualized and dysfunctional) and concrete/experiential (problem-focused and adaptive). They constitute a transdiagnostic process involved in many psychopathological states but have received little attention in schizophrenia, as earlier studies only indexed increased ruminations (related to dysfunctional repetitive thoughts) without jointly exploring both modes. This study explored the two repetitive thinking modes, beyond ruminations, to determine their imbalance in schizophrenia. Thirty stabilized patients with schizophrenia and 30 matched controls completed the Repetitive Response Scale and the Mini Cambridge-Exeter Repetitive Thought Scale, both measuring repetitive thinking modes. Complementary measures related to schizophrenic symptomatology, depression and anxiety were also conducted. Compared to controls, patients with schizophrenia presented an imbalance between repetitive thinking modes, with increased abstract/analytic and reduced concrete/experiential thoughts, even after controlling for comorbidities. Schizophrenia is associated with stronger dysfunctional repetitive thoughts (i.e. abstract thinking) and impaired ability to efficiently use repetitive thinking for current problem-solving (i.e. concrete thinking). This imbalance confirms the double-faced nature of repetitive thinking modes, whose influence on schizophrenia's symptomatology should be further investigated. The present results also claim for evaluating these processes in clinical settings and for rehabilitating the balance between opposite repetitive thinking modes. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Repetitive thinking, executive functioning, and depressive mood in the elderly.

    Science.gov (United States)

    Philippot, Pierre; Agrigoroaei, Stefan

    2017-11-01

    Previous findings and the depressive-executive dysfunction hypothesis suggest that the established association between executive functioning and depression is accounted for by repetitive thinking. Investigating the association between executive functioning, repetitive thinking, and depressive mood, the present study empirically tested this mediational model in a sample of older adults, while focusing on both concrete and abstract repetitive thinking. This latter distinction is important given the potential protective role of concrete repetitive thinking, in contrast to the depletive effect of abstract repetitive thinking. A sample of 43 elderly volunteers, between 75 and 95 years of age, completed tests of executive functioning (the Stroop test, the Trail Making test, and the Fluency test), and questionnaires of repetitive thinking and depression. Positive correlations were observed between abstract repetitive thinking and depressive mood, and between concrete repetitive thinking and executive functioning; a negative correlation was observed between depressive mood and executive functioning. Further, mediational analysis evidenced that the relation between executive functioning and depressive mood was mediated by abstract repetitive thinking. The present data provide, for the first time, empirical support to the depressive-executive dysfunction hypothesis: the lack of executive resources would favor a mode of abstract repetitive thinking, which in turn would deplete mood. It suggests that clinical intervention targeting depression in the elderly should take into consideration repetitive thinking modes and the executive resources needed to disengage from rumination.

  3. [Direct assays of radiation-induced DNA base lesions in mammalian cells.] Final progress report, February 1, 1984-June 30, 1986

    International Nuclear Information System (INIS)

    Wheeler, K.T.

    1986-01-01

    Adenine (Ade), 2'-deoxyadenosine (dAdo) and 5'-deoxyadenosine monophosphate (5'-dAMP) were irradiated with 50 to 15,000 Gy under oxic and hypoxic conditions. HPLC procedures providing satisfactory separation of the adenine damage products formed during irradiation of DNA model compounds were found. Structures of some of the damage products were confirmed to include 8-OHAde, 4,6-diamino-5-formamidopyrimidine, and 8-OH-5'-dAMP. Two damage products of dAdo (8-OHdAdo and the major isomer of 8,5'-cdAdo), the formation of which depends on the presence or absence of oxygen, were determined quantitatively by HPLC. The limit for HPLC detection was estimated as 4 to 50 pmoles for these compounds. This corresponds to a detection limit of about 50 Gy in radiation dose units. These two products were also detected in mixtures of all four nucleosides irradiated with 50 Gy

  4. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

    Science.gov (United States)

    Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

    2009-01-01

    Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

  5. Pull-production in repetitive remanufacturing

    Energy Technology Data Exchange (ETDEWEB)

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele`s pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  6. Pull-production in repetitive remanufacturing

    Energy Technology Data Exchange (ETDEWEB)

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele's pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  7. Synergy Repetition Training versus Task Repetition Training in Acquiring New Skill.

    Science.gov (United States)

    Patel, Vrajeshri; Craig, Jamie; Schumacher, Michelle; Burns, Martin K; Florescu, Ionut; Vinjamuri, Ramana

    2017-01-01

    Traditionally, repetitive practice of a task is used to learn a new skill, exhibiting as immediately improved performance. Research suggests, however, that a more experience-based rather than exposure-based training protocol may allow for better transference of the skill to related tasks. In synergy-based motor control theory, fundamental motor skills, such as hand grasping, are represented with a synergy subspace that captures essential motor patterns. In this study, we propose that motor-skill learning through synergy-based mechanisms may provide advantages over traditional task repetition learning. A new task was designed to highlight the range of motion and dexterity of the human hand. Two separate training strategies were tested in healthy subjects: task repetition training and synergy training versus a control. All three groups showed improvements when retested on the same task. When tested on a similar, but different set of tasks, only the synergy group showed improvements in accuracy (9.27% increase) compared to the repetition (3.24% decline) and control (3.22% decline) groups. A kinematic analysis revealed that although joint angular peak velocities decreased, timing benefits stemmed from the initial feed-forward portion of the task (reaction time). Accuracy improvements may have derived from general improved coordination among the four involved fingers. These preliminary results warrant further investigation of synergy-based motor training in healthy individuals, as well as in individuals undergoing hand-based rehabilitative therapy.

  8. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

    Directory of Open Access Journals (Sweden)

    Hankus Lukasz

    2006-10-01

    Full Text Available Abstract Background Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. Results We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s, repeat sequences found in the query, and alignments. Conclusion Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter and http://www.girinst.org/censor/index.php (Censor.

  9. The role of short-term memory impairment in nonword repetition, real word repetition, and nonword decoding: A case study.

    Science.gov (United States)

    Peter, Beate

    2018-01-01

    In a companion study, adults with dyslexia and adults with a probable history of childhood apraxia of speech showed evidence of difficulty with processing sequential information during nonword repetition, multisyllabic real word repetition and nonword decoding. Results suggested that some errors arose in visual encoding during nonword reading, all levels of processing but especially short-term memory storage/retrieval during nonword repetition, and motor planning and programming during complex real word repetition. To further investigate the role of short-term memory, a participant with short-term memory impairment (MI) was recruited. MI was confirmed with poor performance during a sentence repetition and three nonword repetition tasks, all of which have a high short-term memory load, whereas typical performance was observed during tests of reading, spelling, and static verbal knowledge, all with low short-term memory loads. Experimental results show error-free performance during multisyllabic real word repetition but high counts of sequence errors, especially migrations and assimilations, during nonword repetition, supporting short-term memory as a locus of sequential processing deficit during nonword repetition. Results are also consistent with the hypothesis that during complex real word repetition, short-term memory is bypassed as the word is recognized and retrieved from long-term memory prior to producing the word.

  10. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  11. ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

    Directory of Open Access Journals (Sweden)

    Alves-Ferreira Marcelo

    2008-09-01

    Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

  12. Object color affects identification and repetition priming.

    Science.gov (United States)

    Uttl, Bob; Graf, Peter; Santacruz, Pilar

    2006-10-01

    We investigated the influence of color on the identification of both non-studied and studied objects. Participants studied black and white and color photos of common objects and memory was assessed with an identification test. Consistent with our meta-analysis of prior research, we found that objects were easier to identify from color than from black and white photos. We also found substantial priming in all conditions, and study-to-test changes in an object's color reduced the magnitude of priming. Color-specific priming effects were large for color-complex objects, but minimal for color-simple objects. The pattern and magnitude of priming effects was not influenced either by the extent to which an object always appears in the same color (i.e., whether a color is symptomatic of an object) or by the object's origin (natural versus fabricated). We discuss the implications of our findings for theoretical accounts of object perception and repetition priming.

  13. PROJECT IMPLEMENTATION IN ORGANISATIONS OF REPETITIVE ACTIVITIES

    Directory of Open Access Journals (Sweden)

    Marek WIRKUS

    2015-04-01

    Full Text Available The study presents the implementation of projects in organisations that achieve business objectives through the imple-mentation of repetitive actions. Projects in these organisations are, on the one hand, treated as marginal activities, while the results of these projects have significant impact on the delivery of main processes, e.g. through the introduction of new products. Human capital and solutions in this field bear impact on the success of projects in these organisations, which is not always conducive to smooth implementation of projects. Conflict results from the nature of a project, which is a one-time and temporary process, so organisational solutions are also temporary. It influences on attitudes and com-mitment of the project contractors. The paper identifies and analyses factors which affect the success of the projects.

  14. Low-Intensity Repetitive Exercise Induced Rhabdomyolysis

    Directory of Open Access Journals (Sweden)

    Mina Tran

    2015-01-01

    Full Text Available Rhabdomyolysis is a rare condition caused by the proteins of damaged muscle cells entering the bloodstream and damaging the kidneys. Common symptoms of rhabdomyolysis are muscle pain and fatigue in conjunction with dark urine; kidney damage is a common symptom among these patients. We present a case of a 23-year-old woman who displayed myalgia in the upper extremities caused by low-intensity and high-repetition exercise. She was successfully diagnosed and treated for exertional rhabdomyolysis. This patient had no significant medical history that would induce this condition. We urge the emergency medical community to observe and monitor patients that complain of myalgia to ensure they are not suffering from rhabdomyolysis even in atypical cases.

  15. Repetitively pulsed power for meat pasteurization

    International Nuclear Information System (INIS)

    Patterson, E.L.; Kaye, R.J.; Neau, E.L.

    1994-01-01

    Electronic pasteurization of meat offers the potential for drastically reducing the incidence of food poisoning caused by biological pathogens accidentally introduced into meat products. Previous work has shown that γ-rays are an effective method of destroying E. coli 0157:H7, Salmonella, C. jejuni, L. monocytogenes, Listeria, and S. aureus bacteria types. The concern with the use of γ-rays is that radioactive material must be used in the pasteurization process that can lead to some market resistance and activist pressure on the meat industry. The use of accelerator generated high average power electron beams, at energies less than 10 MeV, or X-rays, with energies below 5 MeV, have been approved by the FDA for use in pasteurizing foods. Accelerator produced electronic pasteurization has the advantage that no radioactive material inventory is required. Electronic pasteurization has the additional benefit that it removes bacterial pathogens on the meat surface as well as within the volume of the meat product. High average power, repetitively-pulsed, broad-area electron beam sources being developed in the RHEPP program are suitable for large scale meat treatment in packing plant environments. RHEPP-II, which operates at 2.5 MeV and 25 kA at pulse repetition frequencies up to 120 Hz has adequate electron energy to penetrate hamburger patties which comprise about half of the beef consumption in the United States. Ground beef also has the highest potential for contamination since considerable processing is required in its production. A meat pasteurization facility using this size of accelerator source should be capable of treating 10 6 pounds of hamburger patties per hour to a dose of up to 3 kGy (300 kilorads). The RHEPP modular accelerator technology can easily be modified for other production rates and types of products

  16. FEMA Hazard Mitigation Assistance Severe Repetitive Loss (SRL) Data

    Data.gov (United States)

    Department of Homeland Security — This dataset contains closed and obligated projects funded under the following Hazard Mitigation Assistance (HMA) grant programs: Severe Repetitive Loss (SRL). The...

  17. FEMA Hazard Mitigation Assistance Repetitive Flood Claims (RFC) Data

    Data.gov (United States)

    Department of Homeland Security — This dataset contains closed and obligated projects funded under the following Hazard Mitigation Assistance (HMA) grant programs: Repetitive Flood Claims (RFC). The...

  18. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes.

    Science.gov (United States)

    Li, Shu-Fen; Zhang, Guo-Jun; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

    2016-05-01

    The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

  19. Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae).

    Science.gov (United States)

    García, G; Ríos, N; Gutiérrez, V

    2015-06-01

    Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45%) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25%). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family.

  20. The Golden Ratio of Gait Harmony: Repetitive Proportions of Repetitive Gait Phases

    Directory of Open Access Journals (Sweden)

    Marco Iosa

    2013-01-01

    Full Text Available In nature, many physical and biological systems have structures showing harmonic properties. Some of them were found related to the irrational number known as the golden ratio that has important symmetric and harmonic properties. In this study, the spatiotemporal gait parameters of 25 healthy subjects were analyzed using a stereophotogrammetric system with 25 retroreflective markers located on their skin. The proportions of gait phases were compared with , the value of which is about 1.6180. The ratio between the entire gait cycle and stance phase resulted in 1.620 ± 0.058, that between stance and the swing phase was 1.629 ± 0.173, and that between swing and the double support phase was 1.684 ± 0.357. All these ratios did not differ significantly from each other (, , repeated measure analysis of variance or from (, resp., t-tests. The repetitive gait phases of physiological walking were found in turn in repetitive proportions with each other, revealing an intrinsic harmonic structure. Harmony could be the key for facilitating the control of repetitive walking. Harmony is a powerful unifying factor between seemingly disparate fields of nature, including human gait.

  1. Photocathodes for High Repetition Rate Light Sources

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Zvi, Ilan [Stony Brook Univ., NY (United States). Dept. of Physics and Astronomy. Center for Accelerator Science and Education

    2014-04-20

    This proposal brought together teams at Brookhaven National Laboratory (BNL), Lawrence Berkeley National Laboratory (LBNL) and Stony Brook University (SBU) to study photocathodes for high repetition rate light sources such as Free Electron Lasers (FEL) and Energy Recovery Linacs (ERL). Below details the Principal Investigators and contact information. Each PI submits separately for a budget through his corresponding institute. The work done under this grant comprises a comprehensive program on critical aspects of the production of the electron beams needed for future user facilities. Our program pioneered in situ and in operando diagnostics for alkali antimonide growth. The focus is on development of photocathodes for high repetition rate Free Electron Lasers (FELs) and Energy Recovery Linacs (ERLs), including testing SRF photoguns, both normal-­conducting and superconducting. Teams from BNL, LBNL and Stony Brook University (SBU) led this research, and coordinated their work over a range of topics. The work leveraged a robust infrastructure of existing facilities and the support was used for carrying out the research at these facilities. The program concentrated in three areas: a) Physics and chemistry of alkali-­antimonide cathodes (BNL – LBNL) b) Development and testing of a diamond amplifier for photocathodes (SBU -­ BNL) c) Tests of both cathodes in superconducting RF photoguns (SBU) and copper RF photoguns (LBNL) Our work made extensive use of synchrotron radiation materials science techniques, such as powder-­ and single-­crystal diffraction, x-­ray fluorescence, EXAFS and variable energy XPS. BNL and LBNL have many complementary facilities at the two light sources associated with these laboratories (NSLS and ALS, respectively); use of these will be a major thrust of our program and bring our understanding of these complex materials to a new level. In addition, CHESS at Cornell will be used to continue seamlessly throughout the NSLS dark period and

  2. Visual attention to advertising : The impact of motivation and repetition

    NARCIS (Netherlands)

    Pieters, RGM; Rosbergen, E; Hartog, M; Corfman, KP; Lynch, JG

    1996-01-01

    Using eye-tracking data, we examine the impact of motivation and repetition on visual attention to advertisements differing in argument quality. Our analyses indicate that repetition leads to an overall decrease in the amount of attention. However, while at first high motivation subjects attend to

  3. Repetitively pulsed, double discharge TEA CO/sub 2/ laser

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, D C; James, D J; Ramsden, S A

    1975-10-01

    The design and operation of a repetitively pulsed TEA CO/sub 2/ laser is described. Average powers of up to 400 W at a repetition frequency of 200 pulses/s have been obtained. The system has also been used to provide long pulses (over 20 ..mu..s) and tunable single axial mode pulses.

  4. Effects of repetition and temperature on Contingent Electrical Stimulation

    DEFF Research Database (Denmark)

    Castrillon, Eduardo E.; Zhou, Xinwen; Svensson, Peter

    ) activity associated with bruxism. Repetition of the electrical stimulus and skin surface temperature (ST) may affect the perception of CES and possibly also the inhibitory EMG effects.Objectives: To determine the effects of stimulus repetition and skin ST on the perception of CES.  Methods: Healthy...

  5. Repetition Blindness: Out of Sight or Out of Mind?

    Science.gov (United States)

    Morris, Alison L.; Harris, Catherine L.

    2004-01-01

    Does repetition blindness represent a failure of perception or of memory? In Experiment 1, participants viewed rapid serial visual presentation (RSVP) sentences. When critical words (C1 and C2) were orthographically similar, C2 was frequently omitted from serial report; however, repetition priming for C2 on a postsentence lexical decision task was…

  6. Evidence-Based Behavioral Interventions for Repetitive Behaviors in Autism

    Science.gov (United States)

    Boyd, Brian A.; McDonough, Stephen G.; Bodfish, James W.

    2012-01-01

    Restricted and repetitive behaviors (RRBs) are a core symptom of autism spectrum disorders (ASD). There has been an increased research emphasis on repetitive behaviors; however, this research primarily has focused on phenomenology and mechanisms. Thus, the knowledge base on interventions is lagging behind other areas of research. The literature…

  7. Pre-Lexical Disorders in Repetition Conduction Aphasia

    Science.gov (United States)

    Sidiropoulos, Kyriakos; de Bleser, Ria; Ackermann, Hermann; Preilowski, Bruno

    2008-01-01

    At the level of clinical speech/language evaluation, the repetition type of conduction aphasia is characterized by repetition difficulties concomitant with reduced short-term memory capacities, in the presence of fluent spontaneous speech as well as unimpaired naming and reading abilities. It is still unsettled which dysfunctions of the…

  8. Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment

    Directory of Open Access Journals (Sweden)

    Manuela Silva

    2012-07-01

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

  9. Repetitive exposure: Brain and reflex measures of emotion and attention

    Science.gov (United States)

    Ferrari, Vera; Bradley, Margaret M.; Codispoti, Maurizio; Lang, Peter J.

    2010-01-01

    Effects of massed repetition on the modulation of the late positive potential elicited during affective picture viewing were investigated in two experiments. Despite a difference in the number of repetitions across studies (from 5 to 30), results were quite similar: the late positive potential continued to be enhanced when viewing emotional, compared to neutral, pictures. On the other hand, massed repetition did prompt a reduction in the late positive potential that was most pronounced for emotional pictures. Startle probe P3 amplitude generally increased with repetition, suggesting diminished attention allocation to repeated pictures. The blink reflex, however, continued to be modulated by hedonic valence, despite massive massed repetition. Taken together, the data suggest that the amplitude of the late positive potential during picture viewing reflects both motivational significance and attention allocation. PMID:20701711

  10. Repetition and Emotive Communication in Music Versus Speech

    Directory of Open Access Journals (Sweden)

    Elizabeth Hellmuth eMargulis

    2013-04-01

    Full Text Available Music and speech are often placed alongside one another as comparative cases. Their relative overlaps and disassociations have been well explored (e.g. Patel, 2010. But one key attribute distinguishing these two domains has often been overlooked: the greater preponderance of repetition in music in comparison to speech. Recent fMRI studies have shown that familiarity – achieved through repetition – is a critical component of emotional engagement with music (Pereira et al., 2011. If repetition is fundamental to emotional responses to music, and repetition is a key distinguisher between the domains of music and speech, then close examination of the phenomenon of repetition might help clarify the ways that music elicits emotion differently than speech.

  11. Transgenerational effects of environmental enrichment on repetitive motor behavior development.

    Science.gov (United States)

    Bechard, Allison R; Lewis, Mark H

    2016-07-01

    The favorable consequences of environmental enrichment (EE) on brain and behavior development are well documented. Much less is known, however, about transgenerational benefits of EE on non-enriched offspring. We explored whether transgenerational effects of EE might extend to the development of repetitive motor behaviors in deer mice. Repetitive motor behaviors are invariant patterns of movement that, across species, can be reduced by EE. We found that EE not only attenuated the development of repetitive behavior in dams, but also in their non-enriched offspring. Moreover, maternal behavior did not seem to mediate the transgenerational effect we found, although repetitive behavior was affected by reproductive experience. These data support a beneficial transgenerational effect of EE on repetitive behavior development and suggest a novel benefit of reproductive experience. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Repetitive low-frequency stimulation reduces epileptiform synchronization in limbic neuronal networks.

    Science.gov (United States)

    D'Arcangelo, G; Panuccio, G; Tancredi, V; Avoli, M

    2005-01-01

    Deep-brain electrical or transcranial magnetic stimulation may represent a therapeutic tool for controlling seizures in patients presenting with epileptic disorders resistant to antiepileptic drugs. In keeping with this clinical evidence, we have reported that repetitive electrical stimuli delivered at approximately 1 Hz in mouse hippocampus-entorhinal cortex (EC) slices depress the EC ability to generate ictal activity induced by the application of 4-aminopyridine (4AP) or Mg(2+)-free medium (Barbarosie, M., Avoli, M., 1997. CA3-driven hippocampal-entorhinal loop controls rather than sustains in vitro limbic seizures. J. Neurosci. 17, 9308-9314.). Here, we confirmed a similar control mechanism in rat brain slices analyzed with field potential recordings during 4AP (50 microM) treatment. In addition, we used intrinsic optical signal (IOS) recordings to quantify the intensity and spatial characteristics of this inhibitory influence. IOSs reflect the changes in light transmittance throughout the entire extent of the slice, and are thus reliable markers of limbic network epileptiform synchronization. First, we found that in the presence of 4AP, the IOS increases, induced by a train of electrical stimuli (10 Hz for 1 s) or by recurrent, single-shock stimulation delivered at 0.05 Hz in the deep EC layers, are reduced in intensity and area size by low-frequency (1 Hz), repetitive stimulation of the subiculum; these effects were observed in all limbic areas contained in the slice. Second, by testing the effects induced by repetitive subicular stimulation at 0.2-10 Hz, we identified maximal efficacy when repetitive stimuli are delivered at 1 Hz. Finally, we discovered that similar, but slightly less pronounced, inhibitory effects occur when repetitive stimuli at 1 Hz are delivered in the EC, suggesting that the reduction of IOSs seen during repetitive stimulation is pathway dependent as well as activity dependent. Thus, the activation of limbic networks at low frequency

  13. Repetitive switching for an electromagnetic rail gun

    Science.gov (United States)

    Gruden, J. M.

    1983-12-01

    Previous testing on a repetitive opening switch for inductive energy storage has proved the feasibility of the rotary switch concept. The concept consists of a rotating copper disk (rotor) with a pie-shaped insulator section and brushes which slide along each of the rotor surfaces. While on top of the copper surface, the brushes and rotor conduct current allowing the energy storage inductor to charge. When the brushes slide onto the insulator section, the current cannot pass through the rotor and is diverted into the load. This study investigates two new brush designs and a rotor modification designed to improve the current commutating capabilities of the switch. One brush design (fringe fiber) employs carbon fibers on the leading and trailing edge of the brush to increase the resistive commutating action as the switch opens and closes. The other brush design uses fingers to conduct current to the rotor surface, effectively increasing the number of brush contact points. The rotor modification was the placement of tungsten inserts at the copper-insulator interfaces.

  14. Repetitive Interrogation of 2-Level Quantum Systems

    Science.gov (United States)

    Prestage, John D.; Chung, Sang K.

    2010-01-01

    Trapped ion clocks derive information from a reference atomic transition by repetitive interrogations of the same quantum system, either a single ion or ionized gas of many millions of ions. Atomic beam frequency standards, by contrast, measure reference atomic transitions in a continuously replenished "flow through" configuration where initial ensemble atomic coherence is zero. We will describe some issues and problems that can arise when atomic state selection and preparation of the quantum atomic system is not completed, that is, optical pumping has not fully relaxed the coherence and also not fully transferred atoms to the initial state. We present a simple two-level density matrix analysis showing how frequency shifts during the state-selection process can cause frequency shifts of the measured clock transition. Such considerations are very important when a low intensity lamp light source is used for state selection, where there is relatively weak relaxation and re-pumping of ions to an initial state and much weaker 'environmental' relaxation of the atomic coherence set-up in the atomic sample.

  15. Detection and Identification of Bursaphelenchus Species with DNA Fingerprinting and Polymerase Chain Reaction

    OpenAIRE

    Harmey, Judith H.; Harmey, Matthew A.

    1993-01-01

    We have evaluated the potential of DNA-based methods to identify and differentiate Bursaphelenchus spp. and isolates. The isolation of a DNA probe, designated X14, and development of a DNA fingerprinting method for the identification and differentiation of Bursaphelenchus species and strains is described. Polymerase chain reaction (PCR) amplification of DNA isolated from Bursaphelenchus species using two primers derived from the sequence of the cloned repetitive DNA fragment X14 resulted in m...

  16. Polymerase chain reaction-mediated DNA fingerprinting for epidemiological studies on Campylobacter spp

    NARCIS (Netherlands)

    Giesendorf, B A; Goossens, H; Niesters, H G; Van Belkum, A; Koeken, A; Endtz, H P; Stegeman, H; Quint, W G

    The applicability of polymerase chain reaction (PCR)-mediated DNA typing, with primers complementary to dispersed repetitive DNA sequences and arbitrarily chosen DNA motifs, to study the epidemiology of campylobacter infection was evaluated. With a single PCR reaction and simple gel electrophoresis,

  17. Development of repetitive railgun pellet accelerator and steady-state solid hydrogen extruder

    International Nuclear Information System (INIS)

    Oda, Y.; Azuma, K.; Onozuka, M.; Kasai, S.; Hasegawa, K.

    1995-01-01

    Development of a railgun pellet accelerator and a steady-state solid hydrogen extruder has been conducted. A railgun accelerator has been investigated for a high-speed repetitive pellet acceleration. The final objective is to develop a railgun system that can achieve a 5km/s speed-class repetitive (2Hz) pellet injection. Improvement in the acceleration efficiency showed a pellet velocity of more than 2km/s using augment rails and a ceramic insulator applied to a 1m-long railgun. The other investigation focused on the development of a steady-state solid hydrogen extruder for continuous pellet injection. Screw-driven extruding system has been chosen to extrude the solid hydrogen filament continuously. Theoretical considerations suggest that temperature control of the system is important in future research. (orig.)

  18. Development of repetitive railgun pellet accelerator and steady-state solid hydrogen extruder

    Energy Technology Data Exchange (ETDEWEB)

    Oda, Y. [Mitsubishi Heavy Industries Ltd., Kobe (Japan); Azuma, K. [Mitsubishi Heavy Industries Ltd., Kobe (Japan); Onozuka, M. [Mitsubishi Heavy Industries Ltd., Kobe (Japan); Kasai, S. [Japan Atomic Energy Research Inst., Ibaraki (Japan); Hasegawa, K. [Japan Atomic Energy Research Inst., Ibaraki (Japan)

    1995-12-31

    Development of a railgun pellet accelerator and a steady-state solid hydrogen extruder has been conducted. A railgun accelerator has been investigated for a high-speed repetitive pellet acceleration. The final objective is to develop a railgun system that can achieve a 5km/s speed-class repetitive (2Hz) pellet injection. Improvement in the acceleration efficiency showed a pellet velocity of more than 2km/s using augment rails and a ceramic insulator applied to a 1m-long railgun. The other investigation focused on the development of a steady-state solid hydrogen extruder for continuous pellet injection. Screw-driven extruding system has been chosen to extrude the solid hydrogen filament continuously. Theoretical considerations suggest that temperature control of the system is important in future research. (orig.).

  19. RS-20 type repetitive generator with planar configuration of plasma opening switch

    Energy Technology Data Exchange (ETDEWEB)

    Agalakov, V P; Barinov, N U; Belenki, G S [Kurchatov Inst., Moscow (Russian Federation); and others

    1997-12-31

    The existing experience with the production of repetitive rate accelerators with a high peak power (in excess of 10{sup 10} W) and an average power above 50 kW makes it possible to resolve a number of physics and technology tasks which are connected with the reliability and life of the accelerator. The design and results on optimization of a simple plasma opening switch (POS) are discussed. The final design of the POS provided voltages of up to 2 MV and had a life of more than 105 pulses including 4 hours of continuous operation under 4 Hz repetition rate and wall plug power 65 kW. This unit was tested at the RS-20 type accelerator both at the Kurchatov Institute and at the Northwest Institute of Nuclear Technology in China. (author). 5 figs., 1 ref.

  20. Dispersed repetitive sequences in eukaryotic genomes and their possible biological significance

    International Nuclear Information System (INIS)

    Georgiev, G.P.; Kramerov, D.A.; Ryskov, A.P.; Skryabin, K.G.; Lukanidin, E.M.

    1983-01-01

    In this paper is described the properties of a novel mouse mdg-like element, the A2 sequence, which is the most abundant repetitive sequence. We also characterized an ubiquitous B2 sequence that represents, after B1, the dominant family among the short interspersed repeats of the mouse genome. The existence of some putative transposition intermediates was shown for repeats of both A and B types of the mouse genome. These are closed circular DNA of the A type and small polyadenylated B + RNAs. The fundamental question that arises is whether these sequences are simply selfish DNA capable of transpositions or do they fulfill some useful biological functions within the genome. 66 references, 11 figures, 1 table

  1. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Pech, Jiří; Steinhaisl, J.; Macas, Jiří

    2013-01-01

    Roč. 29, č. 6 (2013), s. 792-793 ISSN 1367-4803 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) OC10037 Institutional support: RVO:60077344 Keywords : repetitiveDNA * computational analysis * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.621, year: 2013

  2. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  3. Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.

    Science.gov (United States)

    Rebollo, Rita; Mager, Dixie L

    2016-01-01

    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method used in our laboratory to detect, quantify, and compare mammalian endogenous retrovirus DNA methylation. More specifically we describe methylated DNA immunoprecipitation (MeDIP) followed by quantitative PCR.

  4. Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae

    Directory of Open Access Journals (Sweden)

    Quanwen Dou

    2016-10-01

    Full Text Available Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14, and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28, were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two species imply that the autopolyploid origin of H. brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.

  5. Initiation of the microgene polymerization reaction with non-repetitive homo-duplexes

    International Nuclear Information System (INIS)

    Itsko, Mark; Zaritsky, Arieh; Rabinovitch, Avinoam; Ben-Dov, Eitan

    2008-01-01

    Microgene Polymerization Reaction (MPR) is used as an experimental system to artificially simulate evolution of short, non-repetitive homo-duplex DNA into multiply-repetitive products that can code for functional proteins. Blunt-end ligation by DNA polymerase is crucial in expansion of homo-duplexes (HDs) into head-to-tail multiple repeats in MPR. The propagation mechanism is known, but formation of the initial doublet (ID) by juxtaposing two HDs and polymerization through the gap has been ambiguous. Initiation events with pairs of HDs using Real-Time PCR were more frequent at higher HD concentrations and slightly below the melting temperature. A process molecularity of about 3.1, calculated from the amplification efficiency and the difference in PCR cycles at which propagation was detected at varying HD concentrations, led to a simple mechanism for ID formation: the gap between two HDs is bridged by a third. Considering thermodynamic aspects of the presumed intermediate 'nucleation complex' can predict relative propensity for the process with other HDs

  6. Repetitive transcranial magnetic stimulation in psychiatry

    Directory of Open Access Journals (Sweden)

    Biswa Ranjan Mishra

    2011-01-01

    Full Text Available Repetitive transcranial magnetic stimulation (rTMS is a non-invasive and relatively painless tool that has been used to study various cognitive functions as well as to understand the brain-behavior relationship in normal individuals as well as in those with various neuropsychiatric disorders. It has also been used as a therapeutic tool in various neuropsychiatric disorders because of its ability to specifically modulate distinct brain areas. Studies have shown that repeated stimulation at low frequency produces long-lasting inhibition, which is called as long-term depression, whereas repeated high-frequency stimulation can produce excitation through long-term potentiation. This paper reviews the current status of rTMS as an investigative and therapeutic modality in various neuropsychiatric disorders. It has been used to study the cortical and subcortical functions, neural plasticity and brain mapping in normal individuals and in various neuropsychiatric disorders. rTMS has been most promising in the treatment of depression, with an overall milder adverse effect profile compared with electroconvulsive therapy. In other neuropsychiatric disorders such as schizophrenia, mania, epilepsy and substance abuse, it has been found to be useful, although further studies are required to establish therapeutic efficacy. It appears to be ineffective in the treatment of obsessive compulsive disorder. There is a paucity of studies of efficacy and safety of rTMS in pediatric and geriatric population. Although it appears safe, further research is required to optimize its efficacy and reduce the side-effects. Magnetic seizure therapy, which involves producing seizures akin to electroconvulsive therapy, appears to be of comparable efficacy in the treatment of depression with less cognitive adverse effects.

  7. Repetition-based Interactive Facade Modeling

    KAUST Repository

    AlHalawani, Sawsan

    2012-07-01

    Modeling and reconstruction of urban environments has gained researchers attention throughout the past few years. It spreads in a variety of directions across multiple disciplines such as image processing, computer graphics and computer vision as well as in architecture, geoscience and remote sensing. Having a virtual world of our real cities is very attractive in various directions such as entertainment, engineering, governments among many others. In this thesis, we address the problem of processing a single fa cade image to acquire useful information that can be utilized to manipulate the fa cade and generate variations of fa cade images which can be later used for buildings\\' texturing. Typical fa cade structures exhibit a rectilinear distribution where in windows and other elements are organized in a grid of horizontal and vertical repetitions of similar patterns. In the firt part of this thesis, we propose an efficient algorithm that exploits information obtained from a single image to identify the distribution grid of the dominant elements i.e. windows. This detection method is initially assisted with the user marking the dominant window followed by an automatic process for identifying its repeated instances which are used to define the structure grid. Given the distribution grid, we allow the user to interactively manipulate the fa cade by adding, deleting, resizing or repositioning the windows in order to generate new fa cade structures. Having the utility for the interactive fa cade is very valuable to create fa cade variations and generate new textures for building models. Ultimately, there is a wide range of interesting possibilities of interactions to be explored.

  8. Epithelial topography for repetitive tooth formation

    Directory of Open Access Journals (Sweden)

    Marcia Gaete

    2015-12-01

    Full Text Available During the formation of repetitive ectodermally derived organs such as mammary glands, lateral line and teeth, the tissue primordium iteratively initiates new structures. In the case of successional molar development, new teeth appear sequentially in the posterior region of the jaw from Sox2+ cells in association with the posterior aspect of a pre-existing tooth. The sequence of molar development is well known, however, the epithelial topography involved in the formation of a new tooth is unclear. Here, we have examined the morphology of the molar dental epithelium and its development at different stages in the mouse in vivo and in molar explants. Using regional lineage tracing we show that within the posterior tail of the first molar the primordium for the second and third molar are organized in a row, with the tail remaining in connection with the surface, where a furrow is observed. The morphology and Sox2 expression of the tail retains characteristics reminiscent of the earlier stages of tooth development, such that position along the A-P axes of the tail correlates with different temporal stages. Sox9, a stem/progenitor cell marker in other organs, is expressed mainly in the suprabasal epithelium complementary with Sox2 expression. This Sox2 and Sox9 expressing molar tail contains actively proliferating cells with mitosis following an apico-basal direction. Snail2, a transcription factor implicated in cell migration, is expressed at high levels in the tip of the molar tail while E-cadherin and laminin are decreased. In conclusion, our studies propose a model in which the epithelium of the molar tail can grow by posterior movement of epithelial cells followed by infolding and stratification involving a population of Sox2+/Sox9+ cells.

  9. Understanding communicative actions: a repetitive TMS study.

    Science.gov (United States)

    Stolk, Arjen; Noordzij, Matthijs L; Volman, Inge; Verhagen, Lennart; Overeem, Sebastiaan; van Elswijk, Gijs; Bloem, Bas; Hagoort, Peter; Toni, Ivan

    2014-02-01

    Despite the ambiguity inherent in human communication, people are remarkably efficient in establishing mutual understanding. Studying how people communicate in novel settings provides a window into the mechanisms supporting the human competence to rapidly generate and understand novel shared symbols, a fundamental property of human communication. Previous work indicates that the right posterior superior temporal sulcus (pSTS) is involved when people understand the intended meaning of novel communicative actions. Here, we set out to test whether normal functioning of this cerebral structure is required for understanding novel communicative actions using inhibitory low-frequency repetitive transcranial magnetic stimulation (rTMS). A factorial experimental design contrasted two tightly matched stimulation sites (right pSTS vs left MT+, i.e., a contiguous homotopic task-relevant region) and tasks (a communicative task vs a visual tracking task that used the same sequences of stimuli). Overall task performance was not affected by rTMS, whereas changes in task performance over time were disrupted according to TMS site and task combinations. Namely, rTMS over pSTS led to a diminished ability to improve action understanding on the basis of recent communicative history, while rTMS over MT+ perturbed improvement in visual tracking over trials. These findings qualify the contributions of the right pSTS to human communicative abilities, showing that this region might be necessary for incorporating previous knowledge, accumulated during interactions with a communicative partner, to constrain the inferential process that leads to action understanding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. EVOLUTIONARY RELATIONSHIPS BETWEEN 4 SPECIES OF CLADOPHORA (CLADOPHORALES, CHLOROPHYTA) BASED ON DNA-DNA HYBRIDIZATION

    NARCIS (Netherlands)

    BOT, PVM; BRUSSAARD, CPD; STAM, WT; VANDENHOEK, C

    1991-01-01

    Analysis of the reassociation kinetics of the DNA from Cladophora pellucida (Huds.) Kutz. indicates that the genome of this benthic alga is comprised of approximately 75% repetitive sequences. Single-copy sequences reassociated with a rate constant of 1.8 x 10(-3) M-1.s-1, which corresponds to a

  11. Progress in developing repetitive pulse systems utilizing inductive energy storage

    Energy Technology Data Exchange (ETDEWEB)

    Honig, E.M.

    1983-01-01

    High-power, fast-recovery vacuum switches were used in a new repetitive counterpulse and transfer circuit to deliver a 5-kHz pulse train with a peak power of 75 MW (at 8.6 kA) to a 1-..cap omega.. load, resulting in the first demonstration of fully controlled, high-power, high-repetition-rate operation of an inductive energy-storage and transfer system with nondestructive switches. New circuits, analytical and experimental results, and feasibility of 100-kV repetitive pulse generation are discussed. A new switching concept for railgun loads is presented.

  12. Electrical strength of vacuum gap at repetitive breakdown

    International Nuclear Information System (INIS)

    Dubinin, N.P.; Chistyakov, N.P.

    1983-01-01

    The investigation of repetitive pulse breakdown of vacuum space, which electrodes have been subjected to various treatment in vacuum and inert gas, is carried out. In case of electrode warm-up in vacuum up to 400 deg C as well as electronic heating up to 900 deg C the voltage in case of repetitive breakdown hasncreased approximately twice and in case of a through treatment, which is accomplished by a high-current glow discharge in inert gas, the maximum high voltage in case of the first breakdown at repetitive breakdown has decreased by 30...40%, remaining 2-3 times higher than in the first case

  13. Regulation of rDNA stability by sumoylation

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2009-01-01

    Repair of DNA lesions by homologous recombination relies on the copying of genetic information from an intact homologous sequence. However, many eukaryotic genomes contain repetitive sequences such as the ribosomal gene locus (rDNA), which poses a risk for illegitimate recombination. Therefore, t......6 complex and sumoylation of Rad52, which directs DNA double-strand breaks in the rDNA to relocalize from within the nucleolus to the nucleoplasm before association with the recombination machinery. The relocalization before repair is important for maintaining rDNA stability. The focus...

  14. Neural dynamics during repetitive visual stimulation

    Science.gov (United States)

    Tsoneva, Tsvetomira; Garcia-Molina, Gary; Desain, Peter

    2015-12-01

    Objective. Steady-state visual evoked potentials (SSVEPs), the brain responses to repetitive visual stimulation (RVS), are widely utilized in neuroscience. Their high signal-to-noise ratio and ability to entrain oscillatory brain activity are beneficial for their applications in brain-computer interfaces, investigation of neural processes underlying brain rhythmic activity (steady-state topography) and probing the causal role of brain rhythms in cognition and emotion. This paper aims at analyzing the space and time EEG dynamics in response to RVS at the frequency of stimulation and ongoing rhythms in the delta, theta, alpha, beta, and gamma bands. Approach.We used electroencephalography (EEG) to study the oscillatory brain dynamics during RVS at 10 frequencies in the gamma band (40-60 Hz). We collected an extensive EEG data set from 32 participants and analyzed the RVS evoked and induced responses in the time-frequency domain. Main results. Stable SSVEP over parieto-occipital sites was observed at each of the fundamental frequencies and their harmonics and sub-harmonics. Both the strength and the spatial propagation of the SSVEP response seem sensitive to stimulus frequency. The SSVEP was more localized around the parieto-occipital sites for higher frequencies (>54 Hz) and spread to fronto-central locations for lower frequencies. We observed a strong negative correlation between stimulation frequency and relative power change at that frequency, the first harmonic and the sub-harmonic components over occipital sites. Interestingly, over parietal sites for sub-harmonics a positive correlation of relative power change and stimulation frequency was found. A number of distinct patterns in delta (1-4 Hz), theta (4-8 Hz), alpha (8-12 Hz) and beta (15-30 Hz) bands were also observed. The transient response, from 0 to about 300 ms after stimulation onset, was accompanied by increase in delta and theta power over fronto-central and occipital sites, which returned to baseline

  15. The Effect of Repetition on Tempo Preferences of Elementary Children.

    Science.gov (United States)

    Moskovitz, Elisa M.

    1992-01-01

    Reports on a study of children's preferences between slow and fast tempo classical music excerpts. Finds that students preferred music with a slow tempo. Concludes that repetition had a positive effect on children's preferences. (CFR)

  16. Is perfectionism associated with academic burnout through repetitive negative thinking?

    Science.gov (United States)

    Garratt-Reed, David; Howell, Joel; Hayes, Lana; Boyes, Mark

    2018-01-01

    Academic burnout is prevalent among university students, although understanding of what predicts burnout is limited. This study aimed to test the direct and indirect relationship between two dimensions of perfectionism (Perfectionistic Concerns and Perfectionistic Strivings) and the three elements of Academic Burnout (Exhaustion, Inadequacy, and Cynicism) through Repetitive Negative Thinking. In a cross-sectional survey, undergraduate students ( n  = 126, M age = 23.64, 79% female) completed well-validated measures of Perfectionism, Repetitive Negative Thinking, and Academic Burnout. Perfectionistic Concerns was directly associated with all elements of burnout, as well as indirectly associated with Exhaustion and Cynicism via Repetitive Negative Thinking. Perfectionistic Strivings was directly associated with less Inadequacy and Cynicism; however, there were no indirect associations between Perfectionistic Strivings and Academic Burnout operating through Repetitive Negative Thinking. Repetitive Negative Thinking was also directly related to more burnout Exhaustion and Inadequacy, but not Cynicism. It is concluded that future research should investigate whether interventions targeting Perfectionistic Concerns and Repetitive Negative Thinking can reduce Academic Burnout in university students.

  17. Negative effects of item repetition on source memory.

    Science.gov (United States)

    Kim, Kyungmi; Yi, Do-Joon; Raye, Carol L; Johnson, Marcia K

    2012-08-01

    In the present study, we explored how item repetition affects source memory for new item-feature associations (picture-location or picture-color). We presented line drawings varying numbers of times in Phase 1. In Phase 2, each drawing was presented once with a critical new feature. In Phase 3, we tested memory for the new source feature of each item from Phase 2. Experiments 1 and 2 demonstrated and replicated the negative effects of item repetition on incidental source memory. Prior item repetition also had a negative effect on source memory when different source dimensions were used in Phases 1 and 2 (Experiment 3) and when participants were explicitly instructed to learn source information in Phase 2 (Experiments 4 and 5). Importantly, when the order between Phases 1 and 2 was reversed, such that item repetition occurred after the encoding of critical item-source combinations, item repetition no longer affected source memory (Experiment 6). Overall, our findings did not support predictions based on item predifferentiation, within-dimension source interference, or general interference from multiple traces of an item. Rather, the findings were consistent with the idea that prior item repetition reduces attention to subsequent presentations of the item, decreasing the likelihood that critical item-source associations will be encoded.

  18. Recency, repetition, and the multidimensional basis of recognition memory.

    Science.gov (United States)

    Buchsbaum, Bradley R; Lemire-Rodger, Sabrina; Bondad, Ashley; Chepesiuk, Alexander

    2015-02-25

    Recency and repetition are two factors that have large effects on human memory performance. One way of viewing the beneficial impact of these variables on recognition memory is to assume that both factors modulate a unidimensional memory trace strength. Although previous functional neuroimaging studies have indicated that recency and repetition may modulate similar brain structures, particularly in the region of the inferior parietal cortex, there is extensive behavioral evidence that human subjects can make independent and accurate recognition memory judgments about both an item's recency and its frequency. In the present study, we used fMRI to examine patterns of brain activity during recognition memory for auditory-verbal stimuli that were parametrically and orthogonally manipulated in terms of recency and number of repetitions. We found in a continuous recognition paradigm that the lateral inferior parietal cortex, a region that has previously been associated with recollective forms of memory, is highly sensitive to recency but not repetition. In a multivariate analysis of whole-brain activation patterns, we found orthogonal components that dissociated recency and repetition variables, indicating largely independent neural bases underlying these two factors. The results demonstrate that although both recency and repetition dramatically improve recognition memory performance, the neural bases for this improvement are dissociable, and thus are difficult to explain in terms of access to a unitary memory trace. Copyright © 2015 the authors 0270-6474/15/353544-11$15.00/0.

  19. Properties of water surface discharge at different pulse repetition rates

    International Nuclear Information System (INIS)

    Ruma,; Yoshihara, K.; Hosseini, S. H. R.; Sakugawa, T.; Akiyama, H.; Akiyama, M.; Lukeš, P.

    2014-01-01

    The properties of water surface discharge plasma for variety of pulse repetition rates are investigated. A magnetic pulse compression (MPC) pulsed power modulator able to deliver pulse repetition rates up to 1000 Hz, with 0.5 J per pulse energy output at 25 kV, was used as the pulsed power source. Positive pulse with a point-to-plane electrode configuration was used for the experiments. The concentration and production yield of hydrogen peroxide (H 2 O 2 ) were quantitatively measured and orange II organic dye was treated, to evaluate the chemical properties of the discharge reactor. Experimental results show that the physical and chemical properties of water surface discharge are not influenced by pulse repetition rate, very different from those observed for under water discharge. The production yield of H 2 O 2 and degradation rate per pulse of the dye did not significantly vary at different pulse repetition rates under a constant discharge mode on water surface. In addition, the solution temperature, pH, and conductivity for both water surface and underwater discharge reactors were measured to compare their plasma properties for different pulse repetition rates. The results confirm that surface discharge can be employed at high pulse repetition rates as a reliable and advantageous method for industrial and environmental decontamination applications.

  20. Epigenetic and Transcriptional Modifications in Repetitive Elements in Petrol Station Workers Exposed to Benzene and MTBE

    Directory of Open Access Journals (Sweden)

    Federica Rota

    2018-04-01

    Full Text Available Benzene, a known human carcinogen, and methyl tert-butyl ether (MTBE, not classifiable as to its carcinogenicity, are fuel-related pollutants. This study investigated the effect of these chemicals on epigenetic and transcriptional alterations in DNA repetitive elements. In 89 petrol station workers and 90 non-occupationally exposed subjects the transcriptional activity of retrotransposons (LINE-1, Alu, the methylation on repeated-element DNA, and of H3K9 histone, were investigated in peripheral blood lymphocytes. Median work shift exposure to benzene and MTBE was 59 and 408 µg/m3 in petrol station workers, and 4 and 3.5 µg/m3, in controls. Urinary benzene (BEN-U, S-phenylmercapturic acid, and MTBE were significantly higher in workers than in controls, while trans,trans-muconic acid (tt-MA was comparable between the two groups. Increased BEN-U was associated with increased Alu-Y and Alu-J expression; moreover, increased tt-MA was associated with increased Alu-Y and Alu-J and LINE-1 (L1-5′UTR expression. Among repetitive element methylation, only L1-Pa5 was hypomethylated in petrol station workers compared to controls. While L1-Ta and Alu-YD6 methylation was not associated with benzene exposure, a negative association with urinary MTBE was observed. The methylation status of histone H3K9 was not associated with either benzene or MTBE exposure. Overall, these findings only partially support previous observations linking benzene exposure with global DNA hypomethylation.

  1. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  2. DNA fingerprints come to court

    International Nuclear Information System (INIS)

    Anon.

    1988-01-01

    DNA fingerprinting, a new technique, which produces a visual representation of a person's genome, enables the identification of perpetrators from as little as a single hair root, providing they have left some biologic evidence-hair, skin cells, blood, or semen-at the scene of the crime. DNA fingerprinting was developed by British geneticist Alec Jeffreys, PhD, in 1985. Jeffreys, professor genetics at the University of Leicester, built upon a discovery, five years earlier, of certain hypervariable regions called minisatellites in unexpressed areas of DNA. The hypervariability was evidenced in the number of repetitions of certain sequences of base pairs. It was this aspect that revealed to Jeffreys something that had eluded other investigators. He realized that these minisatellite regions had a potential for identification far greater than that of conventional genetic markers, which are defined by restriction fragment length polymorphisms (RFLPs). RFLPs are characterized by the substitution of one base pair for another, resulting in the presence or absence of a restriction enzyme site. Thus, each offers a limited number of alleles. In contrast, minisatellite regions have an accordion-like range of length, as the number of repetitions of a given sequence varies widely from person to person

  3. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  4. The repetitive portion of the Xenopus IgH Mu switch region mediates orientation-dependent class switch recombination.

    Science.gov (United States)

    Zhang, Zheng Z; Pannunzio, Nicholas R; Lu, Zhengfei; Hsu, Ellen; Yu, Kefei; Lieber, Michael R

    2015-10-01

    Vertebrates developed immunoglobulin heavy chain (IgH) class switch recombination (CSR) to express different IgH constant regions. Most double-strand breaks for Ig CSR occur within the repetitive portion of the switch regions located upstream of each set of constant domain exons for the Igγ, Igα or Igϵ heavy chain. Unlike mammalian switch regions, Xenopus switch regions do not have a high G-density on the non-template DNA strand. In previous studies, when Xenopus Sμ DNA was moved to the genome of mice, it is able to support substantial CSR when it is used to replace the murine Sγ1 region. Here, we tested both the 2kb repetitive portion and the 4.6 kb full-length portions of the Xenopus Sμ in both their natural (forward) orientation relative to the constant domain exons, as well as the opposite (reverse) orientation. Consistent with previous work, we find that the 4.6 kb full-length Sμ mediates similar levels of CSR in both the forward and reverse orientations. Whereas, the forward orientation of the 2kb portion can restore the majority of the CSR level of the 4.6 kb full-length Sμ, the reverse orientation poorly supports R-looping and no CSR. The forward orientation of the 2kb repetitive portion has more GG dinucleotides on the non-template strand than the reverse orientation. The correlation of R-loop formation with CSR efficiency, as demonstrated in the 2kb repetitive fragment of the Xenopus switch region, confirms a role played by R-looping in CSR that appears to be conserved through evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Word and nonword repetition in patients with Schizophrenia

    Directory of Open Access Journals (Sweden)

    Alireza Farnam

    2015-08-01

    Full Text Available Introduction: The assessment of the verbal repetition is important in the study of acquired language disorders and neuropsychology. It is helpful in differential diagnosis of aphasia subtypes, auditory breakdowns, and working memory (WM performance. Though different linguistic disorders have been identified in patients with schizophrenia, very little is known about their verbal repetition ability. Methods: The present study was conducted in the inpatient ward of Razi Psychiatric Hospital, Tabriz University of Medical Sciences, Iran, during the year 2013. Participants were: 30 patients diagnosed with schizophrenia during the maintenance phase of treatment and 30 healthy people as control group. They were asked to repeat 15 words and 15 nonwords immediately. The stimuli were 1, 2, and 3 syllabic in Turkish language. Any incorrect repetition scored 1 and correct repetitions scored 0. Lexicalization errors were compared between groups too. Results: Both groups repeated words better than nonwords. Patients showed lower ability to repeat nonwords than controls, especially in 3 syllabics. There was no significant difference in the repetition of words between groups though it was better in controls. Patients with schizophrenia made more errors in both words and nonwords and lexicalization errors were twice more. Conclusion: Lower ability to repeat nonwords (than words in patients with schizophrenia may show the involvement of phonological loop of WM. More lexicalization errors may take place because of dis-inhibition.

  6. Quantifying repetitive speech in autism spectrum disorders and language impairment.

    Science.gov (United States)

    van Santen, Jan P H; Sproat, Richard W; Hill, Alison Presmanes

    2013-10-01

    We report on an automatic technique for quantifying two types of repetitive speech: repetitions of what the child says him/herself (self-repeats) and of what is uttered by an interlocutor (echolalia). We apply this technique to a sample of 111 children between the ages of four and eight: 42 typically developing children (TD), 19 children with specific language impairment (SLI), 25 children with autism spectrum disorders (ASD) plus language impairment (ALI), and 25 children with ASD with normal, non-impaired language (ALN). The results indicate robust differences in echolalia between the TD and ASD groups as a whole (ALN + ALI), and between TD and ALN children. There were no significant differences between ALI and SLI children for echolalia or self-repetitions. The results confirm previous findings that children with ASD repeat the language of others more than other populations of children. On the other hand, self-repetition does not appear to be significantly more frequent in ASD, nor does it matter whether the child's echolalia occurred within one (immediate) or two turns (near-immediate) of the adult's original utterance. Furthermore, non-significant differences between ALN and SLI, between TD and SLI, and between ALI and TD are suggestive that echolalia may not be specific to ALN or to ASD in general. One important innovation of this work is an objective fully automatic technique for assessing the amount of repetition in a transcript of a child's utterances. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.

  7. Autism and exergaming: effects on repetitive behaviors and cognition

    Directory of Open Access Journals (Sweden)

    Anderson-Hanley C

    2011-09-01

    Full Text Available Cay Anderson-Hanley, Kimberly Tureck, Robyn L Schneiderman Department of Psychology, Union College, Schenectady, NY, USA Abstract: Autism is a neurodevelopmental disorder that leads to impairment in social skills and delay in language development, and results in repetitive behaviors and restricted interests that impede academic and social involvement. Physical exercise has been shown to decrease repetitive behaviors in autistic children and improve cognitive function across the life-span. Exergaming combines physical and mental exercise simultaneously by linking physical activity movements to video game control and may yield better compliance with exercise. In this investigation, two pilot studies explored the potential behavioral and cognitive benefits of exergaming. In Pilot I, twelve children with autism spectrum disorders completed a control task and an acute bout of Dance Dance Revolution (DDR; in Pilot II, ten additional youths completed an acute bout of cyber cycling. Repetitive behaviors and executive function were measured before and after each activity. Repetitive behaviors significantly decreased, while performance on Digits Backwards improved following the exergaming conditions compared with the control condition. Additional research is needed to replicate these findings, and to explore the application of exergaming for the management of behavioral disturbance and to increase cognitive control in children on the autism spectrum. Keywords: autism, repetitive behaviors, exergaming, exercise, executive function

  8. Nanosecond radar system based on repetitive pulsed relativistic BWO

    International Nuclear Information System (INIS)

    Bunkin, B.V.; Gaponov-Grekhov, A.V.; Eltchaninov, A.S.; Zagulov, F.Ya.; Korovin, S.D.; Mesyats, G.A.; Osipov, M.L.; Otlivantchik, E.A.; Petelin, M.I.; Prokhorov, A.M.

    1993-01-01

    The paper presents the results of studies of a nanosecond radar system based on repetitive pulsed relativistic BWO. A pulsed power repetitive accelerator producing electron beams of electron energy 500-700 keV and current 5 kA in pulses of duraction 10 ns with a repetition rate of 100 pps is described. The results of experiments with a high-voltage gas-filled spark gap and a cold-cathode vacuum diode under the conditions of high repetition rates are given. Also presented are the results of studies of a relativistic BWO operating with a wavelength of 3 cm. It is shown that for a high-current beam electron energy of 500-700 keV, the BWO efficiency can reach 35%, the microwave power being 10 9 W. A superconducting solenoid creating a magnetic field of 30 kOe was used for the formation and transportation of the high-current electron beam. In conclusion, the outcome of tests of a nanosecond radar station based on a pulsed power repetitive accelerator and a relativistic BWO is reported

  9. RPERT: Repetitive-Projects Evaluation and Review Technique

    Directory of Open Access Journals (Sweden)

    Remon Fayek Aziz

    2014-03-01

    Full Text Available Estimating expected completion probability of any repetitive construction project with a specified/certain duration including repetitive identical activities by using program evaluation and review technique is the most essential part in construction areas since the activities were had optimistic, most likely and pessimistic durations. This paper focuses on the calculation of expected completion probability of any repetitive construction project within a specified/certain duration (contract duration by using Line Of Balance technique (LOB in case of single or multiple number of crews integrated with Program Evaluation and Review Technique (PERT. Repetitive-Projects Evaluation and Review Technique (RPERT, which is a simplified software, will generate the expected project completion probability of a specified/certain duration (contract duration. RPERT software is designed by java programming code system to provide a number of new and unique capabilities, including: (1 Viewing the expected project completion probability according to a set of specified durations per each identical activity (optimistic time, most likely time, and pessimistic time in the analyzed project; (2 Providing seamless integration with available project time calculations. In order to provide the aforementioned capabilities of RPERT, the system is implemented and developed in four main modules: (1 A user interface module; (2 A database module; (3 A running module; and (4 A processing module. At the end, an illustrative example will be presented to demonstrate and verify the applications of proposed software (RPERT, by using probabilistic calculations for repetitive construction projects.

  10. Development of a recombinant DNA assay system for the detection of genetic change in astronauts' cells

    International Nuclear Information System (INIS)

    Atchley, S.V.; Chen, D.J.C.; Strniste, G.F.; Walters, R.A.; Moyzis, R.K.

    1984-01-01

    We are developing a new recombinant DNA system for the detection and measurement of genetic change in humans caused by exposure to low level ionizing radiation. A unique feature of the method is the use of cloned repetitive DNA probes to assay human DNA for structural changes during or after irradiation. Repetitive sequences exist in different families. Collectively they constitute over 25% of the DNA in a human cell. Repeat families have between 10 and 500,000 members. We have constructed repetitive DNA sequence libraries using recombinant DNA techniques. From these libraries we have isolated and characterized individual repeats comprising 75 to 90% of the mass of human repetitive DNA. Repeats used in our assay system exist in tandem arrays in the genome. Perturbation of these sequences in a cell, followed by detection with a repeat probe, produces a new, multimeric ''ladder'' pattern on an autoradiogram. The repeat probe used in our initial study is complementary to 1% of human DNA. Therefore, the sensitivity of this method is several orders of magnitude better than existing assays. Preliminary evidence from human skin cells exposed to acute, low-dose x-ray treatments indicates that DNA is affected at a dose as low as 5R. The radiation doses used in this system are well within the range of doses received by astronauts during spaceflight missions. Due to its small material requirements, this technique could easily be adapted for use in space. 16 refs., 1 fig

  11. Design, fabricate, and test a 1.06μ repetitively pulsed laser. Final report

    International Nuclear Information System (INIS)

    Eggleston, J.M.; Crawford, E.A.

    1985-01-01

    The results of a program to develop the Thomson scattering diagnostic laser are described. Background material and technical justification for the design approach are given. Principal results of the developmental program were the construction of a rep rated slab glass amplifier, and the accumulation of the design knowledge necessary to build such amplifiers for maximum performance. Significant advances were made in reducing second order optical distortions

  12. Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.

    Science.gov (United States)

    Hribová, Eva; Neumann, Pavel; Matsumoto, Takashi; Roux, Nicolas; Macas, Jirí; Dolezel, Jaroslav

    2010-09-16

    Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement. In this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. 'Calcutta 4') genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones. A low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic

  13. Body-focused repetitive behavior disorders in ICD-11

    Directory of Open Access Journals (Sweden)

    Jon E. Grant

    2014-01-01

    Full Text Available This article addresses the question of how body-focused repetitive behavior disorders (e.g., trichotillomania and skin-picking disorder should be characterized in ICD-11. The article reviews the historical nosology of the two disorders and the current approaches in DSM-5 and ICD-10. Although data are limited and mixed regarding the optimal relationship between body-focused repetitive behavior disorders and nosological categories, these conditions should be included within the obsessive-compulsive and related disorders category, as this is how most clinicians see these behaviors, and as this may optimize clinical utility. The descriptions of these disorders should largely mirror those in DSM-5, given the evidence from recent field surveys. The recommendations regarding ICD-11 and body-focused repetitive behavior disorders should promote the global identification and treatment of these conditions in primary care settings.

  14. Repetitive control of an electrostatic microbridge actuator: theory and simulation

    International Nuclear Information System (INIS)

    Zhao, Haiyu; Rahn, Christopher D

    2010-01-01

    Electrostatic microactuators are used extensively in MEMS sensors, RF switches and microfluidic pumps. The high bandwidth operation required by these applications complicates the implementation of feedback controllers. This paper designs, proves stability and simulates a feedforward repetitive controller for an electrostatic microbridge. High residual stress creates tension in the microbridge that dominates bending stiffness so a pinned string model with uniform electrostatic force loading is used for model-based control. The control objective is to force the microbridge displacement to follow prescribed spatial and periodic time trajectories. Viscous damping ensures boundedness of the distributed transverse displacement in response to bounded inputs. The average displacement is measured by capacitive sensing and processed offline using a repetitive control algorithm that updates a high speed waveform generator's parameters. Simulations show that the performance depends on the amount of damping. With less than 1% damping in a representative microbridge structure, repetitive control reduces the midspan displacement overshoot by 83%

  15. Illusory sensation of movement induced by repetitive transcranial magnetic stimulation

    DEFF Research Database (Denmark)

    Christensen, Mark Schram; Lundbye-Jensen, Jesper; Grey, Michael James

    2010-01-01

    Human movement sense relies on both somatosensory feedback and on knowledge of the motor commands used to produce the movement. We have induced a movement illusion using repetitive transcranial magnetic stimulation over primary motor cortex and dorsal premotor cortex in the absence of limb movement...... and its associated somatosensory feedback. Afferent and efferent neural signalling was abolished in the arm with ischemic nerve block, and in the leg with spinal nerve block. Movement sensation was assessed following trains of high-frequency repetitive transcranial magnetic stimulation applied over...... premotor cortex stimulation was less affected by sensory and motor deprivation than was primary motor cortex stimulation. We propose that repetitive transcranial magnetic stimulation over dorsal premotor cortex produces a corollary discharge that is perceived as movement....

  16. Risk factors for hand-wrist disorders in repetitive work

    DEFF Research Database (Denmark)

    Thomsen, J. F.; Mikkelsen, S.; Andersen, JH

    2007-01-01

    OBJECTIVES: To identify the risk of hand-wrist disorders related to repetitive movements, use of hand force and wrist position in repetitive monotonous work. METHODS: Using questionnaires and physical examinations, the prevalence and incidence of hand-wrist pain and possible extensor tendonitis...... (wrist pain and palpation tenderness) were determined in 3123 employees in 19 industrial settings. With the use of questionnaires and video recordings of homogenous work tasks number of wrist movements, hand force requirements and wrist position were analysed as risk factors for hand-wrist disorders......, controlling for potential personal and psychosocial confounders. All participants were re-examined three times during a follow-up period of three years. RESULTS: Force but not repetition and position was related to hand-wrist pain and possible tendonitis in the baseline analyses showing an exposure...

  17. Comparison of concentric and eccentric bench press repetitions to failure.

    Science.gov (United States)

    Kelly, Stephen B; Brown, Lee E; Hooker, Steven P; Swan, Pamela D; Buman, Matthew P; Alvar, Brent A; Black, Laurie E

    2015-04-01

    Eccentric muscle actions (ECC) are characterized by muscle lengthening, despite actin-myosin crossbridge formation. Muscles acting eccentrically are capable of producing higher levels of force compared with muscles acting concentrically. The purpose of this study was to determine whether ECC bench press yields greater strength than concentric (CON) as determined by 1 repetition maximum (1RM). Additionally, a comparison was made examining differences in the number of repetitions to failure at different relative intensities of 1RM. Thirty healthy men (age = 24.63 ± 5.6 years) were tested for 1RM in CON and ECC bench press and the number of repetitions completed at 60, 70, 80, and 90% 1RM. For CON repetitions, the weight was mechanically lowered to the chest, and the participant pressed it up until the elbows were fully extended. The ECC bench press consisted of lowering a barbell from a fully extended elbow position to the chest in a continuous controlled manner for 3 seconds as determined by electronic metronome. Paired t-tests showed that ECC 1RM (115.99 ± 31.08 kg) was significantly (p ≤ 0.05) greater than CON 1RM (93.56 ± 26.56 kg), and the number of repetitions completed at 90% 1RM was significantly (p ≤ 0.05) greater in ECC (7.67 ± 3.24) as compared with CON (4.57 ± 2.21). There were no significant differences in number of completed repetitions during CON and ECC bench press at 60, 70, and 80% 1RM. These data indicate that ECC actions yield increased force capabilities (∼120%) as compared with CON in the bench press and may be less prone to fatigue, especially at higher intensities. These differences suggest a need to develop unique strategies for training eccentrically.

  18. Repetitive DNAs highlight the role of chromosomal fusions in the karyotype evolution of Dascyllus species (Pomacentridae, Perciformes).

    Science.gov (United States)

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

    2016-04-01

    The Dascyllus genus consists of 11 species spread over vast regions of the Indo-Pacific, showing remarkable reductions in the diploid chromosome numbers (2n). The present study analyzed the karyotypes and other chromosomal characteristics of D. trimaculatus (2n = 48; 2st + 46a; NF = 50), D. carneus (2n = 48; 2st + 46a; NF = 50) and D. aruanus (2n = 30; 18m + 2st + 10a; NF = 50) from the Thailand Gulf (Pacific Ocean) and D. melanurus (2n = 48; 2st + 46a; NF = 50) from the Andaman Sea (Indian Ocean), employing conventional cytogenetic analyses and the chromosomal mapping of repetitive DNAs, using 18S and 5S rDNA, telomeric sequences and (CA)15, (GA)15, and (CAA)10 microsatellites as probes. The C-positive heterochromatin was found in the centromeric regions of most chromosomal pairs and 18S rDNA phenotypes were single in all species. However, in D. aruanus (2n = 30), which harbors nine metacentric pairs; the 5S rDNA sites were located in the centromeric region of the shortest one. The mapping of the telomeric sequences in D. aruanus revealed the presence of interstitial telomeric sites (ITS) in the centromeric region of four metacentric pairs, with one of these pairs also displaying an additional ITS in the long arms. Distinct chromosomal markers confirmed the reduction of the 2n by chromosomal fusions, highlighting the precise characterization of these rearrangements by the cytogenetic mapping of the repetitive DNAs.

  19. Negative effects of item repetition on source memory

    OpenAIRE

    Kim, Kyungmi; Yi, Do-Joon; Raye, Carol L.; Johnson, Marcia K.

    2012-01-01

    In the present study, we explored how item repetition affects source memory for new item–feature associations (picture–location or picture–color). We presented line drawings varying numbers of times in Phase 1. In Phase 2, each drawing was presented once with a critical new feature. In Phase 3, we tested memory for the new source feature of each item from Phase 2. Experiments 1 and 2 demonstrated and replicated the negative effects of item repetition on incidental source memory. Prior item re...

  20. High-repetition-rate short-pulse gas discharge.

    Science.gov (United States)

    Tulip, J; Seguin, H; Mace, P N

    1979-09-01

    A high-average-power short-pulse gas discharge is described. This consists of a volume-preionized transverse discharge of the type used in gas lasers driven by a Blumlein energy storage circuit. The Blumlein circuit is fabricated from coaxial cable, is pulse-charged from a high-repetition-rate Marx-bank generator, and is switched by a high-repetition-rate segmented rail gap. The operation of this discharge under conditions typical of rare-gas halide lasers is described. A maximum of 900 pps was obtained, giving a power flow into the discharge of 30 kW.

  1. Iodine laser of high efficiency and fast repetition rate

    Energy Technology Data Exchange (ETDEWEB)

    Hohla, K; Witte, K J

    1976-07-01

    The scaling laws of an iodine laser of high efficiency and fast repetition rate are reported. The laser is pumped with a new kind of low pressure Hg-UV-lamps which convert 32% of the electrical input in UV-light in the absorption band of the iodine laser and which can be fired up to 100 Hz. Details of a 10 kJ/1 nsec system as dimensions, energy density, repetition rate, flow velocity, gas composition and gas pressure and the overall efficiency are given which is expected to be about 2%.

  2. Dynamics of DNA conformations and DNA-protein interaction

    DEFF Research Database (Denmark)

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...... denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed...... in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent...

  3. [Single-molecule detection and characterization of DNA replication based on DNA origami].

    Science.gov (United States)

    Wang, Qi; Fan, Youjie; Li, Bin

    2014-08-01

    To investigate single-molecule detection and characterization of DNA replication. Single-stranded DNA (ssDNA) as the template of DNA replication was attached to DNA origami by a hybridization reaction based on the complementary base-pairing principle. DNA replication catalyzed by E.coli DNA polymerase I Klenow Fragment (KF) was detected using atomic force microscopy (AFM). The height variations between the ssDNA and the double-stranded DNA (dsDNA), the distribution of KF during DNA replication and biotin-streptavidin (BA) complexes on the DNA strand after replication were detected. Agarose gel electrophoresis was employed to analyze the changes in the DNA after replication. The designed ssDNA could be anchored on the target positions of over 50% of the DNA origami. The KF was capable of binding to the ssDNA fixed on DNA origami and performing its catalytic activities, and was finally dissociated from the DNA after replication. The height of DNA strand increased by about 0.7 nm after replication. The addition of streptavidin also resulted in an DNA height increase to about 4.9 nm due to the formation of BA complexes on the biotinylated dsDNA. The resulting dsDNA and BA complex were subsequently confirmed by agarose gel electrophoresis. The combination of AFM and DNA origami allows detection and characterization of DNA replication at the single molecule level, and this approach provides better insights into the mechanism of DNA polymerase and the factors affecting DNA replication.

  4. Analogous selection processes in declarative and procedural working memory: N-2 list-repetition and task-repetition costs.

    Science.gov (United States)

    Gade, Miriam; Souza, Alessandra S; Druey, Michel D; Oberauer, Klaus

    2017-01-01

    Working memory (WM) holds and manipulates representations for ongoing cognition. Oberauer (Psychology of Learning and Motivation, 51, 45-100, 2009) distinguishes between two analogous WM sub-systems: a declarative WM which handles the objects of thought, and a procedural WM which handles the representations of (cognitive) actions. Here, we assessed whether analogous effects are observed when participants switch between memory sets (declarative representations) and when they switch between task sets (procedural representations). One mechanism assumed to facilitate switching in procedural WM is the inhibition of previously used, but currently irrelevant task sets, as indexed by n-2 task-repetition costs (Mayr & Keele, Journal of Experimental Psychology: General, 129(1), 4-26, 2000). In this study we tested for an analogous effect in declarative WM. We assessed the evidence for n-2 list-repetition costs across eight experiments in which participants switched between memory lists to perform speeded classifications, mental arithmetic, or a local recognition test. N-2 list-repetition costs were obtained consistently in conditions assumed to increase interference between memory lists, and when lists formed chunks in long-term memory. Further analyses across experiments revealed a substantial contribution of episodic memory to n-2 list-repetition costs, thereby questioning the interpretation of n-2 repetition costs as reflecting inhibition. We reanalyzed the data of eight task-switching experiments, and observed that episodic memory also contributes to n-2 task-repetition costs. Taken together, these results show analogous processing principles in declarative and procedural WM, and question the relevance of inhibitory processes for efficient switching between mental sets.

  5. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals

    Directory of Open Access Journals (Sweden)

    Reneker Jeff

    2005-05-01

    Full Text Available Abstract Background Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1. SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches – most of which are irrelevant to the researcher. Results We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the

  6. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  7. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Gurney, Kevin R. [Arizona Univ., Mesa, AZ (United States)

    2015-01-12

    This document constitutes the final report under DOE grant DE-FG-08ER64649. The organization of this document is as follows: first, I will review the original scope of the proposed research. Second, I will present the current draft of a paper nearing submission to Nature Climate Change on the initial results of this funded effort. Finally, I will present the last phase of the research under this grant which has supported a Ph.D. student. To that end, I will present the graduate student’s proposed research, a portion of which is completed and reflected in the paper nearing submission. This final work phase will be completed in the next 12 months. This final workphase will likely result in 1-2 additional publications and we consider the results (as exemplified by the current paper) high quality. The continuing results will acknowledge the funding provided by DOE grant DE-FG-08ER64649.

  8. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    DeTar, Carleton [P.I.

    2012-12-10

    This document constitutes the Final Report for award DE-FC02-06ER41446 as required by the Office of Science. It summarizes accomplishments and provides copies of scientific publications with significant contribution from this award.

  9. Recognition of base J in duplex DNA by J-binding protein

    NARCIS (Netherlands)

    Sabatini, Robert; Meeuwenoord, Nico; van Boom, Jacques H.; Borst, Piet

    2002-01-01

    beta-d-Glucosylhydroxymethyluracil, also called base J, is an unusual modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously found a J-binding

  10. Repetitive Domain-Referenced Testing Using Computers: the TITA System.

    Science.gov (United States)

    Olympia, P. L., Jr.

    The TITA (Totally Interactive Testing and Analysis) System algorithm for the repetitive construction of domain-referenced tests utilizes a compact data bank, is highly portable, is useful in any discipline, requires modest computer hardware, and does not present a security problem. Clusters of related keyphrases, statement phrases, and distractors…

  11. Repetitive endoscopic sinus surgery failure: a role for radical surgery?

    NARCIS (Netherlands)

    Videler, Ward J. M.; Wreesmann, Volkert B.; van der Meulen, Freerk W.; Knegt, Paul P.; Fokkens, Wytske J.

    2006-01-01

    OBJECTIVES: Endoscopic sinus surgery (ESS) is considered to be the golden standard for surgery in patients with chronic rhinosinusitis and nasal polyposis. However, there is still a small group of patients unresponsive despite repetitive surgery. Radical surgery aimed at reduction of the

  12. Nonword Repetition and Language Learning Disorders: A Developmental Contingency Framework

    Science.gov (United States)

    Snowling, Margaret J.

    2006-01-01

    In 1990 Gathercole and Baddeley proposed a strong hypothesis that has generated a wealth of research in the field of language development and disorder. The hypothesis was that phonological memory, as indexed by nonword repetition, is causally related to vocabulary development. Support for the hypothesis came from an impressive range of…

  13. Software-engineering-based model for mitigating Repetitive Strain ...

    African Journals Online (AJOL)

    The incorporation of Information and Communication Technology (ICT) in virtually all facets of human endeavours has fostered the use of computers. This has induced Repetitive Stress Injury (RSI) for continuous and persistent computer users. Proposing a software engineering model capable of enacted RSI force break ...

  14. Intrinsic and Extrinsic Motivation for Stereotypic and Repetitive Behavior

    Science.gov (United States)

    Joosten, Annette V.; Bundy, Anita C.; Einfeld, Stewart L.

    2009-01-01

    This study provides evidence for intrinsic and extrinsic motivators for stereotypical and repetitive behavior in children with autism and intellectual disability and children with intellectual disability alone. We modified the Motivation Assessment Scale (MAS) (1988b); dividing it into intrinsic and extrinsic measures and adding items to assess…

  15. Temporal dynamics of high repetition rate pulsed single longitudinal ...

    Indian Academy of Sciences (India)

    ing (GIG) cavity, single-mode dye laser pumped by high repetition rate ... in a high loss cavity, a detailed theoretical study and optimization of cavity ..... rate for high conversion efficiency and longer pulse width of the single-mode dye laser.

  16. Context-Dependent Repetition Effects on Recognition Memory

    Science.gov (United States)

    Opitz, Bertram

    2010-01-01

    One widely acknowledged way to improve our memory performance is to repeatedly study the to be learned material. One aspect that has received little attention in past research regards the context sensitivity of this repetition effect, that is whether the item is repeated within the same or within different contexts. The predictions of a…

  17. Autism and exergaming: effects on repetitive behaviors and cognition.

    Science.gov (United States)

    Anderson-Hanley, Cay; Tureck, Kimberly; Schneiderman, Robyn L

    2011-01-01

    Autism is a neurodevelopmental disorder that leads to impairment in social skills and delay in language development, and results in repetitive behaviors and restricted interests that impede academic and social involvement. Physical exercise has been shown to decrease repetitive behaviors in autistic children and improve cognitive function across the life-span. Exergaming combines physical and mental exercise simultaneously by linking physical activity movements to video game control and may yield better compliance with exercise. In this investigation, two pilot studies explored the potential behavioral and cognitive benefits of exergaming. In Pilot I, twelve children with autism spectrum disorders completed a control task and an acute bout of Dance Dance Revolution (DDR); in Pilot II, ten additional youths completed an acute bout of cyber cycling. Repetitive behaviors and executive function were measured before and after each activity. Repetitive behaviors significantly decreased, while performance on Digits Backwards improved following the exergaming conditions compared with the control condition. Additional research is needed to replicate these findings, and to explore the application of exergaming for the management of behavioral disturbance and to increase cognitive control in children on the autism spectrum.

  18. Heavy-duty high-repetition-rate generators

    NARCIS (Netherlands)

    Heesch, van E.J.M.; Yan, K.; Pemen, A.J.M.

    2002-01-01

    We present our results on high-power repetitive pulse sources for continuous operation. Two 1-10-kW systems using advanced spark gap technology and a transmission line transformer have been tested for several hundred hours at a 60-MW pulse level. High reliability and above 90% overall efficiency are

  19. Post-exercise cortical depression following repetitive passive finger movement.

    Science.gov (United States)

    Otsuka, Ryohei; Sasaki, Ryoki; Tsuiki, Shota; Kojima, Sho; Onishi, Hideaki

    2017-08-24

    This study aimed to clarify the influence of range of repetitive passive finger movement on corticospinal excitability. Thirteen healthy subjects participated in this study. Passive index finger adduction-abduction movements were performed from 15° abduction to 15° adduction, 15° abduction to 0°, 0° to 15° adduction, and 15° adduction to 30° adduction, each at 15°/s for 10min on separate days. Motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation and M- and F-waves were measured before and after each repetitive passive index finger movement protocol to evaluate changes in corticospinal excitability. MEP amplitude significantly decreased after all passive movements, while F-wave amplitude, F-wave persistence, and M-wave amplitude remained stable. These results suggest that cortical excitability decreases after repetitive passive movement. However, the range of repetitive passive movement does not markedly influence the magnitude of cortical depression. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Use of Repetitive Transcranial Magnetic Stimulation for Treatment in Psychiatry

    NARCIS (Netherlands)

    Aleman, Andre

    The potential of noninvasive neurostimulation by repetitive transcranial magnetic stimulation (rTMS) for improving psychiatric disorders has been studied increasingly over the past two decades. This is especially the case for major depression and for auditory verbal hallucinations in schizophrenia.

  1. Repetitive controller for improving grid-connected photovoltaic systems

    NARCIS (Netherlands)

    Almeida, de P.M.; Duarte, J.L.; Ribeiro, P.F.; Barbosa, P.G.

    2014-01-01

    This study presents the modelling and design steps of a discrete time recursive repetitive controller (RC) to be used in a grid-connected photovoltaic (PV) system. It is shown that the linear synchronous reference frame proportional-integral controller, originally designed to control the converter's

  2. Task type and incidental L2 vocabulary learning: Repetition versus ...

    African Journals Online (AJOL)

    This study investigated the effect of task type on incidental L2 vocabulary learning. The different tasks investigated in this study differed in terms of repetition of encounters and task involvement load. In a within-subjects design, 72 Iranian learners of English practised 18 target words in three exercise conditions: three ...

  3. Exact Repetition as Input Enhancement in Second Language Acquisition.

    Science.gov (United States)

    Jensen, Eva Dam; Vinther, Thora

    2003-01-01

    Reports on two studies on input enhancement used to support learners' selection of focus of attention in Spanish second language listening material. Input consisted of video recordings of dialogues between native speakers. Exact repetition and speech rate reduction were examined for effect on comprehension, acquisition of decoding strategies, and…

  4. Repetition of Attempted Suicide Among Immigrants in Europe

    Science.gov (United States)

    Lipsicas, Cendrine Bursztein; Mäkinen, Ilkka Henrik; Wasserman, Danuta; Apter, Alan; Kerkhof, Ad; Michel, Konrad; Renberg, Ellinor Salander; van Heeringen, Kees; Värnik, Airi; Schmidtke, Armin

    2014-01-01

    Objectives To compare frequencies of suicide attempt repetition in immigrants and local European populations, and the timing of repetition in these groups. Method: Data from 7 European countries, comprising 10 574 local and 3032 immigrant subjects, were taken from the World Health Organization European Multicentre Study on Suicidal Behaviour and the ensuing Monitoring Suicidal Behaviour in Europe (commonly referred to as MONSUE) project. The relation between immigrant status and repetition of suicide attempt within 12-months following first registered attempt was analyzed with binary logistic regression, controlling for sex, age, and method of attempt. Timing of repetition was controlled for sex, age, and the recommended type of aftercare. Results: Lower odds of repeating a suicide attempt were found in Eastern European (OR 0.50; 95% CI 0.41 to 0.61, P Europe stands in contrast to their markedly higher tendency to attempt suicide in general, possibly pointing to situational stress factors related to their suicidal crisis that are less persistent over time. Our findings also raise the possibility that suicide attempters and repeaters constitute only partially overlapping populations. PMID:25565687

  5. Understanding the relationship between repetition priming and mere exposure.

    Science.gov (United States)

    Butler, Laurie T; Berry, Dianne C

    2004-11-01

    Over the last two decades interest in implicit memory, most notably repetition priming, has grown considerably. During the same period, research has also focused on the mere exposure effect. Although the two areas have developed relatively independently, a number of studies has described the mere exposure effect as an example of implicit memory. Tacit in their comparisons is the assumption that the effect is more specifically a demonstration of repetition priming. Having noted that this assumption has attracted relatively little attention, this paper reviews current evidence and shows that it is by no means conclusive. Although some evidence is suggestive of a common underlying mechanism, even a modified repetition priming (perceptual fluency/attribution) framework cannot accommodate all of the differences between the two phenomena. Notwithstanding this, it seems likely that a version of this theoretical framework still offers the best hope of a comprehensive explanation for the mere exposure effect and its relationship to repetition priming. As such, the paper finishes by offering some initial guidance as to ways in which the perceptual fluency/attribution framework might be extended, as well as outlining important areas for future research.

  6. Instruction, Repetition, Discovery: Restoring the Historical Educational Role of Practice

    Science.gov (United States)

    Trninic, Dragan

    2018-01-01

    This conceptual paper considers what it would mean to take seriously Freudenthal's suggestion that mathematics should be taught like swimming. The general claim being made is that "direct instruction" and "discovery" are not opposite but complementary, linked by repetitive yet explorative practice. This claim is elaborated…

  7. Pulsed electron beam generation with fast repetitive double pulse system

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Surender Kumar; Deb, Pankaj; Shyam, Anurag, E-mail: surender80@gmail.com [Energetics and Electromagnetics Division, Bhabha Atomic Research Centre, Visakhapatnam (India); Sharma, Archana [Accelerator and Pulse Power Division, Bhabha Atomic Research Centre, Mumbai (India)

    2014-07-01

    Longer duration high voltage pulse (∼ 100 kV, 260 ns) is generated and reported using helical pulse forming line in compact geometry. The transmission line characteristics of the helical pulse forming line are also used to develop fast repetition double pulse system with very short inter pulse interval. It overcomes the limitations caused due to circuit parameters, power supplies and load characteristics for fast repetitive high voltage pulse generation. The high voltage double pulse of 100 kV, 100 ns with an inter pulse repetition interval of 30 ns is applied across the vacuum field emission diode for pulsed electron beam generation. The electron beam is generated from cathode material by application of negative high voltage (> 100 kV) across the diode by explosive electron emission process. The vacuum field emission diode is made of 40 mm diameter graphite cathode and SS mesh anode. The anode cathode gap was 6 mm and the drift tube diameter was 10 cm. The initial experimental results of pulsed electron beam generation with fast repetitive double pulse system are reported and discussed. (author)

  8. Evidence for the involvement of a nonlexical route in the repetition of familiar words: A comparison of single and dual route models of auditory repetition.

    Science.gov (United States)

    Hanley, J Richard; Dell, Gary S; Kay, Janice; Baron, Rachel

    2004-03-01

    In this paper, we attempt to simulate the picture naming and auditory repetition performance of two patients reported by Hanley, Kay, and Edwards (2002), who were matched for picture naming score but who differed significantly in their ability to repeat familiar words. In Experiment 1, we demonstrate that the model of naming and repetition put forward by Foygel and Dell (2000) is better able to accommodate this pattern of performance than the model put forward by Dell, Schwartz, Martin, Saffran, and Gagnon (1997). Nevertheless, Foygel and Dell's model underpredicted the repetition performance of both patients. In Experiment 2, we attempt to simulate their performance using a new dual route model of repetition in which Foygel and Dell's model is augmented by an additional nonlexical repetition pathway. The new model provided a more accurate fit to the real-word repetition performance of both patients. It is argued that the results provide support for dual route models of auditory repetition.

  9. Narrative Finality

    Directory of Open Access Journals (Sweden)

    Armine Kotin Mortimer

    1981-01-01

    Full Text Available The cloturai device of narration as salvation represents the lack of finality in three novels. In De Beauvoir's Tous les hommes sont mortels an immortal character turns his story to account, but the novel makes a mockery of the historical sense by which men define themselves. In the closing pages of Butor's La Modification , the hero plans to write a book to save himself. Through the thrice-considered portrayal of the Paris-Rome relationship, the ending shows the reader how to bring about closure, but this collective critique written by readers will always be a future book. Simon's La Bataille de Pharsale , the most radical attempt to destroy finality, is an infinite text. No new text can be written. This extreme of perversion guarantees bliss (jouissance . If the ending of De Beauvoir's novel transfers the burden of non-final world onto a new victim, Butor's non-finality lies in the deferral to a future writing, while Simon's writer is stuck in a writing loop, in which writing has become its own end and hence can have no end. The deconstructive and tragic form of contemporary novels proclaims the loss of belief in a finality inherent in the written text, to the profit of writing itself.

  10. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  11. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  12. Active power filter for harmonic compensation using a digital dual-mode-structure repetitive control approach

    DEFF Research Database (Denmark)

    Zou, Zhixiang; Wang, Zheng; Cheng, Ming

    2012-01-01

    This paper presents an digital dual-mode-structure repetitive control approach for the single-phase shunt active power filter (APF), which aims to enhance the tracking ability and eliminate arbitrary order harmonic. The proposed repetitive control scheme blends the characteristics of both odd......-harmonic repetitive control and even-harmonic repetitive control. Moreover, the convergence rate is faster than conventional repetitive controller. Additionally, the parameters have been designed and optimized for the dual-mode structure repetitive control to improve the performance of APF system. Experimental...

  13. solation, characterization and chromosome localization of repetitive DNA sequences in bananas (Musa spp.)

    Czech Academy of Sciences Publication Activity Database

    Valárik, Miroslav; Šimková, Hana; Šafář, Jan; Doleželová, Marie; Doležel, Jaroslav

    2002-01-01

    Roč. 10, - (2002), s. 89-100 ISSN 0967-3849 R&D Projects: GA AV ČR IAA6038204; GA AV ČR IBS5038104 Institutional research plan: CEZ:AV0Z5038910 Keywords : chromosome structure * genome size * in situ hybridization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.828, year: 2002

  14. Meiotic recombination breakpoints are associated with open chromatin and enriched with repetitive DNA elements in potato

    Science.gov (United States)

    Meiotic recombination provides the framework for the genetic variation in natural and artificial populations of eukaryotes through the creation of novel haplotypes. Thus, determining the molecular characteristics of meiotic recombination remains essential for future plant breeding efforts, which hea...

  15. Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes

    Czech Academy of Sciences Publication Activity Database

    Garbus, I.; Romero, J.R.; Valárik, Miroslav; Vanžurová, Hana; Karafiátová, Miroslava; Doležel, Jaroslav; Tranquilli, G.; Helguera, M.; Echenique, V.

    2015-01-01

    Roč. 16, MAY 12 (2015) ISSN 1471-2164 Institutional support: RVO:61389030 Keywords : VIRTUAL GENE ORDER * BAC END SEQUENCES * NEXT-GENERATION Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.867, year: 2015

  16. General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

    Science.gov (United States)

    Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

    2003-01-01

    Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

  17. General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding.

    Science.gov (United States)

    Lucius, Aaron L; Maluf, Nasib K; Fischer, Christopher J; Lohman, Timothy M

    2003-10-01

    Helicase-catalyzed DNA unwinding is often studied using "all or none" assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using "n-step" sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the "kinetic step size", m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using "n-step" sequential mechanisms has previously been limited by an inability to float the number of "unwinding steps", n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, f(ss)(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain f(ss)(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation.

  18. Final Report

    DEFF Research Database (Denmark)

    Heiselberg, Per; Brohus, Henrik; Nielsen, Peter V.

    This final report for the Hybrid Ventilation Centre at Aalborg University describes the activities and research achievement in the project period from August 2001 to August 2006. The report summarises the work performed and the results achieved with reference to articles and reports published...

  19. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE

    Directory of Open Access Journals (Sweden)

    Lavrov Dennis V

    2009-12-01

    Full Text Available Abstract Background The mitochondrial (mt genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

  20. Genesis of multipeaked waves of the esophagus: repetitive contractions or motion artifact?

    Science.gov (United States)

    Sampath, Neha J; Bhargava, Valmik; Mittal, Ravinder K

    2010-06-01

    Multipeaked waves (MPW) in the distal esophagus occur frequently in patients with esophageal spastic motor disorders and diabetes mellitus and are thought to represent repetitive esophageal contractions. We aimed to investigate whether the relative motion between a stationary pressure sensor and contracted peristaltic esophageal segment that moves with respiration leads to the formation of MPW. We mathematically modeled the effect of relative movement between a moving pressure segment and a fixed pressure sensor on the pressure waveform morphology. We conducted retrospective analysis of 100 swallow-induced esophageal contractions in 10 patients, who demonstrated >30% MPW on high-resolution manometry (HRM) during standardized swallows. Finally, using HRM, we determined the effects of suspended breathing and hyperventilation on the waveform morphology in 10 patients prospectively. Modeling revealed that relative movement between a stationary pressure sensor and a moving contracted segment, contraction duration, contraction amplitude, respiratory frequency, and depth of respiration affects the waveform morphology. Retrospective analysis demonstrated a close temporal association with the onset of second and subsequent contractions in MPW with respiratory phase reversals. Numbers of peaks in MPW and respiratory phase reversals were closely related to the duration of contraction. In the prospective study, suspended breathing and hyperventilation resulted in a significant decrease and increase in the MPW frequency as well as the number of peaks within MPW respectively. We conclude that MPW observed during clinical motility studies are not indicative of repetitive esophageal contraction; rather they represent respiration-related movement of the contracted esophageal segment in relation to the stationary pressure sensor.

  1. Fabrication of SLM NiTi Shape Memory Alloy via Repetitive Laser Scanning

    Science.gov (United States)

    Khoo, Zhong Xun; Liu, Yong; Low, Zhi Hong; An, Jia; Chua, Chee Kai; Leong, Kah Fai

    2018-01-01

    Additive manufacturing has the potential to overcome the poor machinability of NiTi shape-memory alloy in fabricating smart structures of complex geometry. In recent years, a number of research activities on selective laser melting (SLM) of NiTi have been carried out to explore the optimal parameters for producing SLM NiTi with the desired phase transformation characteristics and shape-memory properties. Different effects of energy density and processing parameters on the properties of SLM NiTi were reported. In this research, a new approach—repetitive laser scanning—is introduced to meet these objectives as well. The results suggested that the laser absorptivity and heat conductivity of materials before and after the first scan significantly influence the final properties of SLM NiTi. With carefully controlled repetitive scanning process, the fabricated samples have demonstrated shape-memory effect of as high as 5.11% (with an average value of 4.61%) and exhibited comparable transformation characteristics as the NiTi powder used. These results suggest the potential for fabricating complex NiTi structures with similar properties to that of the conventionally produced NiTi parts.

  2. Fabrication of SLM NiTi Shape Memory Alloy via Repetitive Laser Scanning

    Science.gov (United States)

    Khoo, Zhong Xun; Liu, Yong; Low, Zhi Hong; An, Jia; Chua, Chee Kai; Leong, Kah Fai

    2018-03-01

    Additive manufacturing has the potential to overcome the poor machinability of NiTi shape-memory alloy in fabricating smart structures of complex geometry. In recent years, a number of research activities on selective laser melting (SLM) of NiTi have been carried out to explore the optimal parameters for producing SLM NiTi with the desired phase transformation characteristics and shape-memory properties. Different effects of energy density and processing parameters on the properties of SLM NiTi were reported. In this research, a new approach—repetitive laser scanning—is introduced to meet these objectives as well. The results suggested that the laser absorptivity and heat conductivity of materials before and after the first scan significantly influence the final properties of SLM NiTi. With carefully controlled repetitive scanning process, the fabricated samples have demonstrated shape-memory effect of as high as 5.11% (with an average value of 4.61%) and exhibited comparable transformation characteristics as the NiTi powder used. These results suggest the potential for fabricating complex NiTi structures with similar properties to that of the conventionally produced NiTi parts.

  3. Production and processing of siRNA precursor transcripts from the highly repetitive maize genome.

    Directory of Open Access Journals (Sweden)

    Christopher J Hale

    2009-08-01

    Full Text Available Mutations affecting the maintenance of heritable epigenetic states in maize identify multiple RNA-directed DNA methylation (RdDM factors including RMR1, a novel member of a plant-specific clade of Snf2-related proteins. Here we show that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR retrotransposons, the most common repetitive feature in the maize genome. A genetic analysis of DNA transposon repression indicates that RMR1 acts upstream of the RNA-dependent RNA polymerase, RDR2 (MOP1. Surprisingly, we show that non-polyadenylated transcripts from a sampling of LTR retrotransposons are lost in both rmr1 and rdr2 mutants. In contrast, plants deficient for RNA Polymerase IV (Pol IV function show an increase in polyadenylated LTR RNA transcripts. These findings support a model in which Pol IV functions independently of the small RNA accumulation facilitated by RMR1 and RDR2 and support that a loss of Pol IV leads to RNA Polymerase II-based transcription. Additionally, the lack of changes in general genome homeostasis in rmr1 mutants, despite the global loss of 24 nt small RNAs, challenges the perceived roles of siRNAs in maintaining functional heterochromatin in the genomes of outcrossing grass species.

  4. The nitric oxide donor JS-K sensitizes U87 glioma cells to repetitive irradiation.

    Science.gov (United States)

    Heckler, Max; Osterberg, Nadja; Guenzle, Jessica; Thiede-Stan, Nina Kristin; Reichardt, Wilfried; Weidensteiner, Claudia; Saavedra, Joseph E; Weyerbrock, Astrid

    2017-06-01

    As a potent radiosensitizer nitric oxide (NO) may be a putative adjuvant in the treatment of malignant gliomas which are known for their radio- and chemoresistance. The NO donor prodrug JS-K (O2-(2.4-dinitrophenyl) 1-[(4-ethoxycarbonyl) piperazin-1-yl] diazen-1-ium-1,2-diolate) allows cell-type specific intracellular NO release via enzymatic activation by glutathione-S-transferases overexpressed in glioblastoma multiforme. The cytotoxic and radiosensitizing efficacy of JS-K was assessed in U87 glioma cells in vitro focusing on cell proliferation, induction of DNA damage, and cell death. In vivo efficacy of JS-K and repetitive irradiation were investigated in an orthotopic U87 xenograft model in mice. For the first time, we could show that JS-K acts as a potent cytotoxic and radiosensitizing agent in U87 cells in vitro. This dose- and time-dependent effect is due to an enhanced induction of DNA double-strand breaks leading to mitotic catastrophe as the dominant form of cell death. However, this potent cytotoxic and radiosensitizing effect could not be confirmed in an intracranial U87 xenograft model, possibly due to insufficient delivery into the brain. Although NO donor treatment was well tolerated, neither a retardation of tumor growth nor an extended survival could be observed after JS-K and/or radiotherapy.

  5. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  6. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  7. Perseveration and other repetitive verbal behaviors: functional dissociations.

    Science.gov (United States)

    Christman, Sarah S; Boutsen, Frank R; Buckingham, Hugh W

    2004-11-01

    This article will review types of perseveration from a neurolinguistic perspective. During the course of the article, continuous, stuck-in-set, and recurrent perseveration will be placed in contradistinction to several other types of repetitive behaviors commonly associated with neurogenic communication disorders. These include echolalia in mixed transcortical aphasia; conduite d'approche and conduite d'ecart in fluent aphasias; lexical and nonlexical automatisms in nonfluent aphasias; palilalia in neuromotor disorders, such as Parkinson's disease (PD); and sound, syllable, word, and phrase repetitions in neurogenic stuttering. When differentiating these phenomena from perseveration, it is helpful to consider the salient factors that condition observed behaviors in individual patients, such as overall speech fluency, inventory of available utterances, nature of eliciting tasks, and propositionality of responses. Information such as communication disorder diagnosis, underlying etiology, and known sites of lesion from each patient's total clinical profile may also assist with differentiation.

  8. Repetitive motion planning and control of redundant robot manipulators

    CERN Document Server

    Zhang, Yunong

    2013-01-01

    Repetitive Motion Planning and Control of Redundant Robot Manipulators presents four typical motion planning schemes based on optimization techniques, including the fundamental RMP scheme and its extensions. These schemes are unified as quadratic programs (QPs), which are solved by neural networks or numerical algorithms. The RMP schemes are demonstrated effectively by the simulation results based on various robotic models; the experiments applying the fundamental RMP scheme to a physical robot manipulator are also presented. As the schemes and the corresponding solvers presented in the book have solved the non-repetitive motion problems existing in redundant robot manipulators, it is of particular use in applying theoretical research based on the quadratic program for redundant robot manipulators in industrial situations. This book will be a valuable reference work for engineers, researchers, advanced undergraduate and graduate students in robotics fields. Yunong Zhang is a professor at The School of Informa...

  9. Interaction of Repetitively Pulsed High Energy Laser Radiation With Matter

    Science.gov (United States)

    Hugenschmidt, Manfred

    1986-10-01

    The paper is concerned with laser target interaction processes involving new methods of improving the overall energy balance. As expected theoretically, this can be achieved with high repetition rate pulsed lasers even for initially highly reflecting materials, such as metals. Experiments were performed by using a pulsed CO2 laser at mean powers up to 2 kW and repetition rates up to 100 Hz. The rates of temperature rise of aluminium for example were thereby increased by lore than a factor of 3 as compared to cw-radiation of comparable power density. Similar improvements were found for the overall absorptivities that were increased by this method by more than an order of magnitude.

  10. Long-term repetition priming with symmetrical polygons and words.

    Science.gov (United States)

    Kersteen-Tucker, Z

    1991-01-01

    In two different tasks, subjects were asked to make lexical decisions (word or nonword) and symmetry judgments (symmetrical or nonsymmetrical) about two-dimensional polygons. In both tasks, every stimulus was repeated at one of four lags (0, 1, 4, or 8 items interposed between the first and second stimulus presentations). This paradigm, known as repetition priming, revealed comparable short-term priming (Lag 0) and long-term priming (Lags 1, 4, and 8) both for symmetrical polygons and for words. A shorter term component (Lags 0 and 1) of priming was observed for nonwords, and only very short-term priming (Lag 0) was observed for nonsymmetrical polygons. These results indicate that response facilitation accruing from repeated exposure can be observed for stimuli that have no preexisting memory representations and suggest that perceptual factors contribute to repetition-priming effects.

  11. Closed cycle high-repetition-rate pulsed HF laser

    Science.gov (United States)

    Harris, Michael R.; Morris, A. V.; Gorton, Eric K.

    1997-04-01

    The design and performance of a closed cycle high repetition rate HF laser is described. A short pulse, glow discharge is formed in a 10 SF6:1 H2 gas mixture at a total pressure of approximately 110 torr within a 15 by 0.5 by 0.5 cm3 volume. Transverse, recirculated gas flow adequate to enable repetitive operation up to 3 kHz is imposed by a centrifugal fan. The fan also forces the gas through a scrubber cell to eliminate ground state HF from the gas stream. An automated gas make-up system replenishes spent gas removed by the scrubber. Typical mean laser output powers up to 3 W can be maintained for extended periods of operation.

  12. Spared behavioral repetition effects in Alzheimer's disease linked to an altered neural mechanism at posterior cortex.

    Science.gov (United States)

    Broster, Lucas S; Li, Juan; Wagner, Benjamin; Smith, Charles D; Jicha, Gregory A; Schmitt, Frederick A; Munro, Nancy; Haney, Ryan H; Jiang, Yang

    2018-02-20

    Individuals with dementia of the Alzheimer type (AD) classically show disproportionate impairment in measures of working memory, but repetition learning effects are relatively preserved. As AD affects brain regions implicated in both working memory and repetition effects, the neural basis of this discrepancy is poorly understood. We hypothesized that the posterior repetition effect could account for this discrepancy due to the milder effects of AD at visual cortex. Participants with early AD, amnestic mild cognitive impairment (MCI), and healthy controls performed a working memory task with superimposed repetition effects while electroencephalography was collected to identify possible neural mechanisms of preserved repetition effects. Participants with AD showed preserved behavioral repetition effects and a change in the posterior repetition effect. Visual cortex may play a role in maintained repetition effects in persons with early AD.

  13. Characteristics of Partial Discharge and Ozone Generation for Twisted-pair of Enameled Wires under High-repetitive Impulse Voltage Application

    Science.gov (United States)

    Kanazawa, Seiji; Enokizono, Masato; Shibakita, Toshihide; Umehara, Eiji; Toshimitsu, Jun; Ninomiya, Shinji; Taniguchi, Hideki; Abe, Yukari

    In recent years, inverter drive machines such as a hybrid vehicle and an electric vehicle are operated under high voltage pulse with high repetition rate. In this case, inverter surge is generated and affected the machine operation. Especially, the enameled wire of a motor is deteriorated due to the partial discharge (PD) and finally breakdown of the wire will occur. In order to investigate a PD on a resistant enameled wire, characteristics of PD in the twisted pair sample under bipolar repetitive impulse voltages are investigated experimentally. The relationship between the applied voltage and discharge current was measured at PD inception and extinction, and we estimated the repetitive PD inception and extinction voltages experimentally. The corresponding optical emission of the discharge was also observed by using an ICCD camera. Furthermore, ozone concentration due to the discharge was measured during the life-time test of the resistant enameled wires from a working environmental point of view.

  14. High repetition rate burst-mode spark gap

    International Nuclear Information System (INIS)

    Faltens, A.; Reginato, L.; Hester, R.; Chesterman, A.; Cook, E.; Yokota, T.; Dexter, W.

    1978-01-01

    Results are presented on the design and testing of a pressurized gas blown spark gap switch capable of high repetition rates in a burst mode of operation. The switch parameters which have been achieved are as follows: 220-kV, 42-kA, a five pulse burst at 1-kHz, 12-ns risetime, 2-ns jitter at a pulse width of 50-ns

  15. Context-dependent repetition effects on recognition memory.

    OpenAIRE

    Opitz, B

    2010-01-01

    One widely acknowledged way to improve our memory performance is to repeatedly study the to be learned material. One aspect that has received little attention in past research regards the context sensitivity of this repetition effect, that is whether the item is repeated within the same or within different contexts. The predictions of a neuro-computational model (O'Reilly & Norman, 2002) were tested in an experiment requiring participants to study visual objects either once or three times. Cr...

  16. Repetitive nanosecond electron accelerators type URT-1 for radiation technology

    Science.gov (United States)

    Sokovnin, S. Yu.; Balezin, M. E.

    2018-03-01

    The electron accelerator URT-1М-300 for mobile installation was created for radiation disinfecting to correct drawbacks that were found the URT-1M electron accelerator operation (the accelerating voltage up to 1 МV, repetition rate up to 300 pps, electron beam size 400 × 100 mm, the pulse width about 100 ns). Accelerator configuration was changed that allowed to reduce significantly by 20% tank volume with oil where is placed the system of formation high-voltage pulses, thus the average power of the accelerator is increased by 6 times at the expense of increase in pulses repetition rate. Was created the system of the computerized monitoring parameters (output parameters and thermal mode) and remote control of the accelerator (charge voltage, pulse repetition rate), its elements and auxiliary systems (heat of the thyratron, vacuum system), the remote control panel is connected to the installation by the fiber-optical channel, what lightens the work for service personnel. For generating an electron beam up to 400 mm wide there are used metal- ceramic] and metal-dielectric cold cathodes of several emission elements (plates) with a non-uniform distribution of the electron beam current density on the output foil ± 15%. It was found that emission drop of both type of cathodes, during the operation at the high repetition rate (100 pps) is substantial at the beginning of the process, and then proceeds rather slowly that allows for continuous operation up to 40 h. Experiments showed that linear dependence of the voltage and a signal from the pin-diode remains within the range of the charge voltage 45-65 kV. Thus, voltage increases from 690 to 950 kV, and the signal from the pin-diode - from (2,8-4,6)*104 Gy/s. It allows to select electron energy quite precisely with consideration of the radiation technology requirements.

  17. A Repetition Test for Pseudo-Random Number Generators

    OpenAIRE

    Gil, Manuel; Gonnet, Gaston H.; Petersen, Wesley P.

    2017-01-01

    A new statistical test for uniform pseudo-random number generators (PRNGs) is presented. The idea is that a sequence of pseudo-random numbers should have numbers reappear with a certain probability. The expectation time that a repetition occurs provides the metric for the test. For linear congruential generators (LCGs) failure can be shown theoretically. Empirical test results for a number of commonly used PRNGs are reported, showing that some PRNGs considered to have good statistical propert...

  18. Progress toward a microsecond duration, repetitively pulsed, intense- ion beam

    International Nuclear Information System (INIS)

    Davis, H.A.; Olson, J.C.; Reass, W.A.; Coates, D.M.; Hunt, J.W.; Schleinitz, H.M.; Greenly, J.B.

    1996-01-01

    A number of intense ion beams applications are emerging requiring repetitive high-average-power beams. These applications include ablative deposition of thin films, rapid melt and resolidification for surface property enhancement, advanced diagnostic neutral beams for the next generation of Tokamaks, and intense pulsed-neutron sources. We are developing a 200-250 keV, 15 kA, 1 μs duration, 1-30 Hz intense ion beam accelerator to address these applications

  19. Effects of Navigated Repetitive Transcranial Magnetic Stimulation After Stroke.

    Science.gov (United States)

    Chervyakov, Alexander V; Poydasheva, Alexandra G; Lyukmanov, Roman H; Suponeva, Natalia A; Chernikova, Ludmila A; Piradov, Michael A; Ustinova, Ksenia I

    2018-03-01

    The purpose of this study was to test the effects of navigated repetitive transcranial magnetic stimulation, delivered in different modes, on motor impairments and functional limitations after stroke. The study sample included 42 patients (58.5 ± 10.7 years; 26 males) who experienced a single unilateral stroke (1-12 months previously) in the area of the middle cerebral artery. Patients completed a course of conventional rehabilitation, together with 10 sessions of navigated repetitive transcranial magnetic stimulation or sham stimulation. Stimulation was scheduled five times a week over two consecutive weeks in an inpatient clinical setting. Patients were randomly assigned to one of four groups and received sham stimulation (n = 10), low-frequency (1-Hz) stimulation of the nonaffected hemisphere (n = 11), high-frequency (10-Hz) stimulation of the affected hemisphere (n = 13), or sequential combination of low- and high-frequency stimulations (n = 8). Participants were evaluated before and after stimulation with clinical tests, including the arm and hand section of the Fugl-Meyer Assessment Scale, modified Ashworth Scale of Muscle Spasticity, and Barthel Index of Activities of Daily Living. Participants in the three groups receiving navigated repetitive transcranial magnetic stimulation showed improvements in arm and hand functions on the Fugl-Meyer Stroke Assessment Scale. Ashworth Scale of Muscle Spasticity and Barthel Index scores were significantly reduced in groups receiving low- or high-frequency stimulation alone. Including navigated repetitive transcranial magnetic stimulation in a conventional rehabilitation program positively influenced motor and functional recovery in study participants, demonstrating the clinical potential of the method. The results of this study will be used for designing a large-scale clinical trial.

  20. Repetitive display system of line profiles for Doppler broadening measurement

    International Nuclear Information System (INIS)

    Mohri, A.; Narihara, K.; Haba, K.

    1982-10-01

    Line profiles of impurities in visible and ultraviolet regions are repetitively displayed on a CRT with an interval of 250 mu s or 500 mu s, using a system composed of a Czerny-Turner monochromator with 1 m F.L., a self-resonant optical scanner, a photomultiplier shielded against hard X-rays and electronic circuits. The profile resolution is 0.035 nm FWHM. This system can be used in the environment of strong hard X-rays. (author)

  1. Repetitive Observation of Coniferous Samples in ESEM and SEM

    Czech Academy of Sciences Publication Activity Database

    Tihlaříková, Eva; Neděla, Vilém

    2015-01-01

    Roč. 21, S3 (2015), s. 1695-1696 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA14-22777S; GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : SEM * ESEM * biological samples * repetitive observation Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.730, year: 2015

  2. The Influence of Level of Processing on Advertising Repetition Effects.

    OpenAIRE

    Nordhielm, Christie L

    2002-01-01

    This research examines whether or not repetition of features of a stimulus are subject to wear-out effects that have until now only been tested for the stimulus as a whole. When consumers process features in either a shallower or deeper manner, the level of processing performed dictates the effect of repeated feature exposure on their judgments. When repeated exposures to features are processed in a shallower fashion, there is an enhancement in evaluations with no subsequent downturn, whereas...

  3. High repetition rate ultrashort laser cuts a path through fog

    Science.gov (United States)

    de la Cruz, Lorena; Schubert, Elise; Mongin, Denis; Klingebiel, Sandro; Schultze, Marcel; Metzger, Thomas; Michel, Knut; Kasparian, Jérôme; Wolf, Jean-Pierre

    2016-12-01

    We experimentally demonstrate that the transmission of a 1030 nm, 1.3 ps laser beam of 100 mJ energy through fog increases when its repetition rate increases to the kHz range. Due to the efficient energy deposition by the laser filaments in the air, a shockwave ejects the fog droplets from a substantial volume of the beam, at a moderate energy cost. This process opens prospects for applications requiring the transmission of laser beams through fogs and clouds.

  4. High-repetition-rate hydrogen chamber: Preliminary studies

    International Nuclear Information System (INIS)

    1967-01-01

    This report is a conclusion to the tests realised with an experimental bubbles chamber in view to study the possibilities to increase the repetition rate. The more important parameters (the evolution of the bubbles, the expansion system) are considered in a theoretical way. Then the hardware is described. To end, experimental results are compared with the first evaluations. The calculations and the experimentation are against an oscillation system for the expansion. A system with a locking is to he considered. (authors) [fr

  5. The Role of Memory Processes in Repetition Blindness

    Science.gov (United States)

    Johnston, James C.; Hochhaus, Larry; Null, Cynthia H. (Technical Monitor)

    1995-01-01

    We investigated whether Repetition Blindness (RB) in processing RSVP strings depends critically on memory demands. When all items in the sequence had to be reported, strong RB was found. When only the 2 critical items (cued by color) had to be reported, no RB was found. Preliminary results show that imposing a separate memory load, while reporting only the critical items, also produces little RB. Implications for the processing locus of RB will be discussed.

  6. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Stinis, Panos [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-08-07

    This is the final report for the work conducted at the University of Minnesota (during the period 12/01/12-09/18/14) by PI Panos Stinis as part of the "Collaboratory on Mathematics for Mesoscopic Modeling of Materials" (CM4). CM4 is a multi-institution DOE-funded project whose aim is to conduct basic and applied research in the emerging field of mesoscopic modeling of materials.

  7. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  8. A compact, repetitive accelerator for military and industrial applications

    International Nuclear Information System (INIS)

    Zutavern, F.J.; O'Malley, M.W.; Ruebush, M.H.; Rinehart, L.F.; Loubriel, G.M.; Babcock, S.R.; Denison, G.J.

    1998-04-01

    A compact, short pulse, repetitive accelerator has many useful military and commercial applications in biological counter proliferation, materials processing, radiography, and sterilization (medical instruments, waste, and food). The goal of this project was to develop and demonstrate a small, 700 kV accelerator, which can produce 7 kA particle beams with pulse lengths of 10--30 ns at rates up to 50 Hz. At reduced power levels, longer pulses or higher repetition rates (up to 10 kHz) could be achieved. Two switching technologies were tested: (1) spark gaps, which have been used to build low repetition rate accelerators for many years; and (2) high gain photoconductive semiconductor switches (PCSS), a new solid state switching technology. This plan was economical, because it used existing hardware for the accelerator, and the PCSS material and fabrication for one module was relatively inexpensive. It was research oriented, because it provided a test bed to examine the utility of other emerging switching technologies, such as magnetic switches. At full power, the accelerator will produce 700 kV and 7 kA with either the spark gap or PCSS pulser

  9. Sound segregation via embedded repetition is robust to inattention.

    Science.gov (United States)

    Masutomi, Keiko; Barascud, Nicolas; Kashino, Makio; McDermott, Josh H; Chait, Maria

    2016-03-01

    The segregation of sound sources from the mixture of sounds that enters the ear is a core capacity of human hearing, but the extent to which this process is dependent on attention remains unclear. This study investigated the effect of attention on the ability to segregate sounds via repetition. We utilized a dual task design in which stimuli to be segregated were presented along with stimuli for a "decoy" task that required continuous monitoring. The task to assess segregation presented a target sound 10 times in a row, each time concurrent with a different distractor sound. McDermott, Wrobleski, and Oxenham (2011) demonstrated that repetition causes the target sound to be segregated from the distractors. Segregation was queried by asking listeners whether a subsequent probe sound was identical to the target. A control task presented similar stimuli but probed discrimination without engaging segregation processes. We present results from 3 different decoy tasks: a visual multiple object tracking task, a rapid serial visual presentation (RSVP) digit encoding task, and a demanding auditory monitoring task. Load was manipulated by using high- and low-demand versions of each decoy task. The data provide converging evidence of a small effect of attention that is nonspecific, in that it affected the segregation and control tasks to a similar extent. In all cases, segregation performance remained high despite the presence of a concurrent, objectively demanding decoy task. The results suggest that repetition-based segregation is robust to inattention. (c) 2016 APA, all rights reserved).

  10. Repetitive, small-bore two-stage light gas gun

    International Nuclear Information System (INIS)

    Combs, S.K.; Foust, C.R.; Fehling, D.T.; Gouge, M.J.; Milora, S.L.

    1991-01-01

    A repetitive two-stage light gas gun for high-speed pellet injection has been developed at Oak Ridge National Laboratory. In general, applications of the two-stage light gas gun have been limited to only single shots, with a finite time (at least minutes) needed for recovery and preparation for the next shot. The new device overcomes problems associated with repetitive operation, including rapidly evacuating the propellant gases, reloading the gun breech with a new projectile, returning the piston to its initial position, and refilling the first- and second-stage gas volumes to the appropriate pressure levels. In addition, some components are subjected to and must survive severe operating conditions, which include rapid cycling to high pressures and temperatures (up to thousands of bars and thousands of kelvins) and significant mechanical shocks. Small plastic projectiles (4-mm nominal size) and helium gas have been used in the prototype device, which was equipped with a 1-m-long pump tube and a 1-m-long gun barrel, to demonstrate repetitive operation (up to 1 Hz) at relatively high pellet velocities (up to 3000 m/s). The equipment is described, and experimental results are presented. 124 refs., 6 figs., 5 tabs

  11. Pericentric satellite DNA sequences in Pipistrellus pipistrellus (Vespertilionidae; Chiroptera).

    Science.gov (United States)

    Barragán, M J L; Martínez, S; Marchal, J A; Fernández, R; Bullejos, M; Díaz de la Guardia, R; Sánchez, A

    2003-09-01

    This paper reports the molecular and cytogenetic characterization of a HindIII family of satellite DNA in the bat species Pipistrellus pipistrellus. This satellite is organized in tandem repeats of 418 bp monomer units, and represents approximately 3% of the whole genome. The consensus sequence from five cloned monomer units has an A-T content of 62.20%. We have found differences in the ladder pattern of bands between two populations of the same species. These differences are probably because of the absence of the target sites for the HindIII enzyme in most monomer units of one population, but not in the other. Fluorescent in situ hybridization (FISH) localized the satellite DNA in the pericentromeric regions of all autosomes and the X chromosome, but it was absent from the Y chromosome. Digestion of genomic DNAs with HpaII and its isoschizomer MspI demonstrated that these repetitive DNA sequences are not methylated. Other bat species were tested for the presence of this repetitive DNA. It was absent in five Vespertilionidae and one Rhinolophidae species, indicating that it could be a species/genus specific, repetitive DNA family.

  12. LET-effects in DNA

    International Nuclear Information System (INIS)

    Kraft, G.; Taucher-Scholz, G.; Heilmann, J.

    1994-11-01

    In this contribution, an introductory view on the physical properties of ions is given and the cellular response to high LET radiation is summarized. Then the measurements of strand break induction of DNA in solution and in intracellular DNA are reported and compared to cell survival. The possibility of changes in the quality of the lesions is discussed and finally the present status of model calculations in comparison to the experiments is given. (orig./HSI)

  13. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition

    NARCIS (Netherlands)

    Westra, E.R.; Semenova, E.; Datsenko, K.A.; Jackson, R.N.; Wiedenheft, B.; Severinov, K.; Brouns, S.J.J.

    2013-01-01

    Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat), into which invader DNA fragments are incorporated. CRISPR transcripts

  14. Inverted U-shaped model: How frequent repetition affects perceived risk

    OpenAIRE

    Xi Lu; Xiaofei Xie; Lu Liu

    2015-01-01

    We asked how repeated media reports on technological hazards influence an individual's risk perception. We looked for two contradictory effects, an increasing effect of repetition on perceived risk with the first few repetitions and a decreasing effect with later repetitions, leading to the inverted U-shaped pattern. In an experiment, we demonstrated the inverted U-shaped relationship between the repetition and perceived risk in the context of food risk. The finding broaden...

  15. Repetitive Treatment with Diluted Bee Venom Attenuates the Induction of Below-Level Neuropathic Pain Behaviors in a Rat Spinal Cord Injury Model.

    Science.gov (United States)

    Kang, Suk-Yun; Roh, Dae-Hyun; Choi, Jung-Wan; Ryu, Yeonhee; Lee, Jang-Hern

    2015-07-10

    The administration of diluted bee venom (DBV) into an acupuncture point has been utilized traditionally in Eastern medicine to treat chronic pain. We demonstrated previously that DBV has a potent anti-nociceptive efficacy in several rodent pain models. The present study was designed to examine the potential anti-nociceptive effect of repetitive DBV treatment in the development of below-level neuropathic pain in spinal cord injury (SCI) rats. DBV was applied into the Joksamli acupoint during the induction and maintenance phase following thoracic 13 (T13) spinal hemisection. We examined the effect of repetitive DBV stimulation on SCI-induced bilateral pain behaviors, glia expression and motor function recovery. Repetitive DBV stimulation during the induction period, but not the maintenance, suppressed pain behavior in the ipsilateral hind paw. Moreover, SCI-induced increase in spinal glia expression was also suppressed by repetitive DBV treatment in the ipsilateral dorsal spinal cord. Finally, DBV injection facilitated motor function recovery as indicated by the Basso-Beattie-Bresnahan rating score. These results indicate that the repetitive application of DBV during the induction phase not only decreased neuropathic pain behavior and glia expression, but also enhanced locomotor functional recovery after SCI. This study suggests that DBV acupuncture can be a potential clinical therapy for SCI management.

  16. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  17. Three-dimensional rail cooling analysis for a repetitively fired railgun

    International Nuclear Information System (INIS)

    Liu, H.P.

    1991-01-01

    This paper reports on a three-dimensional (3-D) rail cooling analysis for fabrication and demonstration of a stand-alone repetitive fire compulsator driven 9 MJ gun system which has been performed to assure the entire rail can be maintained below its thermal limit for multiple shots. The 3-D rail thermal model can predict the temperature, pressure, and convective heat transfer coefficient variations of the coolant along the 10 m long copper rail. The 9-MJ projectiles will be fired every 20 s for 3 min. Water cooling was used in the model for its high cooling capacity. Single liquid phase heat transfer was assumed in the cooling analysis. For multiple shots, the temperature difference between the rail and the water was enhanced due to accumulated heat in the rail. As a result, the heat removal by water increased from shot-to-shot. The rail temperature initially increased and finally stabilized after a number of shots

  18. Don't Throw out the Baby with the Bathwater: Verbal Repetition, Mnemonics, and Active Learning

    Science.gov (United States)

    Saber, Jane Lee; Johnson, Richard D.

    2008-01-01

    The effectiveness of using verbal repetition and first-letter acronyms to teach a common marketing framework was examined in two experiments. In Experiment 1, 345 undergraduate students were exposed to the framework using one of four conditions: control, verbal repetition, acronym, and verbal repetition plus acronym in a traditional learning…

  19. Repetition suppression and multi-voxel pattern similarity differentially track implicit and explicit visual memory.

    Science.gov (United States)

    Ward, Emily J; Chun, Marvin M; Kuhl, Brice A

    2013-09-11

    Repeated exposure to a visual stimulus is associated with corresponding reductions in neural activity, particularly within visual cortical areas. It has been argued that this phenomenon of repetition suppression is related to increases in processing fluency or implicit memory. However, repetition of a visual stimulus can also be considered in terms of the similarity of the pattern of neural activity elicited at each exposure--a measure that has recently been linked to explicit memory. Despite the popularity of each of these measures, direct comparisons between the two have been limited, and the extent to which they differentially (or similarly) relate to behavioral measures of memory has not been clearly established. In the present study, we compared repetition suppression and pattern similarity as predictors of both implicit and explicit memory. Using functional magnetic resonance imaging, we scanned 20 participants while they viewed and categorized repeated presentations of scenes. Repetition priming (facilitated categorization across repetitions) was used as a measure of implicit memory, and subsequent scene recognition was used as a measure of explicit memory. We found that repetition priming was predicted by repetition suppression in prefrontal, parietal, and occipitotemporal regions; however, repetition priming was not predicted by pattern similarity. In contrast, subsequent explicit memory was predicted by pattern similarity (across repetitions) in some of the same occipitotemporal regions that exhibited a relationship between priming and repetition suppression; however, explicit memory was not related to repetition suppression. This striking double dissociation indicates that repetition suppression and pattern similarity differentially track implicit and explicit learning.

  20. The effect of event repetition on the production of story grammar in children's event narratives.

    Science.gov (United States)

    Feltis, Brooke B; Powell, Martine B; Roberts, Kim P

    2011-03-01

    This study examined the effect of event repetition on the amount and nature of story-grammar produced by children when recalling the event. Children aged 4 years (N=50) and 7 years (N=56) participated in either 1 or 6 occurrences of a highly similar event where details varied across the occurrences. Half the children in each age and event group recalled the last/single occurrence 5-6 days later and the other half recalled the last/single occurrence after 5-6 weeks (the final and single occurrence was the same). Children's free recall responses were classified according to the number and proportion of story-grammar elements (Stein & Glenn, 1979-setting, initiating event, internal response, plan, attempt, direct consequence, and resolution) as well as the prevalence of causal links between the individual story-grammar elements. More story-grammar detail and more links between individual story-grammar elements were reported about the final compared to single occurrence. The amount of story-grammar increased with age and decreased over time. Further, an interaction was revealed such that the effect of retention interval on the production of story-grammar was negligible for older children who experienced the repeated event. Event repetition has a beneficial effect on the production of children's story-grammar content in situations where event details varied from occasion to occasion. This study highlights the importance of eliciting free recall when conducting evidential interviews with child witnesses about repeated events. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Repetition suppression and repetition enhancement underlie auditory memory-trace formation in the human brain: an MEG study.

    Science.gov (United States)

    Recasens, Marc; Leung, Sumie; Grimm, Sabine; Nowak, Rafal; Escera, Carles

    2015-03-01

    The formation of echoic memory traces has traditionally been inferred from the enhanced responses to its deviations. The mismatch negativity (MMN), an auditory event-related potential (ERP) elicited between 100 and 250ms after sound deviation is an indirect index of regularity encoding that reflects a memory-based comparison process. Recently, repetition positivity (RP) has been described as a candidate ERP correlate of direct memory trace formation. RP consists of repetition suppression and enhancement effects occurring in different auditory components between 50 and 250ms after sound onset. However, the neuronal generators engaged in the encoding of repeated stimulus features have received little interest. This study intends to investigate the neuronal sources underlying the formation and strengthening of new memory traces by employing a roving-standard paradigm, where trains of different frequencies and different lengths are presented randomly. Source generators of repetition enhanced (RE) and suppressed (RS) activity were modeled using magnetoencephalography (MEG) in healthy subjects. Our results show that, in line with RP findings, N1m (~95-150ms) activity is suppressed with stimulus repetition. In addition, we observed the emergence of a sustained field (~230-270ms) that showed RE. Source analysis revealed neuronal generators of RS and RE located in both auditory and non-auditory areas, like the medial parietal cortex and frontal areas. The different timing and location of neural generators involved in RS and RE points to the existence of functionally separated mechanisms devoted to acoustic memory-trace formation in different auditory processing stages of the human brain. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  3. The development of interactive multimedia based on auditory, intellectually, repetition in repetition algorithm learning to increase learning outcome

    Science.gov (United States)

    Munir; Sutarno, H.; Aisyah, N. S.

    2018-05-01

    This research aims to find out how the development of interactive multimedia based on auditory, intellectually, and repetition can improve student learning outcomes. This interactive multimedia is developed through 5 stages. Analysis stages include the study of literature, questionnaire, interviews and observations. The design phase is done by the database design, flowchart, storyboards and repetition algorithm material while the development phase is done by the creation of web-based framework. Presentation material is adapted to the model of learning such as auditory, intellectually, repetition. Auditory points are obtained by recording the narrative material that presented by a variety of intellectual points. Multimedia as a product is validated by material and media experts. Implementation phase conducted on grade XI-TKJ2 SMKN 1 Garut. Based on index’s gain, an increasing of student learning outcomes in this study is 0.46 which is fair due to interest of student in using interactive multimedia. While the multimedia assessment earned 84.36% which is categorized as very well.

  4. Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences

    Czech Academy of Sciences Publication Activity Database

    Matyášek, Roman; Fulneček, Jaroslav; Kovařík, Aleš

    2013-01-01

    Roč. 34, č. 17 (2013), s. 2511-2521 ISSN 0173-0835 R&D Projects: GA ČR(CZ) GA206/09/1751; GA ČR(CZ) GAP501/10/0208; GA ČR(CZ) GA13-10057S Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : HIGHLY REPETITIVE DNA * DOUBLE-HELICAL DNA * CURVED DNA Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 3.161, year: 2013

  5. Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

    Science.gov (United States)

    Freeman, S.; Pham, M.; Rodriguez, R.J.

    1993-01-01

    Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

  6. DNA Self-Assembly: From Chirality to Evolution

    Directory of Open Access Journals (Sweden)

    Youri Timsit

    2013-04-01

    Full Text Available Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are tightly packed into stable right-handed crossovers. Simple packing rules that are imposed by DNA geometry and sequence dictate the overall architecture of higher order DNA structures. Close DNA-DNA interactions also provide the missing link between local interactions and DNA topology, thus explaining how type II DNA topoisomerases may sense locally the global topology. Finally this paper proposes that through its influence on DNA self-assembled structures, DNA chirality played a critical role during the early steps of evolution.

  7. Ultrafast, high repetition rate, ultraviolet, fiber-laser-based source: application towards Yb+ fast quantum-logic.

    Science.gov (United States)

    Hussain, Mahmood Irtiza; Petrasiunas, Matthew Joseph; Bentley, Christopher D B; Taylor, Richard L; Carvalho, André R R; Hope, Joseph J; Streed, Erik W; Lobino, Mirko; Kielpinski, David

    2016-07-25

    Trapped ions are one of the most promising approaches for the realization of a universal quantum computer. Faster quantum logic gates could dramatically improve the performance of trapped-ion quantum computers, and require the development of suitable high repetition rate pulsed lasers. Here we report on a robust frequency upconverted fiber laser based source, able to deliver 2.5 ps ultraviolet (UV) pulses at a stabilized repetition rate of 300.00000 MHz with an average power of 190 mW. The laser wavelength is resonant with the strong transition in Ytterbium (Yb+) at 369.53 nm and its repetition rate can be scaled up using high harmonic mode locking. We show that our source can produce arbitrary pulse patterns using a programmable pulse pattern generator and fast modulating components. Finally, simulations demonstrate that our laser is capable of performing resonant, temperature-insensitive, two-qubit quantum logic gates on trapped Yb+ ions faster than the trap period and with fidelity above 99%.

  8. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Jarillo-Herrero, Pablo [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2017-02-07

    This is the final report of our research program on electronic transport experiments on Topological Insulator (TI) devices, funded by the DOE Office of Basic Energy Sciences. TI-based electronic devices are attractive as platforms for spintronic applications, and for detection of emergent properties such as Majorana excitations , electron-hole condensates , and the topological magneto-electric effect . Most theoretical proposals envision geometries consisting of a planar TI device integrated with materials of distinctly different physical phases (such as ferromagnets and superconductors). Experimental realization of physics tied to the surface states is a challenge due to the ubiquitous presence of bulk carriers in most TI compounds as well as degradation during device fabrication.

  9. Understanding work related musculoskeletal pain: does repetitive work cause stress symptoms?

    DEFF Research Database (Denmark)

    Bonde, J. P.; Mikkelsen, S.; Andersen, JH

    2005-01-01

    for development of regional pain in repetitive work, stress symptoms would likely be on the causal path. AIMS: To examine whether objective measures of repetitive monotonous work are related to occurrence and development of stress symptoms. METHODS: In 1994-95, 2033 unskilled workers with continuous repetitive...... Profile Inventory. RESULTS: Repetitive work, task cycle time, and quantified measures of repetitive upper extremity movements including force requirements were not related to occurrence of stress symptoms at baseline or development of stress symptoms during three years of follow up. CONCLUSIONS......: The findings do not indicate that repetitive work is associated with stress symptoms, but small effects cannot be ruled out. Thus the results question the importance of mental stress mechanisms in the causation of regional pain related to repetitive work. However, the findings should be interpreted...

  10. A characterization of linearly repetitive cut and project sets

    Science.gov (United States)

    Haynes, Alan; Koivusalo, Henna; Walton, James

    2018-02-01

    For the development of a mathematical theory which can be used to rigorously investigate physical properties of quasicrystals, it is necessary to understand regularity of patterns in special classes of aperiodic point sets in Euclidean space. In one dimension, prototypical mathematical models for quasicrystals are provided by Sturmian sequences and by point sets generated by substitution rules. Regularity properties of such sets are well understood, thanks mostly to well known results by Morse and Hedlund, and physicists have used this understanding to study one dimensional random Schrödinger operators and lattice gas models. A key fact which plays an important role in these problems is the existence of a subadditive ergodic theorem, which is guaranteed when the corresponding point set is linearly repetitive. In this paper we extend the one-dimensional model to cut and project sets, which generalize Sturmian sequences in higher dimensions, and which are frequently used in mathematical and physical literature as models for higher dimensional quasicrystals. By using a combination of algebraic, geometric, and dynamical techniques, together with input from higher dimensional Diophantine approximation, we give a complete characterization of all linearly repetitive cut and project sets with cubical windows. We also prove that these are precisely the collection of such sets which satisfy subadditive ergodic theorems. The results are explicit enough to allow us to apply them to known classical models, and to construct linearly repetitive cut and project sets in all pairs of dimensions and codimensions in which they exist. Research supported by EPSRC grants EP/L001462, EP/J00149X, EP/M023540. HK also gratefully acknowledges the support of the Osk. Huttunen foundation.

  11. Relationship to carcinogenesis of repetitive low-dose radiation exposure

    International Nuclear Information System (INIS)

    Ootsuyama, Akira

    2016-01-01

    We studied the carcinogenic effects caused by repetitive irradiation at a low dose, which has received attention in recent years, and examined the experimental methods used to evaluate radiation-induced carcinogenesis. For this experiment, we selected a mouse with as few autochthonous cancers as possible. Skin cancer was selected as the target for analysis, because it is a rare cancer in mice. Beta-rays were selected as the radiation source. The advantage of using beta-rays is weaker penetration power into tissues, thus protecting organs, such as the digestive and hematogenous organs. The benefit of our experimental method is that only skin cancer requires monitoring, and it is possible to perform long-term experiments. The back skin of mice was exposed repetitively to beta-rays three times a week until the occurrence of cancer or death, and the dose per exposure ranged from 0.5 to 11.8 Gy. With the high-dose range (2.5-11.8 Gy), the latency period and carcinogenic rate were almost the same in each experimental group. When the dose was reduced to 1-1.5 Gy, the latency period increased, but the carcinogenic rate remained. When the dose was further reduced to 0.5 Gy, skin cancer never happened, even though we continued irradiation until death of the last mouse in this group. The lifespan of 0.5 Gy group mice was the same as that of the controls. We showed that the 0.5 Gy dose did not cause cancer, even in mice exposed repetitively throughout their life span, and thus refer to 0.5 Gy as the threshold-like dose. (author)

  12. Robustification and Optimization in Repetitive Control For Minimum Phase and Non-Minimum Phase Systems

    Science.gov (United States)

    Prasitmeeboon, Pitcha

    repetitive control FIR compensator. The aim is to reduce the final error level by using real time frequency response model updates to successively increase the cutoff frequency, each time creating the improved model needed to produce convergence zero error up to the higher cutoff. Non-minimum phase systems present a difficult design challenge to the sister field of Iterative Learning Control. The third topic investigates to what extent the same challenges appear in RC. One challenge is that the intrinsic non-minimum phase zero mapped from continuous time is close to the pole of repetitive controller at +1 creating behavior similar to pole-zero cancellation. The near pole-zero cancellation causes slow learning at DC and low frequencies. The Min-Max cost function over the learning rate is presented. The Min-Max can be reformulated as a Quadratically Constrained Linear Programming problem. This approach is shown to be an RC design approach that addresses the main challenge of non-minimum phase systems to have a reasonable learning rate at DC. Although it was illustrated that using the Min-Max objective improves learning at DC and low frequencies compared to other designs, the method requires model accuracy at high frequencies. In the real world, models usually have error at high frequencies. The fourth topic addresses how one can merge the quadratic penalty to the Min-Max cost function to increase robustness at high frequencies. The topic also considers limiting the Min-Max optimization to some frequencies interval and applying an FIR zero-phase low-pass filter to cutoff the learning for frequencies above that interval.

  13. Additional biological therapies for attention-deficit hyperactivity disorder: repetitive transcranical magnetic stimulation of 1 Hz helps to reduce methylphenidate

    Directory of Open Access Journals (Sweden)

    Helmut Niederhofer

    2011-12-01

    Full Text Available Excessive hyperactivity, impulsiveness and attentional difficulties characterize attentiondeficit hyperactivity disorder (ADHD. The aim of this case report is to signal the possible therapeutic effectiveness of the repetitive transcranial magnetic stimulation (rTMS. Low frequency (1Hz, 1200 stim/die for five days was applied on the impending scalp in the motor additional area of a patient suffering from combined type ADHD who received methylphenidate (MPH. We saw a significant improvement, especially according to criteria associated with hyperactivity. The improvement lasted for at least three weeks and suggested the final reduction in dosage of MPH.to 10 mg.

  14. High-repetition intra-cavity source of Compton radiation

    International Nuclear Information System (INIS)

    Pogorelsky, I; Polyanskiy, M; Agustsson, R; Campese, T; Murokh, A; Ovodenko, A; Shaftan, T

    2014-01-01

    We report our progress in developing a high-power Compton source for a diversity of applications ranging from university-scale compact x-ray light sources and metrology tools for EUV lithography, to high-brilliance gamma-sources for nuclear analysis. Our conceptual approach lies in multiplying the source’s repetition rate and increasing its average brightness by placing the Compton interaction point inside the optical cavity of an active laser. We discuss considerations in its design, our simulations, and tests of the laser’s cavity that confirm the feasibility of the proposed concept. (paper)

  15. Repetitive Transcranial Magnetic Stimulation in Patients with Hereditary Spastic Paraplegia

    Directory of Open Access Journals (Sweden)

    Mehmet Ağırman

    2011-06-01

    Full Text Available Hereditary spastic paraplegia (HSPP is a heterogeneous genetic disease characterized by progressive spasticity of lower extremities. Spasticity is a major cause of long-term disability in HSPP and significantly affects the functional life of patients. Repetitive transcranial magnetic stimulation (rTMS is widely used in diagnosis and treatment of many neurological and psychiatric diseases. Although the positive impacts of rTMS for spasticity have been reported, no study has been found on HSPP. We present two HSPP patients treated with low frequency rTMS (20 minutes at a frequency of 1 Hz (1200 pulses, for a period of 10 treatment sessions.

  16. Repetitive Transcranial Magnetic Stimulation in Patients with Hereditary Spastic Paraplegia

    Directory of Open Access Journals (Sweden)

    Mehmet Ağırman

    2011-06-01

    Full Text Available Hereditary spastic paraplegia (HSPP is a heterogeneous genetic disease characterized by progressive spasticity of lower extremities. Spasticity is a major cause of long-term disability in HSPP and significantly affects the functional life of patients. Repetitive transcranial magnetic stimulation (rTMS is widely used in diagnosis and treatment of many neurological and psychiatric diseases. Although the positive impacts of rTMS for spasticity have been reported, no study has been found on HSPP. We present two HSPP patients treated with low frequency rTMS (20 minutes at a frequency of 1 Hz (1200 pulses, for a period of 10 treatment sessions

  17. About the Infinite Repetition of Histories in Space

    Directory of Open Access Journals (Sweden)

    Manuel Alfonseca

    2014-08-01

    Full Text Available This paper analyzes two different proposals, one by Ellis and Brundrit, based on classical relativistic cosmology, the other by Garriga and Vilenkin, based on the DH interpretation of quantum mechanics, both concluding that, in an infinite universe, planets and beings must be repeated an infinite number of times. We point to possible shortcomings in these arguments. We conclude that the idea of an infinite repetition of histories in space cannot be considered strictly speaking a consequence of current physics and cosmology. Such ideas should be seen rather as examples of «ironic science» in the terminology of John Horgan.

  18. ARCA II - a new apparatus for fast, repetitive HPLC separations

    International Nuclear Information System (INIS)

    Schaedel, M.; Bruechle, W.; Jaeger, E.; Schimpf, E.; Kratz, J.V.; Scherer, U.W.; Zimmermann, H.P.

    1989-04-01

    The microcomputer controlled Automated Rapid Chemistry Apparatus, ARCA, is described in its newly designed version for the study of chemical properties of element 105 in aqueous solutions. This improved version, ARCA II, is adapted to the needs of fast and repetitive separations to be carried out in a chemically inert automated micro high performance liquid chromatography system. As an example, the separation of several group IIIB, IVB, and VB elements in the system triisooctylamine/hydrochloric acid within 30 s is demonstrated. Furthermore, a new method for the fast preparation of samples for α-particle spectroscopy by evaporation of the aqueous effluent with an intense light source is presented. (orig.)

  19. Design of a repetitively pulsed megajoule dense-plasma focus

    International Nuclear Information System (INIS)

    Zucker, O.; Bostick, W.; Gullickson, R.; Long, J.; Luce, J.; Sahlin, H.

    1975-01-01

    This report describes a 1 pulse per second, dense-plasma-focus (DPF) materials-testing device capable of delivering a minimum of 10 15 neutrons per pulse. Moderate scaling up from existing designs is shown to be sufficient to provide 2 x 10 13 neutrons/ cm 2 . s to a suitable target. The average power consumption, which has become a major issue due to the energy crisis, is analyzed with respect to other plasma devices and is shown to be highly favorable. Also discussed is a novel approach to capacitor-bank and switch design with respect to repetitive-pulse operation. (auth)

  20. Environmentally stable picosecond Yb fiber laser with low repetition rate

    Science.gov (United States)

    Baumgartl, M.; Abreu-Afonso, J.; Díez, A.; Rothhardt, M.; Limpert, J.; Tünnermann, A.

    2013-04-01

    A SESAM-mode-locked, all-polarization-maintaining Ytterbium fiber laser producing picosecond pulses with narrow spectral bandwidth is presented. A simple linear all-fiber cavity without dispersion compensation is realized using a uniform fiber Bragg grating (FBG). Different cavity lengths are investigated and repetition rates down to 0.7 MHz are obtained. Bandwidth and pulse duration of the output pulses are mainly determined by the choice of FBG. Pulses between 30 and 200 ps are generated employing different FBGs with bandwidths between 17 and 96 pm. The experimental results are in good agreement with numerical simulations. The laser holds great potential for simple amplification setups without pulse picking.

  1. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  2. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  3. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Robert C. [Texas A& M University; Kamon, Teruki [Texas A& M University; Toback, David [Texas A& M University; Safonov, Alexei [Texas A& M University; Dutta, Bhaskar [Texas A& M University; Dimitri, Nanopoulos [Texas A& M University; Pope, Christopher [Texas A& M University; White, James [Texas A& M University

    2013-11-18

    Overview The High Energy Physics Group at Texas A&M University is submitting this final report for our grant number DE-FG02-95ER40917. This grant has supported our wide range of research activities for over a decade. The reports contained here summarize the latest work done by our research team. Task A (Collider Physics Program): CMS & CDF Profs. T. Kamon, A. Safonov, and D. Toback co-lead the Texas A&M (TAMU) collider program focusing on CDF and CMS experiments. Task D: Particle Physics Theory Our particle physics theory task is the combined effort of Profs. B. Dutta, D. Nanopoulos, and C. Pope. Task E (Underground Physics): LUX & NEXT Profs. R. Webb and J. White(deceased) lead the Xenon-based underground research program consisting of two main thrusts: the first, participation in the LUX two-phase xenon dark matter search experiment and the second, detector R&D primarily aimed at developing future detectors for underground physics (e.g. NEXT and LZ).

  4. Divergence of gene body DNA methylation and evolution of plant duplicate genes.

    Directory of Open Access Journals (Sweden)

    Jun Wang

    Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

  5. P2-19: The Effect of item Repetition on Item-Context Association Depends on the Prior Exposure of Items

    Directory of Open Access Journals (Sweden)

    Hongmi Lee

    2012-10-01

    Full Text Available Previous studies have reported conflicting findings on whether item repetition has beneficial or detrimental effects on source memory. To reconcile such contradictions, we investigated whether the degree of pre-exposure of items can be a potential modulating factor. The experimental procedures spanned two consecutive days. On Day 1, participants were exposed to a set of unfamiliar faces. On Day 2, the same faces presented on the previous day were used again in half of the participants, whereas novel faces were used for the other half. Day 2 procedures consisted of three successive phases: item repetition, source association, and source memory test. In the item repetition phase, half of the face stimuli were repeatedly presented while participants were making male/female judgments. During the source association phase, both the repeated and the unrepeated faces appeared in one of the four locations on the screen. Finally, participants were tested on the location in which a given face was presented during the previous phase and reported the confidence of their memory. Source memory accuracy was measured as the percentage of correct non-guess trials. As results, we found a significant interaction between prior exposure and repetition. Repetition impaired source memory when the items had been pre-exposed on Day 1, while it led to greater accuracy in novel ones. These results show that pre-experimental exposure can modulate the effects of repetition on associative binding between an item and its contextual information, suggesting that pre-existing representation and novelty signal interact to form new episodic memory.

  6. Repetitive pulse accelerator technology for light ion inertial confinement fusion

    International Nuclear Information System (INIS)

    Buttram, M.T.

    1985-01-01

    Successful ignition of an inertial confinement fusion (ICF) pellet is calculated to require that several megajoules of energy be deposited in the pellet's centimeter-sized shell within 10 ns. This implies a driver power of several hundreds of terawatts and power density around 100 TW/cm 2 . The Sandia ICF approach is to deposit the energy with beams of 30 MV lithium ions. The first accelerator capable of producing these beams (PBFA II, 100 TW) will be used to study beam formation and target physics on a single pulse basis. To utilize this technology for power production, repetitive pulsing at rates that may be as high as 10 Hz will be required. This paper will overview the technologies being studied for a repetitively pulsed ICF accelerator. As presently conceived, power is supplied by rotating machinery providing 16 MJ in 1 ms. The generator output is transformed to 3 MV, then switched into a pulse compression system using laser triggered spark gaps. These must be synchronized to about 1 ns. Pulse compression is performed with saturable inductor switches, the output being 40 ns, 1.5 MV pulses. These are transformed to 30 MV in a self-magnetically insulated cavity adder structure. Space charge limited ion beams are drawn from anode plasmas with electron counter streaming being magnetically inhibited. The ions are ballistically focused into the entrances of guiding discharge channels for transport to the pellet. The status of component development from the prime power to the ion source will be reviewed

  7. Verbal behavior in Alzheimer's disease patients: Analysis of phrase repetition.

    Science.gov (United States)

    Cecato, Juliana Francisca; Martinellil, José Eduardo; Bartholomeu, Luana Luz; Basqueira, Ana Paula; Yassuda, Mônica Sanches; Aprahamian, Ivan

    2010-01-01

    Language problems in the elderly with AD are due to the fact that deterioration occurs not only in semantic memory, but in a group of cognitive factors, evidenced by a deficiency in search strategies for linguistic information. To evaluate phrase repetition in two cognitive tests, the MMSE and MoCA, in a group of Alzheimer disease patients (AD) and normal controls. A Cross-sectional study was conducted involving 20 patients who sought medical assistance at a geriatric institute in Jundiaí, São Paulo. The subjects underwent a detailed clinical examination and neuropsychometric evaluation. All subjects with AD met DSM-IV and NINCDS-ADRDA criteria. Ten patients received a diagnosis of AD and 10 were healthy subjects, forming the control group (CG). All participants correctly answered the phrase from the MMSE (phrase 1). The MoCA phrases (phrases 2 and 3) were correct in 80% and 90%, respectively in the CG and in 40% and 50%, respectively in the AD group. The MoCA test proved more effective in evaluating the echoic behavior in AD patients compared to the MMSE. The simpler phrase repetition task in the MMSE was found to be less sensitive in detecting mild language decline in AD patients.

  8. Identification of multiple modes of axisymmetric or circularly repetitive structures

    International Nuclear Information System (INIS)

    Kopff, P.

    1983-01-01

    The axisymmetric structures, or those composed with circularly repetitive elements, often display multiple modes, which are not easy to separate by modal identification of experimental responses. To be able to solve in situ some problems related to the vibrational behaviour of reactor vessels or other such huge structures, ELECTRICITY DE FRANCE developed a few years ago, experimental capabilities providing heavy harmonic driving forces, and elaborate data acquisition, signal processing and modal identification software, self-contained in an integrated mobile test facility. The modal analysis techniques we have developed with the LABORATOIRE DE MECANIQUE Appliquee of University of BESANCON (FRANCE) were especially suited for identification of multiple or separation of quasi-multiple modes, i.e. very close and strongly coupled resonances. Besides, the curve fitting methods involved, compute the same complex eigen-frequencies for all the vibration pick-ups, for better accuracy of the related eigen-vector components. Moreover, the latest extensions of these algorithms give us the means to deal with non-linear behaviour. The performances of these programs are drawn from some experimental results on axisymmetric or circularly repetitive structure, we tested in our laboratory to validate the computational hypothesis used in models for seismic responses of breeder reactor vessels. (orig.)

  9. Verbal behavior in Alzheimer disease patients: Analysis of phrase repetition

    Directory of Open Access Journals (Sweden)

    Juliana Francisca Cecato

    Full Text Available Abstract Language problems in the elderly with AD are due to the fact that deterioration occurs not only in semantic memory, but in a group of cognitive factors, evidenced by a deficiency in search strategies for linguistic information. Objectives: To evaluate phrase repetition in two cognitive tests, the MMSE and MoCA, in a group of Alzheimer disease patients (AD and normal controls. Methods: A Cross-sectional study was conducted involving 20 patients who sought medical assistance at a geriatric institute in Jundiaí, São Paulo. The subjects underwent a detailed clinical examination and neuropsychometric evaluation. All subjects with AD met DSM-IV and NINCDS-ADRDA criteria. Ten patients received a diagnosis of AD and 10 were healthy subjects, forming the control group (CG. Results: All participants correctly answered the phrase from the MMSE (phrase 1. The MoCA phrases (phrases 2 and 3 were correct in 80% and 90%, respectively in the CG and in 40% and 50%, respectively in the AD group. Conclusions: The MoCA test proved more effective in evaluating the echoic behavior in AD patients compared to the MMSE. The simpler phrase repetition task in the MMSE was found to be less sensitive in detecting mild language decline in AD patients.

  10. Rotated balance in humans due to repetitive rotational movement

    Science.gov (United States)

    Zakynthinaki, M. S.; Madera Milla, J.; López Diaz De Durana, A.; Cordente Martínez, C. A.; Rodríguez Romo, G.; Sillero Quintana, M.; Sampedro Molinuevo, J.

    2010-03-01

    We show how asymmetries in the movement patterns during the process of regaining balance after perturbation from quiet stance can be modeled by a set of coupled vector fields for the derivative with respect to time of the angles between the resultant ground reaction forces and the vertical in the anteroposterior and mediolateral directions. In our model, which is an adaption of the model of Stirling and Zakynthinaki (2004), the critical curve, defining the set of maximum angles one can lean to and still correct to regain balance, can be rotated and skewed so as to model the effects of a repetitive training of a rotational movement pattern. For the purposes of our study a rotation and a skew matrix is applied to the critical curve of the model. We present here a linear stability analysis of the modified model, as well as a fit of the model to experimental data of two characteristic "asymmetric" elite athletes and to a "symmetric" elite athlete for comparison. The new adapted model has many uses not just in sport but also in rehabilitation, as many work place injuries are caused by excessive repetition of unaligned and rotational movement patterns.

  11. New solid state opening switches for repetitive pulsed power technology

    Energy Technology Data Exchange (ETDEWEB)

    Lyubutin, S K; Mesyats, G A; Rukin, S N; Slovikovskii, B G; Turov, A M [Russian Academy of Sciences, Ekaterinburg (Russian Federation). Inst. of Electrophysics

    1997-12-31

    In 1991 the authors discovered a semiconductor opening switch (SOS) effect that occurs in p{sup +}-p-n-n{sup +} silicon structures at a current density of up to 60 kA/cm{sup 2}. This effect was used to develop high-power semiconductor opening switches in intermediate inductive storage circuits. The breaking power of the opening switches was as high as 5 GW, the interrupted current being up to 45 kA, reverse voltage up to 1 MV and the current interruption time between 10 and 60 ns. The opening switches were assembled from quantity-produced Russian-made rectifying diodes type SDL with hard recovery characteristic. On the basis of experimental and theoretical investigations of the SOS effect, new SOS diodes were designed and manufactured by the Electrophysical Institute. The paper gives basic parameters of the SOS diodes. The new diodes offer higher values of interrupted current and shorter times of current interruption together with a considerable increase in the energy switching efficiency. The new SOS diodes were used to develop repetitive all-solid-state pulsed generators with an output voltage of up to 250 kV, pulse repetition rate up to 5 kHz, and pulse duration between 10 and 30 ns. (author). 2 tabs., 3 figs., 4 refs.

  12. Application of repetitive pulsed power technology to chemical processing

    International Nuclear Information System (INIS)

    Kaye, R.J.; Hamil, R.

    1995-01-01

    The numerous sites of soil and water contaminated with organic chemicals present an urgent environmental concern that continues to grow. Electron and x-ray irradiation have been shown to be effective methods to destroy a wide spectrum of organic chemicals, nitrates, nitrites, and cyanide in water by breaking molecules to non-toxic products or entirely mineralizing the by-products to gas, water, and salts. Sandia National Laboratories is developing Repetitive High Energy Pulsed Power (RHEPP) technology capable of producing high average power, broad area electron or x-ray beams. The 300 kW RHEPP-II facility accelerates electrons to 2.5 MeV at 25 kA over 1,000 cm 2 in 60 ns pulses at repetition rates of over 100 Hz. Linking this modular treatment capability with the rapid optical-sensing diagnostics and neutral network characterization software algorithms will provide a Smart Waste Treatment (SWaT) system. Such a system would also be applicable for chemical manufacture and processing of industrial waste for reuse or disposal. This talk describes both the HREPP treatment capability and sensing technologies. Measurements of the propagated RHEPP-II beam and dose profiles are presented. Sensors and rapid detection software are discussed with application toward chemical treatment

  13. Evolution of repetitive explosive instabilities in space and time

    International Nuclear Information System (INIS)

    Wilhelmsson, H.

    1984-01-01

    A nonlinear rate equation describing nonlinear, explosive type interaction of waves in plasmas is studied, assuming that amplitude saturation occurs due to nonlinear frequency shifts. Emphasis is put on the space dependence of the solution caused by the assumption of a given initial amplitude distribution in space. An analysis is given of the problem of repetitive peaks governed by the nonlinear rate equation for the time development of the amplitudes of plasma waves and by a Lorentzian shape distribution of the initial amplitudes. For the one-dimensional case, the peaks developed by explosive instability move in the direction of lower initial amplitude values, and the speed and the repetition rate of the peaks are determined. The possible forms of equilibria for the nonlinear rate equation in the explosive case are also studied, including, in addition to the quadratic nonlinearity, diffusion and linear damping effects. A solution to the nonlinear rate equation including diffusion is also given for the case where the quadratic nonlinearity represents recombination. (Auth.)

  14. The effects of poliomyelitis on motor unit behavior during repetitive muscle actions: a case report.

    Science.gov (United States)

    Trevino, Michael A; Herda, Trent J; Cooper, Michael A

    2014-09-06

    for the healthy participants. Finally, healthy participants exhibited changes in all electromyographic parameters during the repetitive muscle actions despite successfully completing all contractions with only a slight reduction in force. Thus, caution is warranted when quantifying muscular fatigue via motor unit firing rates and other electromyographic parameters since the parameters changed despite successful completing of all contractions with only a moderate reduction in strength in healthy subjects.

  15. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  16. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  17. Single DNA denaturation and bubble dynamics

    International Nuclear Information System (INIS)

    Metzler, Ralf; Ambjoernsson, Tobias; Hanke, Andreas; Fogedby, Hans C

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.

  18. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

    Science.gov (United States)

    Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

    2014-04-01

    Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

  19. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

    Science.gov (United States)

    Ishii, Satoshi; Sadowsky, Michael J

    2009-04-01

    A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

  20. Effect of parallel magnetic field on repetitively unipolar nanosecond pulsed dielectric barrier discharge under different pulse repetition frequencies

    Science.gov (United States)

    Liu, Yidi; Yan, Huijie; Guo, Hongfei; Fan, Zhihui; Wang, Yuying; Wu, Yun; Ren, Chunsheng

    2018-03-01

    A magnetic field, with the direction parallel to the electric field, is applied to the repetitively unipolar positive nanosecond pulsed dielectric barrier discharge. The effect of the parallel magnetic field on the plasma generated between two parallel-plate electrodes in quiescent air is experimentally studied under different pulse repetition frequencies (PRFs). It is indicated that only the current pulse in the rising front of the voltage pulse occurs, and the value of the current is increased by the parallel magnetic field under different PRFs. The discharge uniformity is improved with the decrease in PRF, and this phenomenon is also observed in the discharge with the parallel magnetic field. By using the line-ratio technique of optical emission spectra, it is found that the average electron density and electron temperature under the considered PRFs are both increased when the parallel magnetic field is applied. The incremental degree of average electron density is basically the same under the considered PRFs, while the incremental degree of electron temperature under the higher-PRFs is larger than that under the lower-PRFs. All the above phenomena are explained by the effect of parallel magnetic field on diffusion and dissipation of electrons.

  1. Effects of modality and repetition in a continuous recognition memory task: Repetition has no effect on auditory recognition memory.

    Science.gov (United States)

    Amir Kassim, Azlina; Rehman, Rehan; Price, Jessica M

    2018-04-01

    Previous research has shown that auditory recognition memory is poorer compared to visual and cross-modal (visual and auditory) recognition memory. The effect of repetition on memory has been robust in showing improved performance. It is not clear, however, how auditory recognition memory compares to visual and cross-modal recognition memory following repetition. Participants performed a recognition memory task, making old/new discriminations to new stimuli, stimuli repeated for the first time after 4-7 intervening items (R1), or repeated for the second time after 36-39 intervening items (R2). Depending on the condition, participants were either exposed to visual stimuli (2D line drawings), auditory stimuli (spoken words), or cross-modal stimuli (pairs of images and associated spoken words). Results showed that unlike participants in the visual and cross-modal conditions, participants in the auditory recognition did not show improvements in performance on R2 trials compared to R1 trials. These findings have implications for pedagogical techniques in education, as well as for interventions and exercises aimed at boosting memory performance. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. High-repetition-rate hydrogen chamber: Preliminary studies; Chambre a hydrogene a haut taux de repetition: Etudes preliminaires

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-01-01

    This report is a conclusion to the tests realised with an experimental bubbles chamber in view to study the possibilities to increase the repetition rate. The more important parameters (the evolution of the bubbles, the expansion system) are considered in a theoretical way. Then the hardware is described. To end, experimental results are compared with the first evaluations. The calculations and the experimentation are against an oscillation system for the expansion. A system with a locking is to he considered. (authors) [French] Ce rapport est une conclusion aux essais realises avec une chambre a bulles experimentale en vue d'etudier les possibilites d'accroitre les taux de repetition. Les parametres les plus importants (evolution des bulles, mecanique de la detente) sont etudies par voie theorique. Puis l'appareillage est decrit. Enfin, les resultats experimentaux sont compares aux evaluations donnees au debut. Ces calculs et cette experimentation ne sont pas en faveur d'un systeme oscillant pour la detente et il faut envisager un systeme avec verrouillage. (auteurs)

  3. Effects of Replication and Transcription on DNA Structure-Related Genetic Instability.

    Science.gov (United States)

    Wang, Guliang; Vasquez, Karen M

    2017-01-05

    Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.

  4. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification.

    Science.gov (United States)

    Liu, Meng; Yin, Qingxin; McConnell, Erin M; Chang, Yangyang; Brennan, John D; Li, Yingfu

    2018-03-26

    Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  6. Relationship between the number of repetitions and selected percentages of one repetition maximum in free weight exercises in trained and untrained men.

    Science.gov (United States)

    Shimano, Tomoko; Kraemer, William J; Spiering, Barry A; Volek, Jeff S; Hatfield, Disa L; Silvestre, Ricardo; Vingren, Jakob L; Fragala, Maren S; Maresh, Carl M; Fleck, Steven J; Newton, Robert U; Spreuwenberg, Luuk P B; Häkkinen, Keijo

    2006-11-01

    Resistance exercise intensity is commonly prescribed as a percent of 1 repetition maximum (1RM). However, the relationship between percent 1RM and the number of repetitions allowed remains poorly studied, especially using free weight exercises. The purpose of this study was to determine the maximal number of repetitions that trained (T) and untrained (UT) men can perform during free weight exercises at various percentages of 1RM. Eight T and 8 UT men were tested for 1RM strength. Then, subjects performed 1 set to failure at 60, 80, and 90% of 1RM in the back squat, bench press, and arm curl in a randomized, balanced design. There was a significant (p squat than the bench press or arm curl at 60% 1RM for T and UT. At 80 and 90% 1RM, there were significant differences between the back squat and other exercises; however, differences were much less pronounced. No differences in number of repetitions performed at a given exercise intensity were noted between T and UT (except during bench press at 90% 1RM). In conclusion, the number of repetitions performed at a given percent of 1RM is influenced by the amount of muscle mass used during the exercise, as more repetitions can be performed during the back squat than either the bench press or arm curl. Training status of the individual has a minimal impact on the number of repetitions performed at relative exercise intensity.

  7. Two discharge modes of a repetitive nanosecond pulsed helium glow discharge under sub-atmospheric pressure in the repetition frequency range of 20 to 600 kHz

    Science.gov (United States)

    Kikuchi, Yusuke; Maegawa, Takuya; Otsubo, Akira; Nishimura, Yoshimi; Nagata, Masayoshi; Yatsuzuka, Mitsuyasu

    2018-05-01

    Two discharge modes, α and γ, of a repetitive nanosecond pulsed helium glow discharge at a gas pressure of 10 kPa in the repetition frequency range from 20 to 600 kHz are reported for the first time. The pulsed glow discharge is produced in a pair of parallel plate metal electrodes without insertion of dielectrics. The α mode discharge is volumetrically produced in the electrode gap at a low-repetition frequency, whereas the γ mode discharge is localized at the cathode surface at a high-repetition frequency. At high-repetition frequency, the time interval between voltage pulses is shorter than the lifetime of the afterglow produced by the preceding discharge. Then, the γ mode discharge is maintained by a large number of secondary electrons emitted from the cathode exposed to high-density ions and metastable helium atoms in the afterglow. In the α mode discharge with a low-repetition frequency operation, primary electrons due to gas ionization dominate the ionization process. Thus, a large discharge voltage is needed for the excitation of the α mode discharge. It is established that the bifurcation of α-γ discharge mode, accompanied by a decrease in the discharge voltage, occurs at the high-repetition frequency of ∼120 kHz.

  8. Boom-Bust Turnovers of Megabase-Sized Centromeric DNA in Solanum Species: Rapid Evolution of DNA Sequences Associated with Centromeres

    Czech Academy of Sciences Publication Activity Database

    Zhang, H.Q.; Koblížková, Andrea; Wang, K.; Gong, Z.Y.; Oliveira, L.; Torres, G.A.; Wu, Y.; Zhang, W.; Novák, Petr; Buell, C.R.; Macas, Jiří; Jiang, J.

    2014-01-01

    Roč. 26, č. 4 (2014), s. 1436-1447 ISSN 1040-4651 Institutional support: RVO:60077344 Keywords : Alpha-satellite DNA * repetitive sequences * rice centromeres Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.338, year: 2014

  9. Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries

    Science.gov (United States)

    Grünzner, S.; Reddavide, F. V.; Steinfelder, C.; Cui, M.; Busek, M.; Klotzbach, U.; Zhang, Y.; Sonntag, F.

    2017-02-01

    The fast development of DNA-encoded chemical libraries (DECL) in the past 10 years has received great attention from pharmaceutical industries. It applies the selection approach for small molecular drug discovery. Because of the limited choices of DNA-compatible chemical reactions, most DNA-encoded chemical libraries have a narrow structural diversity and low synthetic yield. There is also a poor correlation between the ranking of compounds resulted from analyzing the sequencing data and the affinity measured through biochemical assays. By combining DECL with dynamical chemical library, the resulting DNA-encoded dynamic library (EDCCL) explores the thermodynamic equilibrium of reversible reactions as well as the advantages of DNA encoded compounds for manipulation/detection, thus leads to enhanced signal-to-noise ratio of the selection process and higher library quality. However, the library dynamics are caused by the weak interactions between the DNA strands, which also result in relatively low affinity of the bidentate interaction, as compared to a stable DNA duplex. To take advantage of both stably assembled dual-pharmacophore libraries and EDCCLs, we extended the concept of EDCCLs to heat-induced EDCCLs (hi-EDCCLs), in which the heat-induced recombination process of stable DNA duplexes and affinity capture are carried out separately. To replace the extremely laborious and repetitive manual process, a fully automated device will facilitate the use of DECL in drug discovery. Herein we describe a novel lab-on-a-chip platform for high throughput drug discovery with hi-EDCCL. A microfluidic system with integrated actuation was designed which is able to provide a continuous sample circulation by reducing the volume to a minimum. It consists of a cooled and a heated chamber for constant circulation. The system is capable to generate stable temperatures above 75 °C in the heated chamber to melt the double strands of the DNA and less than 15 °C in the cooled chamber

  10. Optimality based repetitive controller design for track-following servo system of optical disk drives.

    Science.gov (United States)

    Chen, Wentao; Zhang, Weidong

    2009-10-01

    In an optical disk drive servo system, to attenuate the external periodic disturbances induced by inevitable disk eccentricity, repetitive control has been used successfully. The performance of a repetitive controller greatly depends on the bandwidth of the low-pass filter included in the repetitive controller. However, owing to the plant uncertainty and system stability, it is difficult to maximize the bandwidth of the low-pass filter. In this paper, we propose an optimality based repetitive controller design method for the track-following servo system with norm-bounded uncertainties. By embedding a lead compensator in the repetitive controller, both the system gain at periodic signal's harmonics and the bandwidth of the low-pass filter are greatly increased. The optimal values of the repetitive controller's parameters are obtained by solving two optimization problems. Simulation and experimental results are provided to illustrate the effectiveness of the proposed method.

  11. Analysis of T-DNA/Host-Plant DNA Junction Sequences in Single-Copy Transgenic Barley Lines

    Directory of Open Access Journals (Sweden)

    Joanne G. Bartlett

    2014-01-01

    Full Text Available Sequencing across the junction between an integrated transfer DNA (T-DNA and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.

  12. DNA Fingerprinting of Single Colonies of Helicobacter pylori from Gastric Cancer Patients Suggests Infection with a Single Predominant Strain

    OpenAIRE

    Miehlke, Stephan; Thomas, Rachel; Guiterrez, Oscar; Graham, David Y.; Go, Mae F.

    1999-01-01

    In each of six gastric cancer patients, repetitive extragenic palindromic PCR DNA fingerprints of 18 single colonies of Helicobacter pylori from the gastric antrum, corpus, and cardia were identical and matched that of the parental isolate. In three additional gastric cancer patients, 17 of 18 single-colony DNA fingerprints were identical to each other and to the DNA fingerprint of the corresponding parental isolate.

  13. Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

    Czech Academy of Sciences Publication Activity Database

    Puterová, J.; Razumova, O.; Martínek, T.; Alexandrov, O.; Divashuk, M.; Kubát, Z.; Hobza, Roman; Karlov, G.; Kejnovský, E.

    2017-01-01

    Roč. 9, č. 1 (2017), s. 197-212 ISSN 1759-6653 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : sex-chromosomes * repetitive sequences * silene-latifolia * molecular cytogenetics * arabidopsis-thaliana * genome size * evolution * organization * alignment * database * sex chromosomes * genome composition * chromosomal localization * repetitive DNA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 3.979, year: 2016

  14. The effect of laser repetition rate on the LASiS synthesis of biocompatible silver nanoparticles in aqueous starch solution

    Directory of Open Access Journals (Sweden)

    Zamiri R

    2013-01-01

    Full Text Available Reza Zamiri,1 Azmi Zakaria,1,* Hossein Abbastabar Ahangar,2 Majid Darroudi,3 Golnoosh Zamiri,1 Zahid Rizwan,1 Gregor PC Drummen4,* 1Department of Physics, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; 2Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Selangor Darul Ehsan, Malaysia; 3Advanced Materials and Nanotechnology Laboratory, Institute of Advanced Technology (ITMA, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; 4Bionanoscience and Bio-Imaging Program, Cellular Stress and Ageing Program, Bio&Nano-Solutions, Düsseldorf, Germany*These authors contributed to this work equallyAbstract: Laser ablation-based nanoparticle synthesis in solution is rapidly becoming popular, particularly for potential biomedical and life science applications. This method promises one pot synthesis and concomitant bio-functionalization, is devoid of toxic chemicals, does not require complicated apparatus, can be combined with natural stabilizers, is directly biocompatible, and has high particle size uniformity. Size control and reduction is generally determined by the laser settings; that the size and size distribution scales with laser fluence is well described. Conversely, the effect of the laser repetition rate on the final nanoparticle product in laser ablation is less well-documented, especially in the presence of stabilizers. Here, the influence of the laser repetition rate during laser ablation synthesis of silver nanoparticles in the presence of starch as a stabilizer was investigated. The increment of the repetition rate does not negatively influence the ablation efficiency, but rather shows increased productivity, causes a red-shift in the plasmon resonance peak of the silver–starch nanoparticles, an increase in mean particle size and size distribution, and a distinct lack of agglomerate formation. Optimal results were achieved at 10 Hz repetition rate, with a mean particle size of ~10 nm and a

  15. Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

    Science.gov (United States)

    Shoura, Massa J; Gabdank, Idan; Hansen, Loren; Merker, Jason; Gotlib, Jason; Levene, Stephen D; Fire, Andrew Z

    2017-10-05

    Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples. Copyright © 2017 Shoura et al.

  16. Functions of repetition in the discourse of elderly speakers: The role of prosody and gesture

    OpenAIRE

    Bolly, Catherine; Gerstenberg, Annette; 14th International Pragmatics Conference (IPra), Panel session "Age and language use"

    2015-01-01

    Cognitively speaking, repetition can work as a facilitator for both the planning and the understanding of spoken language. It can work as a cohesive and interactive device or, at a higher-level function of discourse, to engage in interaction by creating interpersonal involvement: repetition always conveys altered meaning, as it has to be re-interpreted by the interlocutor “in light of the accretion, juxtaposition, or expansion” (Tannen 2007: 62). Repetition is thus useful for the building of ...

  17. Nonword repetition in lexical decision: support for two opposing processes.

    Science.gov (United States)

    Wagenmakers, Eric-Jan; Zeelenberg, René; Steyvers, Mark; Shiffrin, Richard; Raaijmakers, Jeroen

    2004-10-01

    We tested and confirmed the hypothesis that the prior presentation of nonwords in lexical decision is the net result of two opposing processes: (1) a relatively fast inhibitory process based on global familiarity; and (2) a relatively slow facilitatory process based on the retrieval of specific episodic information. In three studies, we manipulated speed-stress to influence the balance between the two processes. Experiment 1 showed item-specific improvement for repeated nonwords in a standard "respond-when-ready" lexical decision task. Experiment 2 used a 400-ms deadline procedure and showed performance for nonwords to be unaffected by up to four prior presentations. In Experiment 3 we used a signal-to-respond procedure with variable time intervals and found negative repetition priming for repeated nonwords. These results can be accounted for by dual-process models of lexical decision.

  18. Repetitive Bunches from RF-Photo Gun Radiate Coherently

    CERN Document Server

    Van der Geer, C A J; Van der Geer, S B

    2004-01-01

    We consider to feed the laser wake field accelerator of the alpha-X project by a train of low charge pancake electron bunches to reduce undesired expansion due to space-charge forces. To this purpose the photo excitation laser of the rf-injector is split into a train of sub-pulses, such that each of the produced electron bunches falls into a successive ponderomotive well of the plasma accelerator. This way the total accelerated charge is not reduced. The repetitive photo gun can be tested, at low energy, by connecting it directly to the undulator and monitoring the radiation. The assertions are based on the results of new GPT simulations.

  19. Report on computation of repetitive hyperbaric-hypobaric decompression tables

    Science.gov (United States)

    Edel, P. O.

    1975-01-01

    The tables were constructed specifically for NASA's simulated weightlessness training program; they provide for 8 depth ranges covering depths from 7 to 47 FSW, with exposure times of 15 to 360 minutes. These tables were based up on an 8 compartment model using tissue half-time values of 5 to 360 minutes and Workmanline M-values for control of the decompression obligation resulting from hyperbaric exposures. Supersaturation ratios of 1.55:1 to 2:1 were used for control of ascents to altitude following such repetitive dives. Adequacy of the method and the resultant tables were determined in light of past experience with decompression involving hyperbaric-hypobaric interfaces in human exposures. Using these criteria, the method showed conformity with empirically determined values. In areas where a discrepancy existed, the tables would err in the direction of safety.

  20. [Repetitive impulse-associated behavioral disorders in Parkinson's disease].

    Science.gov (United States)

    Katzenschlager, R; Goerlich, K S; van Eimeren, T

    2012-12-01

    Parkinson's disease (PD) is associated with a number of behavioral disorders which may cause considerable social, professional or financial problems. Impulse control disorders (ICDs), such as pathological gambling, binge eating, compulsive shopping and hypersexuality occur in approximately 13-14% of PD patients. Further behavioral disorders are the dopamine dysregulation syndrome (DDS), a substance dependence characterized by craving for dopaminergic substances and punding (prolonged repetitive activities which are not goal-oriented).Treatment-related risk factors are dopamine agonists for ICDs and a high total dopaminergic dose for DDS and punding. Shared risk factors are young age at onset, impulsive personality traits, depression and possibly dyskinesia. At the neuronal level these behavioral disorders seem to be associated with changes in the reward system and dysfunction of the orbitofrontal cortex. The evidence level for management strategies is at present insufficient. For ICDs current clinical practice consists of discontinuation or reduction of dopamine agonists.

  1. Repetitive pulse accelerator technology for light ion inertial confinement fusion

    International Nuclear Information System (INIS)

    Buttram, M.T.

    1985-01-01

    This paper will overview the technologies being studied for a repetitively pulsed ICF accelerator. As presently conceived, power is supplied by rotating machinery providing 16 MJ in 1 ms. The generator output is transformed to 3 MV, then switched into a pulse compression system using laser triggered spark gaps. These must be synchronized to about 1 ns. Pulse compression is performed with saturable inductor switches, the output being 40 ns, 1.5 MV pulses. These are transformed to 30 MV in a self-magnetically insulated cavity adder structure. Space charge limited ion beams are drawn from anode plasmas with electron counter streaming being magnetically inhibited. The ions are ballistically focused into the entrances of guiding discharge channels for transport to the pellet. The status of component development from the prime power to the ion source will be reviewed

  2. High repetition rate driver circuit for modulation of injection lasers

    International Nuclear Information System (INIS)

    Dornan, B.R.; Goel, J.; Wolkstein, H.J.

    1981-01-01

    An injection laser modulator comprises a self-biased field effect transistor (FET) and an injection laser to provide a quiescent state during which lasing of the injection laser occurs in response to a high repetition rate signal of pulse coded modulation (pcm). The modulator is d.c. coupled to an input pulse source of pcm rendering it compatible with an input pulse referenced to ground and not being subject to voltage level shifting of the input pulse. The modulator circuit in its preferred and alternate embodiments provides various arrangements for high impedance input and low impedance output matching. In addition, means are provided for adjusting the bias of the FET as well as the bias of the injection laser

  3. A high repetition rate XUV seeding source for FLASH2

    International Nuclear Information System (INIS)

    Willner, Arik

    2012-05-01

    Improved performance of free-electron laser (FEL) light sources in terms of timing stability, pulse shape and spectral properties of the amplified FEL pulses is of interest in material science, the fields of ultrafast dynamics, biology, chemistry and even special branches in industry. A promising scheme for such an improvement is direct seeding with high harmonic generation (HHG) in a noble gas target. A free-electron laser seeded by an external extreme ultraviolet (XUV) source is planned for FLASH2 at DESY in Hamburg. The requirements for the XUV/soft X-ray source can be summarized as follows: A repetition rate of at least 100 kHz in a 10 Hz burst is needed at variable wavelengths from 10 to 40 nm and pulse energies of several nJ within a single laser harmonic. This application requires a laser amplifier system with exceptional parameters, mJ-level pulse energy, 10-15 fs pulse duration at 100 kHz (1 MHz) burst repetition rate. A new optical parametric chirped-pulse amplification (OPCPA) system is under development in order to meet these requirements, and very promising results have been achieved in the last three years. In parallel to this development, a new HHG concept is necessary to sustain high average power of the driving laser system and to generate harmonics with high conversion efficiencies. Currently, the highest conversion efficiency with HHG has been demonstrated using gas-filled capillary targets. For our application, only a free-jet target can be used for HHG, in order to overcome damage threshold limitations of HHG target optics at a high repetition rate. A novel dual-gas multijet gas target has been developed and first experiments show remarkable control of the degree of phase matching forming the basis for improved control of the harmonic photon flux and the XUV pulse characteristics. The basic idea behind the dual-gas concept is the insertion of matching zones in between multiple HHG sources. These matching sections are filled with hydrogen which

  4. A high repetition rate XUV seeding source for FLASH2

    Energy Technology Data Exchange (ETDEWEB)

    Willner, Arik

    2012-05-15

    Improved performance of free-electron laser (FEL) light sources in terms of timing stability, pulse shape and spectral properties of the amplified FEL pulses is of interest in material science, the fields of ultrafast dynamics, biology, chemistry and even special branches in industry. A promising scheme for such an improvement is direct seeding with high harmonic generation (HHG) in a noble gas target. A free-electron laser seeded by an external extreme ultraviolet (XUV) source is planned for FLASH2 at DESY in Hamburg. The requirements for the XUV/soft X-ray source can be summarized as follows: A repetition rate of at least 100 kHz in a 10 Hz burst is needed at variable wavelengths from 10 to 40 nm and pulse energies of several nJ within a single laser harmonic. This application requires a laser amplifier system with exceptional parameters, mJ-level pulse energy, 10-15 fs pulse duration at 100 kHz (1 MHz) burst repetition rate. A new optical parametric chirped-pulse amplification (OPCPA) system is under development in order to meet these requirements, and very promising results have been achieved in the last three years. In parallel to this development, a new HHG concept is necessary to sustain high average power of the driving laser system and to generate harmonics with high conversion efficiencies. Currently, the highest conversion efficiency with HHG has been demonstrated using gas-filled capillary targets. For our application, only a free-jet target can be used for HHG, in order to overcome damage threshold limitations of HHG target optics at a high repetition rate. A novel dual-gas multijet gas target has been developed and first experiments show remarkable control of the degree of phase matching forming the basis for improved control of the harmonic photon flux and the XUV pulse characteristics. The basic idea behind the dual-gas concept is the insertion of matching zones in between multiple HHG sources. These matching sections are filled with hydrogen which

  5. Intrinsic and extrinsic motivation for stereotypic and repetitive behavior.

    Science.gov (United States)

    Joosten, Annette V; Bundy, Anita C; Einfeld, Stewart L

    2009-03-01

    This study provides evidence for intrinsic and extrinsic motivators for stereotypical and repetitive behavior in children with autism and intellectual disability and children with intellectual disability alone. We modified the Motivation Assessment Scale (MAS) (1988b); dividing it into intrinsic and extrinsic measures and adding items to assess anxiety as an intrinsic motivator. Rasch analysis of data from 279 MASs (74 children) revealed that the items formed two unidimensional scales. Anxiety was a more likely intrinsic motivator than sensory seeking for children with dual diagnoses; the reverse was true for children with intellectual disability only. Escape and gaining a tangible object were the most common extrinsic motivators for those with dual diagnoses and attention and escape for children with intellectual disability.

  6. Repetition blindness for natural images of objects with viewpoint changes

    Directory of Open Access Journals (Sweden)

    Stephane eBuffat

    2013-01-01

    Full Text Available When stimuli are repeated in a rapid serial visual presentation (RSVP, observers sometimes fail to report the second occurrence of a target. This phenomenon is referred to as repetition blindness (RB. We report an RSVP experiment with photographs in which we manipulated object viewpoints between the first and second occurrences of a target (0-, 45-, or 90-degree changes, and spatial frequency content. Natural images were spatially filtered to produce low, medium, or high spatial-frequency stimuli. RB was observed for all filtering conditions. Surprisingly, for full-spectrum images, RB increased significantly as the viewpoint reached 90 degrees. For filtered images, a similar pattern of results was found for all conditions except for medium spatial-frequency stimuli. These findings suggest that object recognition in RSVP are subtended by viewpoint-specific representations for all spatial frequencies except medium ones.

  7. Influence of Music Style and Rate on Repetitive Finger Tapping.

    Science.gov (United States)

    Stegemöller, Elizabeth L; Tatz, Joshua R; Warnecke, Alison; Hibbing, Paul; Bates, Brandon; Zaman, Andrew

    2018-03-09

    Auditory cues, including music, are commonly used in the treatment of persons with Parkinson's disease. Yet, how music style and movement rate modulate movement performance in persons with Parkinson's disease have been neglected and remain limited in healthy young populations. The purpose of this study was to determine how music style and movement rate influence movement performance in healthy young adults. Healthy participants were asked to perform repetitive finger movements at two pacing rates (70 and 140 beats per minute) for the following conditions: (a) a tone only, (b) activating music, and (c) relaxing music. Electromyography, movement kinematics, and variability were collected. Results revealed that the provision of music, regardless of style, reduced amplitude variability at both pacing rates. Intermovement interval was longer, and acceleration variability was reduced during both music conditions at the lower pacing rate only. These results may prove beneficial for designing therapeutic interventions for persons with Parkinson's disease.

  8. Repetitive fueling pellet injection in large helical device

    International Nuclear Information System (INIS)

    Yamada, H.; Sakamoto, R.; Viniar, I.; Oda, Y.; Kikuchi, K.; Lukin, A.; Skoblikov, S.; Umov, A.; Takaura, K.; Onozuka, M.; Kato, S.; Sudo, S.

    2003-01-01

    A repetitive pellet injector has been developed for investigation of fueling issues towards the steady-state operation in Large Helical Device (LHD). The goal of this approach is achievement of the plasma operation for longer than 1000 s. A principal technical element of the pellet injector is solidification of hydrogen and extrusion of a solid hydrogen rod through a cryogenic screw extruder cooled by Giffard-McMahon (GM) cryo-coolers. Continuous operation of more than 10000 pellet launches at 10 Hz has been demonstrated. The reliability of pellet launch exceeds 99%. The pellet mass and velocity, the consumption of propellant gas and quality of pellets have been successfully tested to fit the experimental requirement in LHD

  9. Repetitive fueling pellet injection in large helical device

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, H. E-mail: hyamada@lhd.nifs.ac.jp; Sakamoto, R.; Viniar, I.; Oda, Y.; Kikuchi, K.; Lukin, A.; Skoblikov, S.; Umov, A.; Takaura, K.; Onozuka, M.; Kato, S.; Sudo, S

    2003-09-01

    A repetitive pellet injector has been developed for investigation of fueling issues towards the steady-state operation in Large Helical Device (LHD). The goal of this approach is achievement of the plasma operation for longer than 1000 s. A principal technical element of the pellet injector is solidification of hydrogen and extrusion of a solid hydrogen rod through a cryogenic screw extruder cooled by Giffard-McMahon (GM) cryo-coolers. Continuous operation of more than 10000 pellet launches at 10 Hz has been demonstrated. The reliability of pellet launch exceeds 99%. The pellet mass and velocity, the consumption of propellant gas and quality of pellets have been successfully tested to fit the experimental requirement in LHD.

  10. BANSHEE: High-voltage repetitively pulsed electron-beam driver

    International Nuclear Information System (INIS)

    VanHaaften, F.

    1992-01-01

    BANSHEE (Beam Accelerator for a New Source of High-Energy Electrons) this is a high-voltage modulator is used to produce a high-current relativistic electron beam for high-power microwave tube development. The goal of the BANSHEE research is first to achieve a voltage pulse of 700--750 kV with a 1-μs pulse width driving a load of ∼100 Ω, the pulse repetition frequency (PRF) of a few hertz. The ensuing goal is to increase the pulse amplitude to a level approaching 1 MV. We conducted tests using half the modulator with an output load of 200 Ω, up to a level of ∼650 kV at a PRF of 1 Hz and 525 kV at a PRF of 5 Hz. We then conducted additional testing using the complete system driving a load of ∼100 Ω

  11. Repetition rates in heavy ion beam driven fusion reactors

    Science.gov (United States)

    Peterson, Robert R.

    1986-01-01

    The limits on the cavity gas density required for beam propagation and condensation times for material vaporized by target explosions can determine the maximum repetition rate of Heavy Ion Beam (HIB) driven fusion reactors. If the ions are ballistically focused onto the target, the cavity gas must have a density below roughly 10-4 torr (3×1012 cm-3) at the time of propagation; other propagation schemes may allow densities as high as 1 torr or more. In some reactor designs, several kilograms of material may be vaporized off of the target chamber walls by the target generated x-rays, raising the average density in the cavity to 100 tor or more. A one-dimensional combined radiation hydrodynamics and vaporization and condensation computer code has been used to simulate the behavior of the vaporized material in the target chambers of HIB fusion reactors.

  12. Repetition rates in heavy ion beam driven fusion reactors

    International Nuclear Information System (INIS)

    Peterson, R.R.

    1986-01-01

    The limits on the cavity gas density required for beam propagation and condensation times for material vaporized by target explosions can determine the maximum repetition rate of Heavy Ion Beam (HIB) driven fusion reactors. If the ions are ballistically focused onto the target, the cavity gas must have a density below roughly 10 -4 torr (3 x 10 12 cm -3 ) at the time of propagation; other propagation schemes may allow densities as high as 1 torr or more. In some reactor designs, several kilograms of material may be vaporized off of the target chamber walls by the target generated x-rays, raising the average density in the cavity to 100 tor or more. A one-dimensional combined radiation hydrodynamics and vaporization and condensation computer code has been used to simulate the behavior of the vaporized material in the target chambers of HIB fusion reactors

  13. On the non-Poissonian repetition pattern of FRB121102

    Science.gov (United States)

    Oppermann, Niels; Yu, Hao-Ran; Pen, Ue-Li

    2018-04-01

    The Fast Radio Burst FRB121102 has been observed to repeat in an irregular fashion. Using published timing data of the observed bursts, we show that Poissonian statistics are not a good description of this random process. As an alternative, we suggest to describe the intervals between bursts with a Weibull distribution with a shape parameter smaller than one, which allows for the clustered nature of the bursts. We quantify the amount of clustering using the parameters of the Weibull distribution and discuss the consequences that it has for the detection probabilities of future observations and for the optimization of observing strategies. Allowing for this generalization, we find a mean repetition rate of r=5.7^{+3.0}_{-2.0} per day and index k=0.34^{+0.06}_{-0.05} for a correlation function ξ(t) = (t/t0)k - 1.

  14. Dose Measurements in a 20-J Repetitive Plasma Focus

    Science.gov (United States)

    Goudarzi, S.; Babaee, H.; Esmaeli, A.; Nasiri, A.; Mazandarani, A.

    2018-02-01

    In this article, the results of X-ray dose measurements executed using thermoluminescent dosimeters in experiments with a very small (20 J) repetitive plasma focus device named SORENA-1 are presented and analyzed. The working gas in these experiments was Argon. Also, pinch formation in experiments with this device has been observed. This device has been designed and constructed in Plasma and Nuclear Fusion Research School of Nuclear Science and Technology Research Institute of Iran. From these results, it is concluded that we can do experiments with this device using Ar as working gas all over the working days of year, and a good symmetry for measured dose around the device has been seen.

  15. Energy coupling to the plasma in repetitive nanosecond pulse discharges

    International Nuclear Information System (INIS)

    Adamovich, Igor V.; Nishihara, Munetake; Choi, Inchul; Uddi, Mruthunjaya; Lempert, Walter R.

    2009-01-01

    A new analytic quasi-one-dimensional model of energy coupling to nanosecond pulse discharge plasmas in plane-to-plane geometry has been developed. The use of a one-dimensional approach is based on images of repetitively pulsed nanosecond discharge plasmas in dry air demonstrating that the plasma remains diffuse and uniform on a nanosecond time scale over a wide range of pressures. The model provides analytic expressions for the time-dependent electric field and electron density in the plasma, electric field in the sheath, sheath boundary location, and coupled pulse energy. The analytic model predictions are in very good agreement with numerical calculations. The model demonstrates that (i) the energy coupled to the plasma during an individual nanosecond discharge pulse is controlled primarily by the capacitance of the dielectric layers and by the breakdown voltage and (ii) the pulse energy coupled to the plasma during a burst of nanosecond pulses decreases as a function of the pulse number in the burst. This occurs primarily because of plasma temperature rise and resultant reduction in breakdown voltage, such that the coupled pulse energy varies approximately proportionally to the number density. Analytic expression for coupled pulse energy scaling has been incorporated into the air plasma chemistry model, validated previously by comparing with atomic oxygen number density measurements in nanosecond pulse discharges. The results of kinetic modeling using the modified air plasma chemistry model are compared with time-resolved temperature measurements in a repetitively pulsed nanosecond discharge in air, by emission spectroscopy, and purely rotational coherent anti-Stokes Raman spectroscopy showing good agreement.

  16. Repetitive Pediatric Anesthesia in a Non-Hospital Setting

    International Nuclear Information System (INIS)

    Buchsbaum, Jeffrey C.; McMullen, Kevin P.; Douglas, James G.; Jackson, Jeffrey L.; Simoneaux, R. Victor; Hines, Matthew; Bratton, Jennifer; Kerstiens, John; Johnstone, Peter A.S.

    2013-01-01

    Purpose: Repetitive sedation/anesthesia (S/A) for children receiving fractionated radiation therapy requires induction and recovery daily for several weeks. In the vast majority of cases, this is accomplished in an academic center with direct access to pediatric faculty and facilities in case of an emergency. Proton radiation therapy centers are more frequently free-standing facilities at some distance from specialized pediatric care. This poses a potential dilemma in the case of children requiring anesthesia. Methods and Materials: The records of the Indiana University Health Proton Therapy Center were reviewed for patients requiring anesthesia during proton beam therapy (PBT) between June 1, 2008, and April 12, 2012. Results: A total of 138 children received daily anesthesia during this period. A median of 30 fractions (range, 1-49) was delivered over a median of 43 days (range, 1-74) for a total of 4045 sedation/anesthesia procedures. Three events (0.0074%) occurred, 1 fall from a gurney during anesthesia recovery and 2 aspiration events requiring emergency department evaluation. All 3 children did well. One aspiration patient needed admission to the hospital and mechanical ventilation support. The other patient returned the next day for treatment without issue. The patient who fell was not injured. No patient required cessation of therapy. Conclusions: This is the largest reported series of repetitive pediatric anesthesia in radiation therapy, and the only available data from the proton environment. Strict adherence to rigorous protocols and a well-trained team can safely deliver daily sedation/anesthesia in free-standing proton centers

  17. Environmental Enrichment Mitigates Deficits after Repetitive Mild Traumatic Brain Injury.

    Science.gov (United States)

    Liu, Xixia; Qiu, Jianhua; Alcon, Sasha; Hashim, Jumana; Meehan, William P; Mannix, Rebekah

    2017-08-15

    Although environmental enrichment has been shown to improve functional and histologic outcomes in pre-clinical moderate-to-severe traumatic brain injury (TBI), there are a paucity of pre-clinical data regarding enrichment strategies in the setting of repetitive mild traumatic brain injury (rmTBI). Given the vast numbers of athletes and those in the military who sustain rmTBI, the mounting evidence of the long-term and progressive sequelae of rmTBI, and the lack of targeted therapies to mitigate these sequelae, successful enrichment interventions in rmTBI could have large public health significance. Here, we evaluated enrichment strategies in an established pre-clinical rmTBI model. Seventy-one male C57BL/6 mice were randomized to two different housing conditions, environmental enrichment (EE) or normal condition (NC), then subjected to rmTBI injury (seven injuries in 9 days) or sham injury (anesthesia only). Functional outcomes in all four groups (NC-TBI, EE-TBI, NC-sham, and EE-sham) were assessed by motor, exploratory/anxiety, and mnemonic behavioral tests. At the synaptic level, N-methyl d-aspartate receptor (NMDAR) subunit expression of phosphorylated glutamate receptor 1 (GluR1), phosphorylated Ca 2+ /calmodulin-dependent protein kinase II (CaMKII), and calpain were evaluated by western blot. Compared to injured NC-TBI mice, EE-TBI mice had improved memory and decreased anxiety and exploratory activity post-injury. Treatment with enrichment also corresponded to normal NMDAR subunit expression, decreased GluR1 phosphorylation, decreased phosphorylated CaMKII, and normal calpain expression post-rmTBI. These data suggest that enrichment strategies may improve functional outcomes and mitigate synaptic changes post-rmTBI. Given that enrichment strategies are feasible in the clinical setting, particularly for athletes and soldiers for whom the risk of repetitive injury is greatest, these data suggest that clinical trials may be warranted.

  18. Electrophysiological signatures of phonological and semantic maintenance in sentence repetition.

    Science.gov (United States)

    Meltzer, Jed A; Kielar, Aneta; Panamsky, Lilia; Links, Kira A; Deschamps, Tiffany; Leigh, Rosie C

    2017-08-01

    Verbal short-term memory comprises resources for phonological rehearsal, which have been characterized anatomically, and for maintenance of semantic information, which are less understood. Sentence repetition tasks tap both processes interactively. To distinguish brain activity involved in phonological vs. semantic maintenance, we recorded magnetoencephalography during a sentence repetition task, incorporating three manipulations emphasizing one mechanism over the other. Participants heard sentences or word lists and attempted to repeat them verbatim after a 5-second delay. After MEG, participants completed a cued recall task testing how much they remembered of each sentence. Greater semantic engagement relative to phonological rehearsal was hypothesized for 1) sentences vs. word lists, 2) concrete vs. abstract sentences, and 3) well recalled vs. poorly recalled sentences. During auditory perception and the memory delay period, we found highly left-lateralized activation in the form of 8-30 Hz event-related desynchronization. Compared to abstract sentences, concrete sentences recruited posterior temporal cortex bilaterally, demonstrating a neural signature for the engagement of visual imagery in sentence maintenance. Maintenance of arbitrary word lists recruited right hemisphere dorsal regions, reflecting increased demands on phonological rehearsal. Sentences that were ultimately poorly recalled in the post-test also elicited extra right hemisphere activation when they were held in short-term memory, suggesting increased demands on phonological resources. Frontal midline theta oscillations also reflected phonological rather than semantic demand, being increased for word lists and poorly recalled sentences. These findings highlight distinct neural resources for phonological and semantic maintenance, with phonological maintenance associated with stronger oscillatory modulations. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Effects of a cognitive dual task on variability and local dynamic stability in sustained repetitive arm movements using principal component analysis: a pilot study.

    Science.gov (United States)

    Longo, Alessia; Federolf, Peter; Haid, Thomas; Meulenbroek, Ruud

    2018-06-01

    In many daily jobs, repetitive arm movements are performed for extended periods of time under continuous cognitive demands. Even highly monotonous tasks exhibit an inherent motor variability and subtle fluctuations in movement stability. Variability and stability are different aspects of system dynamics, whose magnitude may be further affected by a cognitive load. Thus, the aim of the study was to explore and compare the effects of a cognitive dual task on the variability and local dynamic stability in a repetitive bimanual task. Thirteen healthy volunteers performed the repetitive motor task with and without a concurrent cognitive task of counting aloud backwards in multiples of three. Upper-body 3D kinematics were collected and postural reconfigurations-the variability related to the volunteer's postural change-were determined through a principal component analysis-based procedure. Subsequently, the most salient component was selected for the analysis of (1) cycle-to-cycle spatial and temporal variability, and (2) local dynamic stability as reflected by the largest Lyapunov exponent. Finally, end-point variability was evaluated as a control measure. The dual cognitive task proved to increase the temporal variability and reduce the local dynamic stability, marginally decrease endpoint variability, and substantially lower the incidence of postural reconfigurations. Particularly, the latter effect is considered to be relevant for the prevention of work-related musculoskeletal disorders since reduced variability in sustained repetitive tasks might increase the risk of overuse injuries.

  20. Performance of a high repetition pulse rate laser system for in-gas-jet laser ionization studies with the Leuven laser ion source LISOL

    International Nuclear Information System (INIS)

    Ferrer, R.; Sonnenschein, V.T.; Bastin, B.; Franchoo, S.; Huyse, M.; Kudryavtsev, Yu.; Kron, T.; Lecesne, N.; Moore, I.D.; Osmond, B.; Pauwels, D.; Radulov, D.; Raeder, S.; Rens, L.

    2012-01-01

    The laser ionization efficiency of the Leuven gas cell-based laser ion source was investigated under on- and off-line conditions using two distinctly different laser setups: a low-repetition rate dye laser system and a high-repetition rate Ti:sapphire laser system. A systematic study of the ion signal dependence on repetition rate and laser pulse energy was performed in off-line tests using stable cobalt and copper isotopes. These studies also included in-gas-jet laser spectroscopy measurements on the hyperfine structure of 63 Cu. A final run under on-line conditions in which the radioactive isotope 59 Cu (T 1/2 = 81.5 s) was produced, showed a comparable yield of the two laser systems for in-gas-cell ionization. However, a significantly improved time overlap by using the high-repetition rate laser system for in-gas-jet ionization was demonstrated by an increase of the overall duty cycle, and at the same time, pointed to the need for a better shaped atomic jet to reach higher ionization efficiencies.

  1. The roles of stimulus repetition and hemispheric activation in visual half-field asymmetries.

    Science.gov (United States)

    Sullivan, K F; McKeever, W F

    1985-10-01

    Hardyck, Tzeng, and Wang (1978, Brain and Language, 5, 56-71) hypothesized that ample repetition of a small number of stimuli is required in order to obtain VHF differences in tachistoscopic tasks. Four experiments, with varied levels of repetition, were conducted to test this hypothesis. Three experiments utilized the general task of object-picture naming and one utilized a word-naming task. Naming latencies constituted the dependent measure. The results demonstrate that for the object-naming paradigm repetition is required for RVF superiority to emerge. Repetition was found to be unnecessary for RVF superiority in the word-naming paradigm, with repetition actually reducing RVF superiority. Experiment I suggested the possibility that RVF superiority developed for the second half of the trials as a function of practice or hemispheric activation, regardless of repetition level. Subsequent experiments, better designed to assess this possibility, clearly refuted it. It was concluded that the effect of repetition depends on the processing requirements of the task. We propose that, for tasks which can be processed efficiently by one hemisphere, the effect of repetition will be to reduce VHF asymmetries; but tasks requiring substantial processing by both hemispheres will show shifts to RVF superiority as a function of repetition.

  2. Understanding work related musculoskeletal pain: does repetitive work cause stress symptoms?

    Science.gov (United States)

    Bonde, J P; Mikkelsen, S; Andersen, J H; Fallentin, N; Baelum, J; Svendsen, S W; Thomsen, J F; Frost, P; Kaergaard, A

    2005-01-01

    Pain in the neck and upper extremity is reported with high frequency in repetitive work. Mechanical overload of soft tissues seems a plausible mechanism, but psychological factors have received considerable attention during the past decade. If psychological factors are important for development of regional pain in repetitive work, stress symptoms would likely be on the causal path. To examine whether objective measures of repetitive monotonous work are related to occurrence and development of stress symptoms. In 1994-95, 2033 unskilled workers with continuous repetitive work and 813 workers with varied work were enrolled. Measures of repetitiveness and force requirements were quantified using video observations to obtain individual exposure estimates. Stress symptoms were recorded at baseline and after approximately one, two, and three years by the Setterlind Stress Profile Inventory. Repetitive work, task cycle time, and quantified measures of repetitive upper extremity movements including force requirements were not related to occurrence of stress symptoms at baseline or development of stress symptoms during three years of follow up. The findings do not indicate that repetitive work is associated with stress symptoms, but small effects cannot be ruled out. Thus the results question the importance of mental stress mechanisms in the causation of regional pain related to repetitive work. However, the findings should be interpreted with caution because the stress inventory has not been validated against a gold standard.

  3. Frequency Adaptive Repetitive Control of Grid-Tied Three-Phase PV Inverters

    DEFF Research Database (Denmark)

    Zhou, Keliang; Yang, Yongheng; Blaabjerg, Frede

    2016-01-01

    Repetitive control offers an accurate current control scheme for grid-tied converters to feed high quality sinusoidal current into the grid. However, with grid frequency being treated as a constant value, conventional repetitive controller fail to produce high quality feeding current in the prese......Repetitive control offers an accurate current control scheme for grid-tied converters to feed high quality sinusoidal current into the grid. However, with grid frequency being treated as a constant value, conventional repetitive controller fail to produce high quality feeding current...

  4. Pulse repetition rate multiplication by Talbot effect in a coaxial fiber

    Science.gov (United States)

    Dhingra, Nikhil; Saxena, Geetika Jain; Anand, Jyoti; Sharma, Enakshi K.

    2018-03-01

    We use a coaxial fiber, which is a cylindrical coupled waveguide structure consisting of two concentric cores, the inner rod and an outer ring core as a first order dispersive media to achieve temporal Talbot effect for pulse repetition rate multiplication (PRRM) in high bit rate optical fiber communication. It is observed that for an input Gaussian pulse train with pulse width, 2τ0=1ps at a repetition rate of 40 Gbps (repetition period, T=25ps), an output repetition rate of 640 Gbps can be achieved without significant distortion at a length of 40.92 m.

  5. Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations.

    Science.gov (United States)

    Go, M F; Chan, K Y; Versalovic, J; Koeuth, T; Graham, D Y; Lupski, J R

    1995-07-01

    Helicobacter pylori infection is now accepted as the most common cause of chronic active gastritis and peptic ulcer disease. The etiologies of many infectious diseases have been attributed to specific or clonal strains of bacterial pathogens. Polymerase chain reaction (PCR) amplification of DNA between repetitive DNA sequences, REP elements (REP-PCR), has been utilized to generate DNA fingerprints to examine similarity among strains within a bacterial species. Genomic DNA from H. pylori isolates obtained from 70 individuals (39 duodenal ulcers and 31 simple gastritis) was PCR-amplified using consensus probes to repetitive DNA elements. The H. pylori DNA fingerprints were analyzed for similarity and correlated with disease presentation using the NTSYS-pc computer program. Each H. pylori strain had a distinct DNA fingerprint except for two pairs. Single-colony DNA fingerprints of H. pylori from the same patient were identical, suggesting that each patient harbors a single strain. Computer-assisted cluster analysis of the REP-PCR DNA fingerprints showed two large clusters of isolates, one associated with simple gastritis and the other with duodenal ulcer disease. Cluster analysis of REP-PCR DNA fingerprints of H. pylori strains suggests that duodenal ulcer isolates, as a group, are more similar to one another and different from gastritis isolates. These results suggest that disease-specific strains may exist.

  6. Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis

    Directory of Open Access Journals (Sweden)

    Nilsson Anders

    2010-03-01

    Full Text Available Abstract Background The histone-like protein Hc2 binds DNA in Chlamydia trachomatis and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the hctB gene, which encodes Hc2, were compared. Results This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in Bordetella but was now also found in other genera, including Burkholderia, Herminiimonas, Minibacterium and Ralstonia. Sequence determination resulted in 41 hctB variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements. Conclusions The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the Chlamydiacae. The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis.

  7. Nanomechanical molecular devices made of DNA origami.

    Science.gov (United States)

    Kuzuya, Akinori; Ohya, Yuichi

    2014-06-17

    different cell lines, open their shell, and bind to their target. An intelligent DNA origami "sheath" can mimic the function of suppressors in a transcription regulation system to control the expression of a loaded gene. DNA origami "rolls" are created to construct precisely arranged plasmonic devices with metal nanoparticles. All of their functions are derived from their nanomechanical movement, which is programmable by designing the DNA sequence or by using the significant repository of technical achievements in nucleic acid chemistry. Finally, some studies on detailed structural parameters of DNA origami or their mechanical properties in nanoscale are discussed, which may be useful and inspiring for readers who intend to design new nanomechanical DNA origami devices.

  8. DNA: The Strand that Connects Us All

    Energy Technology Data Exchange (ETDEWEB)

    Kaplan, Matt [Univ. of Arizona, Tucson, AZ (United States). Genetics Core Facility

    2011-03-29

    Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. Dr. Kaplan starts with a short general review of human genetics and the biology behind this form of DNA testing. He looks at how DNA testing is performed and how samples are processed in the University of Arizona laboratory. He also examines examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, he describes the newest project in the UA laboratory, the DNA Shoah Project.

  9. Repair of abasic sites in DNA

    Energy Technology Data Exchange (ETDEWEB)

    Dianov, Grigory L.; Sleeth, Kate M.; Dianova, Irina I.; Allinson, Sarah L

    2003-10-29

    Repair of both normal and reduced AP sites is activated by AP endonuclease, which recognizes and cleaves a phosphodiester bond 5' to the AP site. For a short period of time an incised AP site is occupied by poly(ADP-ribose) polymerase and then DNA polymerase {beta} adds one nucleotide into the repair gap and simultaneously removes the 5'-sugar phosphate. Finally, the DNA ligase III/XRCC1 complex accomplishes repair by sealing disrupted DNA ends. However, long-patch BER pathway, which is involved in the removal of reduced abasic sites, requires further DNA synthesis resulting in strand displacement and the generation of a damage-containing flap that is later removed by the flap endonuclease. Strand-displacement DNA synthesis is accomplished by DNA polymerase {delta}/{epsilon} and DNA ligase I restores DNA integrity. DNA synthesis by DNA polymerase {delta}/{epsilon} is dependent on proliferating cell nuclear antigen, which also stimulates the DNA ligase I and flap endonuclease. These repair events are supported by multiple protein-protein interactions.

  10. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  11. Inhibiting DNA Polymerases as a Therapeutic Intervention against Cancer

    Directory of Open Access Journals (Sweden)

    Anthony J. Berdis

    2017-11-01

    Full Text Available Inhibiting DNA synthesis is an important therapeutic strategy that is widely used to treat a number of hyperproliferative diseases including viral infections, autoimmune disorders, and cancer. This chapter describes two major categories of therapeutic agents used to inhibit DNA synthesis. The first category includes purine and pyrmidine nucleoside analogs that directly inhibit DNA polymerase activity. The second category includes DNA damaging agents including cisplatin and chlorambucil that modify the composition and structure of the nucleic acid substrate to indirectly inhibit DNA synthesis. Special emphasis is placed on describing the molecular mechanisms of these inhibitory effects against chromosomal and mitochondrial DNA polymerases. Discussions are also provided on the mechanisms associated with resistance to these therapeutic agents. A primary focus is toward understanding the roles of specialized DNA polymerases that by-pass DNA lesions produced by DNA damaging agents. Finally, a section is provided that describes emerging areas in developing new therapeutic strategies targeting specialized DNA polymerases.

  12. Hemispheric Asymmetries in Repetition Enhancement and Suppression Effects in the Newborn Brain.

    Science.gov (United States)

    Bouchon, Camillia; Nazzi, Thierry; Gervain, Judit

    2015-01-01

    The repeated presentation of stimuli typically attenuates neural responses (repetition suppression) or, less commonly, increases them (repetition enhancement) when stimuli are highly complex, degraded or presented under noisy conditions. In adult functional neuroimaging research, these repetition effects are considered as neural correlates of habituation. The development and respective functional significance of these effects in infancy remain largely unknown. This study investigates repetition effects in newborns using functional near-infrared spectroscopy, and specifically the role of stimulus complexity in evoking a repetition enhancement vs. a repetition suppression response, following up on Gervain et al. (2008). In that study, abstract rule-learning was found at birth in cortical areas specific to speech processing, as evidenced by a left-lateralized repetition enhancement of the hemodynamic response to highly variable speech sequences conforming to a repetition-based ABB artificial grammar, but not to a random ABC grammar. Here, the same paradigm was used to investigate how simpler stimuli (12 different sequences per condition as opposed to 140), and simpler presentation conditions (blocked rather than interleaved) would influence repetition effects at birth. Results revealed that the two grammars elicited different dynamics in the two hemispheres. In left fronto-temporal areas, we reproduce the early perceptual discrimination of the two grammars, with ABB giving rise to a greater response at the beginning of the experiment than ABC. In addition, the ABC grammar evoked a repetition enhancement effect over time, whereas a stable response was found for the ABB grammar. Right fronto-temporal areas showed neither initial discrimination, nor change over time to either pattern. Taken together with Gervain et al. (2008), this is the first evidence that manipulating methodological factors influences the presence or absence of neural repetition enhancement effects in

  13. Hemispheric Asymmetries in Repetition Enhancement and Suppression Effects in the Newborn Brain.

    Directory of Open Access Journals (Sweden)

    Camillia Bouchon

    Full Text Available The repeated presentation of stimuli typically attenuates neural responses (repetition suppression or, less commonly, increases them (repetition enhancement when stimuli are highly complex, degraded or presented under noisy conditions. In adult functional neuroimaging research, these repetition effects are considered as neural correlates of habituation. The development and respective functional significance of these effects in infancy remain largely unknown.This study investigates repetition effects in newborns using functional near-infrared spectroscopy, and specifically the role of stimulus complexity in evoking a repetition enhancement vs. a repetition suppression response, following up on Gervain et al. (2008. In that study, abstract rule-learning was found at birth in cortical areas specific to speech processing, as evidenced by a left-lateralized repetition enhancement of the hemodynamic response to highly variable speech sequences conforming to a repetition-based ABB artificial grammar, but not to a random ABC grammar.Here, the same paradigm was used to investigate how simpler stimuli (12 different sequences per condition as opposed to 140, and simpler presentation conditions (blocked rather than interleaved would influence repetition effects at birth.Results revealed that the two grammars elicited different dynamics in the two hemispheres. In left fronto-temporal areas, we reproduce the early perceptual discrimination of the two grammars, with ABB giving rise to a greater response at the beginning of the experiment than ABC. In addition, the ABC grammar evoked a repetition enhancement effect over time, whereas a stable response was found for the ABB grammar. Right fronto-temporal areas showed neither initial discrimination, nor change over time to either pattern.Taken together with Gervain et al. (2008, this is the first evidence that manipulating methodological factors influences the presence or absence of neural repetition enhancement

  14. Translation of Syntactic Repetitions as Formal-Aesthetic Marker in Das Brot

    Directory of Open Access Journals (Sweden)

    Rosyidah

    2017-03-01

    Full Text Available Translating repetition as a formal-aesthetic marker in a literary text is a hard task and challenge for translators. The topic of this study is translation of syntactic repetition as formal-aesthetic marker in literary text. The problems examined include: (1 the syntactic repetitions in the source text and (2 the strategies to translate these repetitions carried out by the students. This is a case study with a qualitative approach which is aimed to describe the syntactic repetitions as formal aesthetic markers in the German short story Das Brot written by Wolfgang Borchert and to explain the strategies used by Indonesian students to translate the syntactic repetitions. The research data are repetitive sentences gained from the German short story and from the translated versions done by 60 students. The analysis was carried out interactively and sociosemiotically. The results show that there were repetitions at the sentence level including sentence parts, sentences and content repetition in the source text. The strategies used by the students to translate the repetitions of sentence part and sentence were exact preservation and modified preservation with reduction, implicitation and addition of extra words, avoidance with deletion, explicitation, implicitation, nominalization, and synonymy. In the meantime, content repetitions were translated using the strategy of exact preservation and preservation with modification by adding extra words and using role-based terms of address. Thus, the results lead to two new variations of modified preservation, namely preservation by adding extra words and by changing addressing terms and one new variation of avoidance that is explicitation.

  15. DNA Damage and Pulmonary Hypertension

    Science.gov (United States)

    Ranchoux, Benoît; Meloche, Jolyane; Paulin, Roxane; Boucherat, Olivier; Provencher, Steeve; Bonnet, Sébastien

    2016-01-01

    Pulmonary hypertension (PH) is defined by a mean pulmonary arterial pressure over 25 mmHg at rest and is diagnosed by right heart catheterization. Among the different groups of PH, pulmonary arterial hypertension (PAH) is characterized by a progressive obstruction of distal pulmonary arteries, related to endothelial cell dysfunction and vascular cell proliferation, which leads to an increased pulmonary vascular resistance, right ventricular hypertrophy, and right heart failure. Although the primary trigger of PAH remains unknown, oxidative stress and inflammation have been shown to play a key role in the development and progression of vascular remodeling. These factors are known to increase DNA damage that might favor the emergence of the proliferative and apoptosis-resistant phenotype observed in PAH vascular cells. High levels of DNA damage were reported to occur in PAH lungs and remodeled arteries as well as in animal models of PH. Moreover, recent studies have demonstrated that impaired DNA-response mechanisms may lead to an increased mutagen sensitivity in PAH patients. Finally, PAH was linked with decreased breast cancer 1 protein (BRCA1) and DNA topoisomerase 2-binding protein 1 (TopBP1) expression, both involved in maintaining genome integrity. This review aims to provide an overview of recent evidence of DNA damage and DNA repair deficiency and their implication in PAH pathogenesis. PMID:27338373

  16. DNA testing in homicide investigations.

    Science.gov (United States)

    Prahlow, Joseph A; Cameron, Thomas; Arendt, Alexander; Cornelis, Kenneth; Bontrager, Anthony; Suth, Michael S; Black, Lisa; Tobey, Rebbecca; Pollock, Sharon; Stur, Shawn; Cotter, Kenneth; Gabrielse, Joel

    2017-10-01

    Objectives With the widespread use of DNA testing, police, death investigators, and attorneys need to be aware of the capabilities of this technology. This review provides an overview of scenarios where DNA evidence has played a major role in homicide investigations in order to highlight important educational issues for police, death investigators, forensic pathologists, and attorneys. Methods This was a nonrandom, observational, retrospective study. Data were obtained from the collective files of the authors from casework during a 15-year period, from 2000 through 2014. Results A series of nine scenarios, encompassing 11 deaths, is presented from the standpoint of the police and death investigation, the forensic pathology autopsy performance, the subsequent DNA testing of evidence, and, ultimately, the final adjudication of cases. Details of each case are presented, along with a discussion that focuses on important aspects of sample collection for potential DNA testing, especially at the crime scene and the autopsy. The presentation highlights the diversity of case and evidence types in which DNA testing played a valuable role in the successful prosecution of the case. Conclusions By highlighting homicides where DNA testing contributed to the successful adjudication of cases, police, death investigators, forensic pathologists, and attorneys will be better informed regarding the types of evidence and situations where such testing is of potential value.

  17. DNA mismatch repair deficiency in sporadic colorectal cancer and Lynch Syndrome

    OpenAIRE

    Poulogiannis , George; Frayling , Ian; Arends , Mark

    2009-01-01

    Abstract DNA mismatch repair (MMR) deficiency is one of the best understood forms of genetic instability in colorectal cancer (CRC), and is characterised by the loss of function of the MMR pathway. Failure to repair replication-associated errors due to a defective MMR system allows persistence of mismatch mutations all over the genome, but especially in regions of repetitive DNA known as microsatellites, giving rise to the phenomenon of microsatellite instability (MSI). A high freq...

  18. Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

    DEFF Research Database (Denmark)

    Ziegler, J.O.; Wälther, M.; Linzer, T.R.

    2009-01-01

    Microsatellites are DNA-fragments containing short repetitive motifs with 2-10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during...... on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available....

  19. Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

    Czech Academy of Sciences Publication Activity Database

    Koo, D.H.; Tiwari, V.K.; Hřibová, Eva; Doležel, Jaroslav; Friebe, B.; Gill, B.S.

    2016-01-01

    Roč. 148, č. 4 (2016), s. 314-321 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : in-situ hybridization * chromosome addition lines * resistance genes lr57 * repetitive dna * triticum-ovatum * powdery mildew * plant genome * bread wheat * leaf rust * identification * Aegilops geniculata * Chromosome identification * Fluorescence in situ hybridization * Satellite DNA * Wheat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

  20. Single DNA denaturation and bubble dynamics

    DEFF Research Database (Denmark)

    Metzler, Ralf; Ambjörnsson, Tobias; Hanke, Andreas

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration......, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments...... for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation...

  1. Comparative study of five different DNA fingerprint techniques for molecular typing of Streptococcus pneumoniae strains

    NARCIS (Netherlands)

    P.W.M. Hermans (Peter); M. Sluijter (Marcel); T. Hoogenboezem (Theo); H. Heersma; A.F. van Belkum (Alex); R. de Groot (Ronald)

    1995-01-01

    textabstractThe aim of this study was to identify the strengths and weaknesses of five DNA fingerprint methods for epidemiological typing of Streptococcus pneumoniae. We investigated the usefulness of (i) ribotyping, (ii) BOX fingerprinting with the BOX repetitive sequence of S.

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

    Science.gov (United States)

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

    2018-02-01

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

  3. Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development.

    Science.gov (United States)

    Sun, Cheng; Wyngaard, Grace; Walton, D Brian; Wichman, Holly A; Mueller, Rachel Lockridge

    2014-03-11

    Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution--some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 - 75 Gb, 12-74 Gb of which are lost from pre-somatic cell lineages at germline--soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.

  4. Repetitive Behavior in Rubinstein-Taybi Syndrome: Parallels with Autism Spectrum Phenomenology

    Science.gov (United States)

    Waite, Jane; Moss, Joanna; Beck, Sarah R.; Richards, Caroline; Nelson, Lisa; Arron, Kate; Burbidge, Cheryl; Berg, Katy; Oliver, Chris

    2015-01-01

    Syndrome specific repetitive behavior profiles have been described previously. A detailed profile is absent for Rubinstein-Taybi syndrome (RTS). The Repetitive Behaviour Questionnaire and Social Communication Questionnaire were completed for children and adults with RTS (N = 87), Fragile-X (N = 196) and Down (N = 132) syndromes, and individuals…

  5. High-speed repetitive pellet injector prototype for magnetic confinement fusion devices

    International Nuclear Information System (INIS)

    Frattolillo, A.; Gasparotto, M.; Migliori, S.; Angelone, G.; Baldarelli, M.; Scaramuzzi, F.; Ronci, G.; Reggiori, A.; Riva, G.; Carlevaro, R.; Daminelli, G.B.

    1992-01-01

    The design of a test facility aimed at demonstrating the feasibility of high-speed repetitive acceleration of solid D 2 pellets for fusion applications, developed in a collaboration between Oak Ridge National Laboratory and ENEA Frascati, is presented. The results of tests performed at the CNPM/CNR on the piston wear in a repetitively operating two-stage gun are also reported

  6. The Function of Repeating: The Relation between Word Class and Repetition Type in Developmental Stuttering

    Science.gov (United States)

    Buhr, Anthony P.; Jones, Robin M.; Conture, Edward G.; Kelly, Ellen M.

    2016-01-01

    Background: It is already known that preschool-age children who stutter (CWS) tend to stutter on function words at the beginning of sentences. It is also known that phonological errors potentially resulting in part-word repetitions tend to occur on content words. However, the precise relation between word class and repetition type in preschool-age…

  7. Functional dissociations in top-down control dependent neural repetition priming.

    NARCIS (Netherlands)

    Klaver, P.; Schnaidt, M.; Fell, J.; Ruhlmann, J.; Elger, C.E.; Fernandez, G.S.E.

    2007-01-01

    Little is known about the neural mechanisms underlying top-down control of repetition priming. Here, we use functional brain imaging to investigate these mechanisms. Study and repetition tasks used a natural/man-made forced choice task. In the study phase subjects were required to respond to either

  8. Target-to-Target Repetition Cost and Location Negative Priming Are Dissociable: Evidence for Different Mechanisms

    Science.gov (United States)

    Chao, Hsuan-Fu

    2011-01-01

    In a location-selection task, the repetition of a prior distractor location as the target location would slow down the response. This effect is termed the location negative priming (NP) effect. Recently, it has been demonstrated that repetition of a prior target location as the current target location would also slow down response. Because such…

  9. Changes of the Prefrontal EEG (Electroencephalogram) Activities According to the Repetition of Audio-Visual Learning.

    Science.gov (United States)

    Kim, Yong-Jin; Chang, Nam-Kee

    2001-01-01

    Investigates the changes of neuronal response according to a four time repetition of audio-visual learning. Obtains EEG data from the prefrontal (Fp1, Fp2) lobe from 20 subjects at the 8th grade level. Concludes that the habituation of neuronal response shows up in repetitive audio-visual learning and brain hemisphericity can be changed by…

  10. Repetition suppression in ventral visual cortex is diminished as a function of increasing autistic traits

    NARCIS (Netherlands)

    Ewbank, M.P.; Rhodes, G.; von dem Hagen, E.A.H.; Powell, T.E.; Bright, N.; Stoyanova, R.Z.; Baron-Cohen, S.; Calder, A.J.

    2015-01-01

    Repeated viewing of a stimulus causes a change in perceptual sensitivity, known as a visual aftereffect. Similarly, in neuroimaging, repetitions of the same stimulus result in a reduction in the neural response, known as repetition suppression (RS). Previous research shows that aftereffects for

  11. Cumulative Repetition Effects across Multiple Readings of a Word: Evidence from Eye Movements

    Science.gov (United States)

    Kamienkowski, Juan E.; Carbajal, M. Julia; Bianchi, Bruno; Sigman, Mariano; Shalom, Diego E.

    2018-01-01

    When a word is read more than once, reading time generally decreases in the successive occurrences. This Repetition Effect has been used to study word encoding and memory processes in a variety of experimental measures. We studied naturally occurring repetitions of words within normal texts (stories of around 3,000 words). Using linear mixed…

  12. Electrophysiological Repetition Effects in Persons with Mild Cognitive Impairment depend upon Working Memory Demand.

    Science.gov (United States)

    Broster, Lucas S; Jenkins, Shonna L; Holmes, Sarah D; Edwards, Matthew G; Jicha, Gregory A; Jiang, Yang

    2018-05-07

    Forms of implicit memory, including repetition effects, are preserved relative to explicit memory in clinical Alzheimer's disease. Consequently, cognitive interventions for persons with Alzheimer's disease have been developed that leverage this fact. However, despite the clinical robustness of behavioral repetition effects, altered neural mechanisms of repetition effects are studied as biomarkers of both clinical Alzheimer's disease and pre-morbid Alzheimer's changes in the brain. We hypothesized that the clinical preservation of behavioral repetition effects results in part from concurrent operation of discrete memory systems. We developed two experiments that included probes of emotional repetition effects differing in that one included an embedded working memory task. We found that neural repetition effects manifested in patients with amnestic mild cognitive impairment, the earliest form of clinical Alzheimer's disease, during emotional working memory tasks, but they did not manifest during the task that lacked the embedded working memory manipulation. Specifically, the working memory task evoked neural repetition effects in the P600 time-window, but the same neural mechanism was only minimally implicated in the task without a working memory component. We also found that group differences in behavioral repetition effects were smaller in the experiment with a working memory task. We suggest that cross-domain cognitive challenge can expose "defunct" neural capabilities of individuals with amnestic mild cognitive impairment. Copyright © 2018. Published by Elsevier Ltd.

  13. Relationship between Subtypes of Restricted and Repetitive Behaviors and Sleep Disturbance in Autism Spectrum Disorder

    Science.gov (United States)

    Hundley, Rachel J.; Shui, Amy; Malow, Beth A.

    2016-01-01

    We examined the association of two types of restricted and repetitive behaviors, repetitive sensory motor (RSM) and insistence on sameness (IS), with sleep problems in children with autism spectrum disorder (ASD). Participants included 532 children (aged 2-17) who participated in the Autism Speaks Autism Treatment Network research registry.…

  14. A Framework for Crosslinguistic Nonword Repetition Tests: Effects of Bilingualism and Socioeconomic Status on Children's Performance

    Science.gov (United States)

    Chiat, Shula; Polišenská, Kamila

    2016-01-01

    Purpose: As a recognized indicator of language impairment, nonword repetition has unique potential for distinguishing language impairment from difficulties due to limited experience and knowledge of a language. This study focused on a new Crosslinguistic Nonword Repetition framework, comprising 3 tests that vary the phonological characteristics of…

  15. Task Repetition Effects on L1 Use in EFL Child Task-Based Interaction

    Science.gov (United States)

    Azkarai, Agurtzane; García Mayo, María del Pilar

    2017-01-01

    Research has shown that tasks provide second language (L2) learners with many opportunities to learn the L2. Task repetition has been claimed to benefit L2 learning since familiarity with procedure and/or content gives learners the chance to focus on more specific aspects of language. Most research on task repetition has focused on adult…

  16. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Generation of µW level plateau harmonics at high repetition rate.

    Science.gov (United States)

    Hädrich, S; Krebs, M; Rothhardt, J; Carstens, H; Demmler, S; Limpert, J; Tünnermann, A

    2011-09-26

    The process of high harmonic generation allows for coherent transfer of infrared laser light to the extreme ultraviolet spectral range opening a variety of applications. The low conversion efficiency of this process calls for optimization or higher repetition rate intense ultrashort pulse lasers. Here we present state-of-the-art fiber laser systems for the generation of high harmonics up to 1 MHz repetition rate. We perform measurements of the average power with a calibrated spectrometer and achieved µW harmonics between 45 nm and 61 nm (H23-H17) at a repetition rate of 50 kHz. Additionally, we show the potential for few-cycle pulses at high average power and repetition rate that may enable water-window harmonics at unprecedented repetition rate. © 2011 Optical Society of America

  18. Passing crisis and emergency risk communications: the effects of communication channel, information type, and repetition.

    Science.gov (United States)

    Edworthy, Judy; Hellier, Elizabeth; Newbold, Lex; Titchener, Kirsteen

    2015-05-01

    Three experiments explore several factors which influence information transmission when warning messages are passed from person to person. In Experiment 1, messages were passed down chains of participants using five different modes of communication. Written communication channels resulted in more accurate message transmission than verbal. In addition, some elements of the message endured further down the chain than others. Experiment 2 largely replicated these effects and also demonstrated that simple repetition of a message eliminated differences between written and spoken communication. In a final field experiment, chains of participants passed information however they wanted to, with the proviso that half of the chains could not use telephones. Here, the lack of ability to use a telephone did not affect accuracy, but did slow down the speed of transmission from the recipient of the message to the last person in the chain. Implications of the findings for crisis and emergency risk communication are discussed. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  19. Technique for long and absolute distance measurement based on laser pulse repetition frequency sweeping

    Science.gov (United States)

    Castro Alves, D.; Abreu, Manuel; Cabral, A.; Jost, Michael; Rebordão, J. M.

    2017-11-01

    In this work we present a technique to perform long and absolute distance measurements based on mode-locked diode lasers. Using a Michelson interferometer, it is possible to produce an optical cross-correlation between laser pulses of the reference arm with the pulses from the measurement arm, adjusting externally their degree of overlap either changing the pulse repetition frequency (PRF) or the position of the reference arm mirror for two (or more) fixed frequencies. The correlation of the travelling pulses for precision distance measurements relies on ultra-short pulse durations, as the uncertainty associated to the method is dependent on the laser pulse width as well as on a highly stable PRF. Mode-locked Diode lasers are a very appealing technology for its inherent characteristics, associated to compactness, size and efficiency, constituting a positive trade-off with regard to other mode-locked laser sources. Nevertheless, main current drawback is the non-availability of frequency-stable laser diodes. The laser used is a monolithic mode-locked semiconductor quantum-dot (QD) laser. The laser PRF is locked to an external stabilized RF reference. In this work we will present some of the preliminary results and discuss the importance of the requirements related to laser PRF stability in the final metrology system accuracy.

  20. Modeling age differences in effects of pair repetition and proactive interference using a single parameter.

    Science.gov (United States)

    Stephens, Joseph D W; Overman, Amy A

    2018-02-01

    In this article, we apply the REM model (Shiffrin & Steyvers, 1997) to age differences in associative memory. Using Criss and Shiffrin's (2005) associative version of REM, we show that in a task with pairs repeated across 2 study lists, older adults' reduced benefit of pair repetition can be produced by a general reduction in the diagnosticity of information stored in memory. This reduction can be modeled similarly well by reducing the overall distinctiveness of memory features, or by reducing the accuracy of memory encoding. We report a new experiment in which pairs are repeated across 3 study lists and extend the model accordingly. Finally, we extend the model to previously reported data using the same task paradigm, in which the use of a high-association strategy introduced proactive interference effects in young adults but not older adults. Reducing the diagnosticity of information in memory also reduces the proactive interference effect. Taken together, the modeling and empirical results reported here are consistent with the claim that some age differences that appear to be specific to associative information can be produced via general degradation of information stored in memory. The REM model provides a useful framework for examining age differences in memory as well as harmonizing seemingly conflicting prior modeling approaches for the associative deficit. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  1. Experimental study of plume induced by nanosecond repetitively pulsed spark microdischarges in air at atmospheric pressure

    Science.gov (United States)

    Orriere, Thomas; Benard, Nicolas; Moreau, Eric; Pai, David

    2016-09-01

    Nanosecond repetitively pulsed (NRP) spark discharges have been widely studied due to their high chemical reactivity, low gas temperature, and high ionization efficiency. They are useful in many research areas: nanomaterials synthesis, combustion, and aerodynamic flow control. In all of these fields, particular attention has been devoted to chemical species transport and/or hydrodynamic and thermal effects for applications. The aim of this study is to generate an electro-thermal plume by combining an NRP spark microdischarge in a pin-to-pin configuration with a third DC-biased electrode placed a few centimeters away. First, electrical characterization and optical emission spectroscopy were performed to reveal important plasma processes. Second, particle image velocimetry was combined with schlieren photography to investigate the main characteristics of the generated flow. Heating processes are measured by using the N2(C ->B) (0,2) and (1,3) vibrational bands, and effects due to the confinement of the discharge are described. Moreover, the presence of atomic ions N+ and O+ is discussed. Finally, the electro-thermal plume structure is characterized by a flow velocity around 1.8 m.s-1, and the thermal kernel has a spheroidal shape.

  2. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes.

    Directory of Open Access Journals (Sweden)

    Duílio M Z de A Silva

    Full Text Available Supernumerary (B chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.

  3. Auditory phonological priming in children and adults during word repetition

    Science.gov (United States)

    Cleary, Miranda; Schwartz, Richard G.

    2004-05-01

    Short-term auditory phonological priming effects involve changes in the speed with which words are processed by a listener as a function of recent exposure to other similar-sounding words. Activation of phonological/lexical representations appears to persist beyond the immediate offset of a word, influencing subsequent processing. Priming effects are commonly cited as demonstrating concurrent activation of word/phonological candidates during word identification. Phonological priming is controversial, the direction of effects (facilitating versus slowing) varying with the prime-target relationship. In adults, it has repeatedly been demonstrated, however, that hearing a prime word that rhymes with the following target word (ISI=50 ms) decreases the time necessary to initiate repetition of the target, relative to when the prime and target have no phonemic overlap. Activation of phonological representations in children has not typically been studied using this paradigm, auditory-word + picture-naming tasks being used instead. The present study employed an auditory phonological priming paradigm being developed for use with normal-hearing and hearing-impaired children. Initial results from normal-hearing adults replicate previous reports of faster naming times for targets following a rhyming prime word than for targets following a prime having no phonemes in common. Results from normal-hearing children will also be reported. [Work supported by NIH-NIDCD T32DC000039.

  4. Fusion neutron generation by high-repetitive target injection

    International Nuclear Information System (INIS)

    Kitagawa, Yoneyoshi

    2015-01-01

    Pellet injection and repetitive laser illumination are key technologies for realizing inertial fusion energy. The Graduate School for the Creation of New Photonics Industries, Hamamatsu Photonics K. K. and Toyota Motor Corporation demonstrate the pellet injection, counter laser beams' engagement and neutron generation. Deuterated polystyrene (CD) bead pellets, after free-falling for a distance of 18 cm at 1 Hz, are successfully engaged by two counter laser beams from a diode-pumped, ultra-intense laser HAMA. The laser energy, pulse duration, wavelength and the intensity are 0.63 J per beam, 104 fs, 811 nm and 4.7 x 10 18 W/cm 2 , respectively. The irradiated pellets produce D (D, n) 3 He-reacted neutrons with a maximum yield of 9.5 x 10 4 /4π sr/shot. A straight channel with 10 μm-diameter is found through the beads. The pellet size is 1 mm. The results indicate potentially useful technologies for the next step in realizing inertial fusion energy. The results are reviewed as well as some oversea activities. (author)

  5. LANGUAGE REPETITION AND SHORT-TERM MEMORY: AN INTEGRATIVE FRAMEWORK

    Directory of Open Access Journals (Sweden)

    Steve eMajerus

    2013-07-01

    Full Text Available Short-term maintenance of verbal information is a core factor of language repetition, especially when reproducing multiple or unfamiliar stimuli. Many models of language processing locate the verbal short-term maintenance function in the left posterior superior temporo-parietal area and its connections with the inferior frontal gyrus. However, research in the field of short-term memory has implicated bilateral fronto-parietal networks, involved in attention and serial order processing, as being critical for the maintenance and reproduction of verbal sequences. We present here an integrative framework aimed at bridging research in the language processing and short-term memory fields. This framework considers verbal short-term maintenance as an emergent function resulting from synchronized and integrated activation in dorsal and ventral language processing networks as well as fronto-parietal attention and serial order processing networks. To-be-maintained item representations are temporarily activated in the dorsal and ventral language processing networks, novel phoneme and word serial order information is proposed to be maintained via a right fronto-parietal serial order processing network, and activation in these different networks is proposed to be coordinated and maintained via a left fronto-parietal attention processing network. This framework provides new perspectives for our understanding of information maintenance at the nonword-, word- and sentence-level as well as of verbal maintenance deficits in case of brain injury.

  6. Language repetition and short-term memory: an integrative framework.

    Science.gov (United States)

    Majerus, Steve

    2013-01-01

    Short-term maintenance of verbal information is a core factor of language repetition, especially when reproducing multiple or unfamiliar stimuli. Many models of language processing locate the verbal short-term maintenance function in the left posterior superior temporo-parietal area and its connections with the inferior frontal gyrus. However, research in the field of short-term memory has implicated bilateral fronto-parietal networks, involved in attention and serial order processing, as being critical for the maintenance and reproduction of verbal sequences. We present here an integrative framework aimed at bridging research in the language processing and short-term memory fields. This framework considers verbal short-term maintenance as an emergent function resulting from synchronized and integrated activation in dorsal and ventral language processing networks as well as fronto-parietal attention and serial order processing networks. To-be-maintained item representations are temporarily activated in the dorsal and ventral language processing networks, novel phoneme and word serial order information is proposed to be maintained via a right fronto-parietal serial order processing network, and activation in these different networks is proposed to be coordinated and maintained via a left fronto-parietal attention processing network. This framework provides new perspectives for our understanding of information maintenance at the non-word-, word- and sentence-level as well as of verbal maintenance deficits in case of brain injury.

  7. Variation and Repetition in the Spelling of Young Children

    Science.gov (United States)

    Treiman, Rebecca; Decker, Kristina; Kessler, Brett; Pollo, Tatiana

    2015-01-01

    A number of investigators have suggested that young children, even those do not yet represent the phonological forms of words in their spellings, tend to use different strings of letters for different words. However, empirical evidence that children possess a concept of between-word variation has been weak. In a study by Pollo, Kessler, and Treiman (2009), in fact, prephonological spellers were more likely to write different words in the same way than would be expected on the basis of chance, not less likely. In the present study, preschool-age prephonological and phonological spellers showed a tendency to repeat spellings and parts of spellings that they had recently used. However, even prephonological spellers (mean age 4 years, 8 months) showed more repetition when spelling the same word twice in succession than when spelling different words. The results suggest that children who have not yet learned to use writing to represent the sounds of speech show some knowledge that writing represents words and should thus vary to show differences between them. The results further suggest that in spelling, as in other domains, children have a tendency to repeat recent behaviors. PMID:25637713

  8. Use of repetitive transcranial magnetic stimulation for treatment in psychiatry.

    Science.gov (United States)

    Aleman, André

    2013-08-01

    The potential of noninvasive neurostimulation by repetitive transcranial magnetic stimulation (rTMS) for improving psychiatric disorders has been studied increasingly over the past two decades. This is especially the case for major depression and for auditory-verbal hallucinations in schizophrenia. The present review briefly describes the background of this novel treatment modality and summarizes evidence from clinical trials into the efficacy of rTMS for depression and hallucinations. Evidence for efficacy in depression is stronger than for hallucinations, although a number of studies have reported clinically relevant improvements for hallucinations too. Different stimulation parameters (frequency, duration, location of stimulation) are discussed. There is a paucity of research into other psychiatric disorders, but initial evidence suggests that rTMS may also hold promise for the treatment of negative symptoms in schizophrenia, obsessive compulsive disorder and post-traumatic stress disorder. It can be concluded that rTMS induces alterations in neural networks relevant for psychiatric disorders and that more research is needed to elucidate efficacy and underlying mechanisms of action.

  9. [Repetitive transcranial magnetic stimulation: A potential therapy for cognitive disorders?

    Science.gov (United States)

    Nouhaud, C; Sherrard, R M; Belmin, J

    2017-03-01

    Considering the limited effectiveness of drugs treatments in cognitive disorders, the emergence of noninvasive techniques to modify brain function is very interesting. Among these techniques, repetitive transcranial magnetic stimulation (rTMS) can modulate cortical excitability and have potential therapeutic effects on cognition and behaviour. These effects are due to physiological modifications in the stimulated cortical tissue and their associated circuits, which depend on the parameters of stimulation. The objective of this article is to specify current knowledge and efficacy of rTMS in cognitive disorders. Previous studies found very encouraging results with significant improvement of higher brain functions. Nevertheless, these few studies have limits: a few patients were enrolled, the lack of control of the mechanisms of action by brain imaging, insufficiently formalized technique and variability of cognitive tests. It is therefore necessary to perform more studies, which identify statistical significant improvement and to specify underlying mechanisms of action and the parameters of use of the rTMS to offer rTMS as a routine therapy for cognitive dysfunction. Copyright © 2016 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

  10. Improved discrimination of visual stimuli following repetitive transcranial magnetic stimulation.

    Directory of Open Access Journals (Sweden)

    Michael L Waterston

    Full Text Available BACKGROUND: Repetitive transcranial magnetic stimulation (rTMS at certain frequencies increases thresholds for motor-evoked potentials and phosphenes following stimulation of cortex. Consequently rTMS is often assumed to introduce a "virtual lesion" in stimulated brain regions, with correspondingly diminished behavioral performance. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the effects of rTMS to visual cortex on subjects' ability to perform visual psychophysical tasks. Contrary to expectations of a visual deficit, we find that rTMS often improves the discrimination of visual features. For coarse orientation tasks, discrimination of a static stimulus improved consistently following theta-burst stimulation of the occipital lobe. Using a reaction-time task, we found that these improvements occurred throughout the visual field and lasted beyond one hour post-rTMS. Low-frequency (1 Hz stimulation yielded similar improvements. In contrast, we did not find consistent effects of rTMS on performance in a fine orientation discrimination task. CONCLUSIONS/SIGNIFICANCE: Overall our results suggest that rTMS generally improves or has no effect on visual acuity, with the nature of the effect depending on the type of stimulation and the task. We interpret our results in the context of an ideal-observer model of visual perception.

  11. Combinatorics on words Christoffel words and repetitions in words

    CERN Document Server

    Berstel, Jean; Reutenauer, Christophe; Saliola, Franco V

    2008-01-01

    The two parts of this text are based on two series of lectures delivered by Jean Berstel and Christophe Reutenauer in March 2007 at the Centre de Recherches Mathématiques, Montréal, Canada. Part I represents the first modern and comprehensive exposition of the theory of Christoffel words. Part II presents numerous combinatorial and algorithmic aspects of repetition-free words stemming from the work of Axel Thue-a pioneer in the theory of combinatorics on words. A beginner to the theory of combinatorics on words will be motivated by the numerous examples, and the large variety of exercises, which make the book unique at this level of exposition. The clean and streamlined exposition and the extensive bibliography will also be appreciated. After reading this book, beginners should be ready to read modern research papers in this rapidly growing field and contribute their own research to its development. Experienced readers will be interested in the finitary approach to Sturmian words that Christoffel words offe...

  12. Embryotoxicity following repetitive maternal exposure to scorpion venom

    Directory of Open Access Journals (Sweden)

    BN Hmed

    2012-01-01

    Full Text Available Although it is a frequent accident in a few countries, scorpion envenomation during pregnancy remains scarcely studied. In the present study, the effects of repetitive maternal exposure to Buthus occitanus tunetanus venom are investigated and its possible embryotoxic consequences on rats. Primigravid rats received a daily intraperitoneal dose of 1 mL/kg of saline solution or 300 µg/kg of crude scorpion venom, from the 7th to the 13th day of gestation. On the 21st day, the animals were deeply anesthetized using diethyl-ether. Then, blood was collected for chemical parameter analysis. Following euthanasia, morphometric measurements were carried out. The results showed a significant increase in maternal heart and lung absolute weights following venom treatment. However, the mean placental weight per rat was significantly diminished. Furthermore, blood urea concentration was higher in exposed rats (6.97 ± 0.62 mmol/L than in those receiving saline solution (4.94 ± 0.90 mmol/L. Many organs of venom-treated rat fetuses (brain, liver, kidney and spleen were smaller than those of controls. On the contrary, fetal lungs were significantly heavier in fetuses exposed to venom (3.2 ± 0.4 g than in the others (3.0 ± 0.2 g. Subcutaneous blood clots, microphthalmia and total body and tail shortening were also observed in venom-treated fetuses. It is concluded that scorpion envenomation during pregnancy potentially causes intrauterine fetal alterations and growth impairment.

  13. Power neodymium-glass amplifier of a repetitively pulsed laser

    Energy Technology Data Exchange (ETDEWEB)

    Vinogradov, Aleksandr V; Gaganov, V E; Garanin, Sergey G; Zhidkov, N V; Krotov, V A; Martynenko, S P; Pozdnyakov, E V; Solomatin, I I [Russian Federal Nuclear Center ' All-Russian Research Institute of Experimental Physics' , Sarov, Nizhnii Novgorod region (Russian Federation)

    2011-11-30

    A neodymium-glass diode-pumped amplifier with a zigzag laser beam propagation through the active medium was elaborated; the amplifier is intended for operation in a repetitively pulsed laser. An amplifier unit with an aperture of 20 Multiplication-Sign 25 mm and a {approx}40-cm long active medium was put to a test. The energy of pump radiation amounts to 140 J at a wavelength of 806 nm for a pump duration of 550 {mu}s. The energy parameters of the amplifier were experimentally determined: the small-signal gain per pass {approx}3.2, the linear gain {approx}0.031 cm{sup -1} with a nonuniformity of its distribution over the aperture within 15%, the stored energy of 0.16 - 0.21 J cm{sup -3}. The wavefront distortions in the zigzag laser-beam propagation through the active element of the amplifier did not exceed 0.4{lambda} ({lambda} = 0.63 {mu}m is the probing radiation wavelength).

  14. Power neodymium-glass amplifier of a repetitively pulsed laser

    International Nuclear Information System (INIS)

    Vinogradov, Aleksandr V; Gaganov, V E; Garanin, Sergey G; Zhidkov, N V; Krotov, V A; Martynenko, S P; Pozdnyakov, E V; Solomatin, I I

    2011-01-01

    A neodymium-glass diode-pumped amplifier with a zigzag laser beam propagation through the active medium was elaborated; the amplifier is intended for operation in a repetitively pulsed laser. An amplifier unit with an aperture of 20 × 25 mm and a ∼40-cm long active medium was put to a test. The energy of pump radiation amounts to 140 J at a wavelength of 806 nm for a pump duration of 550 μs. The energy parameters of the amplifier were experimentally determined: the small-signal gain per pass ∼3.2, the linear gain ∼0.031 cm -1 with a nonuniformity of its distribution over the aperture within 15%, the stored energy of 0.16 - 0.21 J cm -3 . The wavefront distortions in the zigzag laser-beam propagation through the active element of the amplifier did not exceed 0.4λ (λ = 0.63 μm is the probing radiation wavelength).

  15. Repetitive transcranial magnetic stimulator with controllable pulse parameters

    Science.gov (United States)

    Peterchev, Angel V.; Murphy, David L.; Lisanby, Sarah H.

    2011-06-01

    The characteristics of transcranial magnetic stimulation (TMS) pulses influence the physiological effect of TMS. However, available TMS devices allow very limited adjustment of the pulse parameters. We describe a novel TMS device that uses a circuit topology incorporating two energy storage capacitors and two insulated-gate bipolar transistor (IGBT) modules to generate near-rectangular electric field pulses with adjustable number, polarity, duration, and amplitude of the pulse phases. This controllable pulse parameter TMS (cTMS) device can induce electric field pulses with phase widths of 10-310 µs and positive/negative phase amplitude ratio of 1-56. Compared to conventional monophasic and biphasic TMS, cTMS reduces energy dissipation up to 82% and 57% and decreases coil heating up to 33% and 41%, respectively. We demonstrate repetitive TMS trains of 3000 pulses at frequencies up to 50 Hz with electric field pulse amplitude and width variability less than the measurement resolution (1.7% and 1%, respectively). Offering flexible pulse parameter adjustment and reduced power consumption and coil heating, cTMS enhances existing TMS paradigms, enables novel research applications and could lead to clinical applications with potentially enhanced potency.

  16. Unraveling the cellular and molecular mechanisms of repetitive magnetic stimulation

    Directory of Open Access Journals (Sweden)

    Florian eMüller-Dahlhaus

    2013-12-01

    Full Text Available Despite numerous clinical studies, which have investigated the therapeutic potential of repetitive transcranial magnetic stimulation (rTMS in various brain diseases, our knowledge of the cellular and molecular mechanisms underlying rTMS-based therapies remains limited. Thus, a deeper understanding of rTMS-induced neural plasticity is required to optimize current treatment protocols. Studies in small animals or appropriate in vitro preparations (including models of brain diseases provide highly useful experimental approaches in this context. State-of-the-art electrophysiological and live-cell imaging techniques that are well established in basic neuroscience can help answering some of the major questions in the field, such as (i which neural structures are activated during TMS, (ii how does rTMS induce Hebbian plasticity, and (iii are other forms of plasticity (e.g., metaplasticity, structural plasticity induced by rTMS? We argue that data gained from these studies will support the development of more effective and specific applications of rTMS in clinical practice.

  17. Left prefrontal repetitive transcranial magnetic stimulation in schizophrenia.

    Science.gov (United States)

    Holi, Matti M; Eronen, Markku; Toivonen, Kari; Toivonen, Päivi; Marttunen, Mauri; Naukkarinen, Hannu

    2004-01-01

    In a double-blind, controlled study, we examined the therapeutic effects of high-frequency left prefrontal repetitive transcranial magnetic stimulation (rTMS) on schizophrenia symptoms. A total of 22 chronic hospitalized schizophrenia patients were randomly assigned to 2 weeks (10 sessions) of real or sham rTMS. rTMS was given with the following parameters: 20 trains of 5-second 10-Hz stimulation at 100 percent motor threshold, 30 seconds apart. Effects on positive and negative symptoms, self-reported symptoms, rough neuropsychological functioning, and hormones were assessed. Although there was a significant improvement in both groups in most of the symptom measures, no real differences were found between the groups. A decrease of more than 20 percent in the total PANSS score was found in 7 control subjects but only 1 subject from the real rTMS group. There was no change in hormone levels or neuropsychological functioning, measured by the MMSE, in either group. Left prefrontal rTMS (with the used parameters) seems to produce a significant nonspecific effect of the treatment procedure but no therapeutic effect in the most chronic and severely ill schizophrenia patients.

  18. Exploring the repetition bias in voluntary task switching.

    Science.gov (United States)

    Mittelstädt, Victor; Dignath, David; Schmidt-Ott, Magdalena; Kiesel, Andrea

    2018-01-01

    In the voluntary task-switching paradigm, participants are required to randomly select tasks. We reasoned that the consistent finding of a repetition bias (i.e., participants repeat tasks more often than expected by chance) reflects reasonable adaptive task selection behavior to balance the goal of random task selection with the goals to minimize the time and effort for task performance. We conducted two experiments in which participants were provided with variable amount of preview for the non-chosen task stimuli (i.e., potential switch stimuli). We assumed that switch stimuli would initiate some pre-processing resulting in improved performance in switch trials. Results showed that reduced switch costs due to extra-preview in advance of each trial were accompanied by more task switches. This finding is in line with the characteristics of rational adaptive behavior. However, participants were not biased to switch tasks more often than chance despite large switch benefits. We suggest that participants might avoid effortful additional control processes that modulate the effects of preview on task performance and task choice.

  19. Repetitive transcranial magnetic stimulation for hallucination in schizophrenia spectrum disorders: A meta-analysis.

    Science.gov (United States)

    Zhang, Yingli; Liang, Wei; Yang, Shichang; Dai, Ping; Shen, Lijuan; Wang, Changhong

    2013-10-05

    This study assessed the efficacy and tolerability of repetitive transcranial magnetic stimulation for treatment of auditory hallucination of patients with schizophrenia spectrum disorders. Online literature retrieval was conducted using PubMed, ISI Web of Science, EMBASE, Medline and Cochrane Central Register of Controlled Trials databases from January 1985 to May 2012. Key words were "transcranial magnetic stimulation", "TMS", "repetitive transcranial magnetic stimulation", and "hallucination". Selected studies were randomized controlled trials assessing therapeutic efficacy of repetitive transcranial magnetic stimulation for hallucination in patients with schizophrenia spectrum disorders. Experimental intervention was low-frequency repetitive transcranial magnetic stimulation in left temporoparietal cortex for treatment of auditory hallucination in schizophrenia spectrum disorders. Control groups received sham stimulation. The primary outcome was total scores of Auditory Hallucinations Rating Scale, Auditory Hallucination Subscale of Psychotic Symptom Rating Scale, Positive and Negative Symptom Scale-Auditory Hallucination item, and Hallucination Change Scale. Secondary outcomes included response rate, global mental state, adverse effects and cognitive function. Seventeen studies addressing repetitive transcranial magnetic stimulation for treatment of schizophrenia spectrum disorders were screened, with controls receiving sham stimulation. All data were completely effective, involving 398 patients. Overall mean weighted effect size for repetitive transcranial magnetic stimulation versus sham stimulation was statistically significant (MD = -0.42, 95%CI: -0.64 to -0.20, P = 0.000 2). Patients receiving repetitive transcranial magnetic stimulation responded more frequently than sham stimulation (OR = 2.94, 95%CI: 1.39 to 6.24, P = 0.005). No significant differences were found between active repetitive transcranial magnetic stimulation and sham stimulation for

  20. A clinical repetitive transcranial magnetic stimulation service in Australia: 6 years on.

    Science.gov (United States)

    Galletly, Cherrie A; Clarke, Patrick; Carnell, Benjamin L; Gill, Shane

    2015-11-01

    There is considerable research evidence for the effectiveness of repetitive transcranial magnetic stimulation in the treatment of depression. However, there is little information about its acceptability and outcomes in clinical settings. This naturalistic study reports on a clinical repetitive transcranial magnetic stimulation service that has been running in Adelaide, South Australia (SA), for 6 years. During this time, 214 complete acute courses were provided to patients with treatment-resistant Major Depressive Disorder. Patients received either sequential bilateral or right unilateral repetitive transcranial magnetic stimulation treatment involving either 18 or 20 sessions given over 6 or 4 weeks respectively. Data included patient demographic details, duration of depression, and medication at the beginning of their repetitive transcranial magnetic stimulation course. The Hamilton Depression Rating Scale was used to assess response to repetitive transcranial magnetic stimulation. Of those undergoing a first-time acute treatment course of repetitive transcranial magnetic stimulation (N = 167), 28% achieved remission, while a further 12% met the criteria for a response to treatment. Most patients (N = 123, 77%) had previously been treated with five or more antidepressant medications, and 77 (47%) had previously received electroconvulsive therapy. Referral rates remained high over the 6 years, indicating acceptance of the treatment by referring psychiatrists. There were no significant adverse events, and the treatment was generally well tolerated. In all, 41 patients (25%) had a second course of repetitive transcranial magnetic stimulation and 6 (4%) patients had a third course; 21 patients subsequently received maintenance repetitive transcranial magnetic stimulation. This naturalistic study showed that repetitive transcranial magnetic stimulation was well accepted by both psychiatrists and patients, and has good efficacy and safety. Furthermore

  1. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    Directory of Open Access Journals (Sweden)

    O'Brien Kimberly

    2008-06-01

    Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

  2. Chromosome mapping of repetitive sequences in four Serrasalmidae species (Characiformes

    Directory of Open Access Journals (Sweden)

    Leila Braga Ribeiro

    2014-01-01

    Full Text Available The Serrasalmidae family is composed of a number of commercially interesting species, mainly in the Amazon region where most of these fishes occur. In the present study, we investigated the genomic organization of the 18S and 5S rDNA and telomeric sequences in mitotic chromosomes of four species from the basal clade of the Serrasalmidae family: Colossoma macropomum, Mylossoma aureum, M. duriventre, and Piaractus mesopotamicus, in order to understand the chromosomal evolution in the family. All the species studied had diploid numbers 2n = 54 and exclusively biarmed chromosomes, but variations of the karyotypic formulas were observed. C-banding resulted in similar patterns among the analyzed species, with heterochromatic blocks mainly present in centromeric regions. The 18S rDNA mapping of C. macropomum and P. mesopotamicus revealed multiple sites of this gene; 5S rDNA sites were detected in two chromosome pairs in all species, although not all of them were homeologs. Hybridization with a telomeric probe revealed signals in the terminal portions of chromosomes in all the species and an interstitial signal was observed in one pair of C. macropomum.

  3. Influence of air flow parameters on nanosecond repetitively pulsed discharges in a pin-annular electrode configuration

    KAUST Repository

    Heitz, Sylvain A; Moeck, Jonas P; Schuller, Thierry; Veynante, Denis; Lacoste, Deanna

    2016-01-01

    The effect of various air flow parameters on the plasma regimes of nanosecond repetitively pulsed (NRP) discharges is investigated at atmospheric pressure. The two electrodes are in a pin-annular configuration, transverse to the mean flow. The voltage pulses have amplitudes up to 15 kV, a duration of 10 ns and a repetition frequency ranging from 15 to 30 kHz. The NRP corona to NRP spark (C-S) regime transition and the NRP spark to NRP corona (S-C) regime transition are investigated for different steady and harmonically oscillating flows. First, the strong effect of a transverse flow on the C-S and S-C transitions, as reported in previous studies, is verified. Second, it is shown that the azimuthal flow imparted by a swirler does not affect the regime transition voltages. Finally, the influence of low frequency harmonic oscillations of the air flow, generated by a loudspeaker, is studied. A strong effect of frequency and amplitude of the incoming flow modulation on the NRP plasma regime is observed. Results are interpreted based on the cumulative effect of the NRP discharges and an analysis of the residence times of fluid particles in the inter-electrode region. © 2016 IOP Publishing Ltd.

  4. Influence of air flow parameters on nanosecond repetitively pulsed discharges in a pin-annular electrode configuration

    KAUST Repository

    Heitz, Sylvain A

    2016-03-16

    The effect of various air flow parameters on the plasma regimes of nanosecond repetitively pulsed (NRP) discharges is investigated at atmospheric pressure. The two electrodes are in a pin-annular configuration, transverse to the mean flow. The voltage pulses have amplitudes up to 15 kV, a duration of 10 ns and a repetition frequency ranging from 15 to 30 kHz. The NRP corona to NRP spark (C-S) regime transition and the NRP spark to NRP corona (S-C) regime transition are investigated for different steady and harmonically oscillating flows. First, the strong effect of a transverse flow on the C-S and S-C transitions, as reported in previous studies, is verified. Second, it is shown that the azimuthal flow imparted by a swirler does not affect the regime transition voltages. Finally, the influence of low frequency harmonic oscillations of the air flow, generated by a loudspeaker, is studied. A strong effect of frequency and amplitude of the incoming flow modulation on the NRP plasma regime is observed. Results are interpreted based on the cumulative effect of the NRP discharges and an analysis of the residence times of fluid particles in the inter-electrode region. © 2016 IOP Publishing Ltd.

  5. Effects of multibuffer supplementation on acid-base balance and 2,3-diphosphoglycerate following repetitive anaerobic exercise.

    Science.gov (United States)

    Kraemer, W J; Gordon, S E; Lynch, J M; Pop, M E; Clark, K L

    1995-12-01

    The purpose of this investigation was to determine the effects of a 3.5-day dietary multibuffer supplement (containing predominantly inorganic phosphate, or Pi, along with bicarbonate and carnosine, i.e., PhosFuel) on repetitive (four trials separated by 2 min rest) Wingate test (WT) performances and whole blood 2,3-diphosphoglycerate (2,3-DPG) concentrations in 10 recreationally trained road cyclists (T) and 10 normally active but untrained (UT) men. A 2-week washout period was utilized between experimental sessions. Venous blood samples were obtained via cannula once before exercise (baseline), immediately post each WT, and 3 min after the final WT (recovery). The data indicate that this supplement does not affect acid-base status with following intense anaerobic exercise and does not improve repetitive WT performance. However, the supplement does enhance post-exercise levels of 2,3-DPG and the 2,3-DPG/Hb ratio in recreationally trained cyclists while improving acute recovery of peak power in these men.

  6. Bright high-repetition-rate source of narrowband extreme-ultraviolet harmonics beyond 22 eV

    Energy Technology Data Exchange (ETDEWEB)

    Wang, He [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Xu, Yiming [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Ulonska, Stefan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Robinson, Joseph S. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Ranitovic, Predrag [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Kaindl, Robert A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division

    2015-06-11

    Novel table-top sources of extreme-ultraviolet light based on high-harmonic generation yield unique insight into the fundamental properties of molecules, nanomaterials or correlated solids, and enable advanced applications in imaging or metrology. Extending high-harmonic generation to high repetition rates portends great experimental benefits, yet efficient extreme-ultraviolet conversion of correspondingly weak driving pulses is challenging. In this article, we demonstrate a highly-efficient source of femtosecond extreme-ultraviolet pulses at 50-kHz repetition rate, utilizing the ultraviolet second-harmonic focused tightly into Kr gas. In this cascaded scheme, a photon flux beyond ≈3 × 1013 s-1 is generated at 22.3 eV, with 5 × 10-5 conversion efficiency that surpasses similar harmonics directly driven by the fundamental by two orders-of-magnitude. The enhancement arises from both wavelength scaling of the atomic dipole and improved spatio-temporal phase matching, confirmed by simulations. Finally, spectral isolation of a single 72-meV-wide harmonic renders this bright, 50-kHz extreme-ultraviolet source a powerful tool for ultrafast photoemission, nanoscale imaging and other applications.

  7. Genetic Diversity in Salmonella Isolates from Ducks and their Environments in Penang, Malaysia using Enterobacterial Repetitive Intergenic Consensus

    Directory of Open Access Journals (Sweden)

    Frederick Adzitey 1, Gulam Rusul Rahmat Ali2*, Nurul Huda2 and Rosma Ahmad3

    2013-07-01

    Full Text Available A total of 107 Salmonella isolates (37 S. typhimurium, 26 S. hadar, 15 S. enteritidis, 15 S. braenderup, and 14 S. albany isolated from ducks and their environments in Penang, Malaysia were typed using enterobacterial repetitive intergenic consensus (ERIC to determine their genetic diversity. Analysis of the Salmonella strains by ERIC produced DNA fingerprints of different sizes for differentiation purposes. The DNA fingerprints or band sizes ranged from 14-8300bp for S. Typhimurium, 146-6593bp for S. hadar, 15-4929bp for S. enteritidis, 14-5142bp for S. braenderup and 7-5712bp for S. albany. Cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. typhimurium were grouped into 10 clusters and 6 singletons, S. Hadar were grouped into 3 clusters and 18 singletons, S. enteritidis were grouped into 3 clusters and 7 singletons, S. braenderup were grouped into 4 clusters and 7 singletons, and S. albany were grouped into 3 clusters and 7 singletons with discriminatory index (D ranging from 0.92-0.98. ERIC proved to be a useful typing tool for determining the genetic diversity of the duck Salmonella strains.

  8. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  9. Characterization and distribution of repetitive elements in association with genes in the human genome.

    Science.gov (United States)

    Liang, Kai-Chiang; Tseng, Joseph T; Tsai, Shaw-Jenq; Sun, H Sunny

    2015-08-01

    Repetitive elements constitute more than 50% of the human genome. Recent studies implied that the complexity of living organisms is not just a direct outcome of a number of coding sequences; the repetitive elements, which do not encode proteins, may also play a significant role. Though scattered studies showed that repetitive elements in the regulatory regions of a gene control gene expression, no systematic survey has been done to report the characterization and distribution of various types of these repetitive elements in the human genome. Sequences from 5' and 3' untranslated regions and upstream and downstream of a gene were downloaded from the Ensembl database. The repetitive elements in the neighboring of each gene were identified and classified using cross-matching implemented in the RepeatMasker. The annotation and distribution of distinct classes of repetitive elements associated with individual gene were collected to characterize genes in association with different types of repetitive elements using systems biology program. We identified a total of 1,068,400 repetitive elements which belong to 37-class families and 1235 subclasses that are associated with 33,761 genes and 57,365 transcripts. In addition, we found that the tandem repeats preferentially locate proximal to the transcription start site (TSS) of genes and the major function of these genes are involved in developmental processes. On the other hand, interspersed repetitive elements showed a tendency to be accumulated at distal region from the TSS and the function of interspersed repeat-containing genes took part in the catabolic/metabolic processes. Results from the distribution analysis were collected and used to construct a gene-based repetitive element database (GBRED; http://www.binfo.ncku.edu.tw/GBRED/index.html). A user-friendly web interface was designed to provide the information of repetitive elements associated with any particular gene(s). This is the first study focusing on the gene

  10. Effectiveness of Non-pharmacological Interventions on Stereotyped and Repetitive Behaviors in Preschool Children With Autism: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Hadi Zarafshan

    2017-03-01

    Full Text Available Objective: The present study aimed to review the literature on non-pharmacological interventions used to treat stereotyped and repetitive behaviors by a systematic method. Methods: Two authors independently performed a search strategy on Medline/PubMed, Scopus and PsycINFO on English articles published up to April 23, 2014 with relevant search keywords. We also reviewed the bibliographies of retrieved articles and conference proceedings to obtain additional citations and references. We used those articles that address any non-pharmacological interventions on reducing stereotyped and repetitive behaviors in preschool children with autism. Four independent reviewers screened relevant articles for inclusion criteria and assessed the quality of eligible articles with CONSORT checklist. Results: In our search, 664 relevant articles were found. After removing duplicates and screening based on title, abstract, and full text, 15 high quality studies were finally included in data analyses. The included articles were published from 1987 to 2013. Three studies were designed as A-B, two as A-B-A and reminders as A-B-A-B. The data and results of 3 clinical trials were synthesized; two of them were parallel randomized clinical trial and another one was designed as cross-over. Interventions were completely heterogeneous in case studies, including non-contingent auditory stimulation, response interruption and redirection, teaching the children to request assistance on the difficult tasks, family-implemented treatment for behavioral inflexibility with treatment approach, vocal or motor response interruption and redirection, brushing, water mist treatment, exposure response prevention, tangible reinforcement or social reinforcement, and music. Interventions in clinical trials included touch therapy, kata techniques training program, and aerobic exercise. Conclusions: The results of our review indicate that different kinds of non-pharmacological interventions can

  11. Actual laser removal of black soiling crust from siliceous sandstone by high pulse repetition rate equipment: effects on surface morphology

    Directory of Open Access Journals (Sweden)

    Iglesias-Campos, M. A.

    2016-03-01

    Full Text Available This research project studies the role of pulse repetition rate in laser removal of black soiling crust from siliceous sandstone, and specifically, how laser fluence correlates with high pulse repetition rates in cleaning practice. The aim is to define practical cleaning processes and determine simple techniques for evaluation based on end-users’ perspective (restorers. Spot and surface tests were made using a Q-switched Nd:YAG laser system with a wide range of pulse repetition rates (5–200 Hz, systematically analysed and compared by macrophotography, portable microscope, stereomicroscope with 3D visualizing and area roughness measurements, SEM imaging and spectrophotometry. The results allow the conclusion that for operation under high pulse repetition rates the average of total energy applied per spot on a treated surface should be attendant upon fluence values in order to provide a systematic and accurate description of an actual laser cleaning intervention.En este trabajo se estudia el papel de la frecuencia de repetición en la limpieza láser de costras de contaminación sobre una arenisca silícea, y concretamente, como se relaciona fluencia y frecuencias elevadas en una limpieza real. Se pretende definir un procedimiento práctico de limpieza y determinar técnicas sencillas de evaluación desde el punto de vista de los usuarios finales (restauradores. Para el estudio se realizaron diferentes ensayos en spot y en superficie mediante un equipo Q-switched Nd:YAG con un amplio rango de frecuencias (5–200 Hz, que se analizaron y compararon sistemáticamente mediante macrofotografía, microscopio portátil, estereomicroscopio con visualización 3D y mediciones de rugosidad en área, imágenes SEM y espectrofotometría. Los resultados permiten proponer que, al trabajar con altas frecuencias, la media de la energía total depositada por spot en la superficie debería acompañar los valores de fluencia para describir y comprender mejor una

  12. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  13. Repetitive Solid Spherical Pellet Injection and Irradiation toward the Repetitive-mode Fast-Ignition Fusion miniReactor CANDY

    International Nuclear Information System (INIS)

    HANAYAMA, Ryohei; KOMEDA, Osamu; NISHIMURA, Yasuhiko; MORI, Yoshitaka; ISHII, Katsuhiro; NAKAYAMA, Suisei; OKIHARA, Shinichiro; FUJITA, Kazuhisa; SEKINE, Takashi; SATO, Nakahiro; KAWASHIMA, Toshiyuki; KAN, Hirofumi; KURITA, Takashi; NAKAMURA, Naoki; KONDO, Takuya; FUJINE, Manabu; AZUMA, Hirozumi; HIOKI, Tatsumi; KAKENO, Mitsutaka; MOTOHIRO, Tomoyoshi

    2016-01-01

    Pellet injection and repetitive laser illumination are key technologies for realizing inertial fusion energy [1-4]. Neutron generator using lasers also requires a repeating pellet target supplier. Here we present the first demonstration of target injection and neutron generation[5]. We injected more than 1300 spherical deuterated polystyrene(C 8 D 8 ) bead pellet targets during 23 minutes at 1 Hz(Fig. 1). After the pellet targets fell for a distance of 18 cm, we applied the synchronized laser-diode-pumped ultra-intense laser HAMA. The laser intensity at the focal point is 5 x 10 18 W/cm 2 , which is high enough to generate neutrons. As a result of the irradiation, we produced 2.45-MeV DD neutrons. Figure 2 shows the neutron time-of-flight signals detected by plastic scintillators coupled to photomultipliers. The neutron energy was calculated by the time-of-flight method. The maximum neutron yield was 9.5 x 10 4 /4π sr. The result is a step toward fusion power and also suggests possible industrial neutron sources. (paper)

  14. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Yun-bo

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs.

  15. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    International Nuclear Information System (INIS)

    Shi, Yun-bo.

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs

  16. A NOR-associated repetitive element present in the genome of two Salmo species (Salmo salar and S. trutta)

    Digital Repository Service at National Institute of Oceanography (India)

    Abuin, M.; Clabby, C.; Martinez, P.; Goswami, U.; Flavin, F.; Wilkins, N.P.; Houghton, J.A.; Powell, R.; Sanchez, L.

    , internal repetition, and long direct repeats with deletions and insertions between individual units. The repetitive element was shown to have a tandem unit arrangement and was estimated to occupy between two and three percent of the Atlantic salmon genome...

  17. Repetitive plasma loads typical for ITER Type-I ELMS; simulation in QSPA Kh-50

    International Nuclear Information System (INIS)

    Tereshin, V.I.; Bandura, A.N.; Byrka, O.V.; Chebotarev, V.V.; Garkusha, I.E.; Makhlaj, V.A.; Solyakov, D.G.; Tsarenko, A.V.; Landman, I.

    2005-01-01

    exposures without formation of corrugations and pits is about 200, which does not depend on the magnitude of target heat load. Further increase of the exposures results in the corrugation structures becoming dominant. Initially the melt layer disintegrates into a set of droplets remaining at the surface. Such evolution seems to be driven by the surface tension forces within a fine network of cracks at the previously irradiated surface, in order to minimize the damaged area. Finally a stabilization of the surface pattern occurs. The onset of intensive evaporation at molten tungsten surface under the repetitive heat loads has also been studied. The evaporation can result in enhanced mass losses: increase of the heat load from 0.75 to 1.1 MJ/m 2 increases mass losses for one order of magnitude and causes bubble structures at the surface. The contribution of evaporation to the surface profile is analyzed. Due to evaporation, the erosion crater grows with the rate equal to 0.04 μm/pulse. It is obtained, that for ELM-like repetitive loads the melt motion driven by plasma pressure gradient does not contribute significantly to the erosion profile. Influence of swelling on the surface profile is also discussed. (author)

  18. Contribution of fronto-striatal regions to emotional valence and repetition under cognitive conflict.

    Science.gov (United States)

    Chun, Ji-Won; Park, Hae-Jeong; Kim, Dai Jin; Kim, Eosu; Kim, Jae-Jin

    2017-07-01

    Conflict processing mediated by fronto-striatal regions may be influenced by emotional properties of stimuli. This study aimed to examine the effects of emotion repetition on cognitive control in a conflict-provoking situation. Twenty-one healthy subjects were scanned using functional magnetic resonance imaging while performing a sequential cognitive conflict task composed of emotional stimuli. The regional effects were analyzed according to the repetition or non-repetition of cognitive congruency and emotional valence between the preceding and current trials. Post-incongruence interference in error rate and reaction time was significantly smaller than post-congruence interference, particularly under repeated positive and non-repeated positive, respectively, and post-incongruence interference, compared to post-congruence interference, increased activity in the ACC, DLPFC, and striatum. ACC and DLPFC activities were significantly correlated with error rate or reaction time in some conditions, and fronto-striatal connections were related to the conflict processing heightened by negative emotion. These findings suggest that the repetition of emotional stimuli adaptively regulates cognitive control and the fronto-striatal circuit may engage in the conflict adaptation process induced by emotion repetition. Both repetition enhancement and repetition suppression of prefrontal activity may underlie the relationship between emotion and conflict adaptation. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Word Recognition during Reading: The Interaction between Lexical Repetition and Frequency

    Science.gov (United States)

    Lowder, Matthew W.; Choi, Wonil; Gordon, Peter C.

    2013-01-01

    Memory studies utilizing long-term repetition priming have generally demonstrated that priming is greater for low-frequency words than for high-frequency words and that this effect persists if words intervene between the prime and the target. In contrast, word-recognition studies utilizing masked short-term repetition priming typically show that the magnitude of repetition priming does not differ as a function of word frequency and does not persist across intervening words. We conducted an eye-tracking while reading experiment to determine which of these patterns more closely resembles the relationship between frequency and repetition during the natural reading of a text. Frequency was manipulated using proper names that were high-frequency (e.g., Stephen) or low-frequency (e.g., Dominic). The critical name was later repeated in the sentence, or a new name was introduced. First-pass reading times and skipping rates on the critical name revealed robust repetition-by-frequency interactions such that the magnitude of the repetition-priming effect was greater for low-frequency names than for high-frequency names. In contrast, measures of later processing showed effects of repetition that did not depend on lexical frequency. These results are interpreted within a framework that conceptualizes eye-movement control as being influenced in different ways by lexical- and discourse-level factors. PMID:23283808

  20. BOLD repetition decreases in object-responsive ventral visual areas depend on spatial attention.

    Science.gov (United States)

    Eger, E; Henson, R N A; Driver, J; Dolan, R J

    2004-08-01

    Functional imaging studies of priming-related repetition phenomena have become widely used to study neural object representation. Although blood oxygenation level-dependent (BOLD) repetition decreases can sometimes be observed without awareness of repetition, any role for spatial attention in BOLD repetition effects remains largely unknown. We used fMRI in 13 healthy subjects to test whether BOLD repetition decreases for repeated objects in ventral visual cortices depend on allocation of spatial attention to the prime. Subjects performed a size-judgment task on a probe object that had been attended or ignored in a preceding prime display of 2 lateralized objects. Reaction times showed faster responses when the probe was the same object as the attended prime, independent of the view tested (identical vs. mirror image). No behavioral effect was evident from unattended primes. BOLD repetition decreases for attended primes were found in lateral occipital and fusiform regions bilaterally, which generalized across identical and mirror-image repeats. No repetition decreases were observed for ignored primes. Our results suggest a critical role for attention in achieving visual representations of objects that lead to both BOLD signal decreases and behavioral priming on repeated presentation.