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Sample records for highly repetitive sequences

  1. 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.

  2. Roles of repetitive sequences

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    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.

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

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    Yandell Mark

    2010-07-01

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

  4. High-throughput scanning of the rat genome using interspersed repetitive sequence-PCR markers.

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    Gösele, C; Hong, L; Kreitler, T; Rossmann, M; Hieke, B; Gross, U; Kramer, M; Himmelbauer, H; Bihoreau, M T; Kwitek-Black, A E; Twigger, S; Tonellato, P J; Jacob, H J; Schalkwyk, L C; Lindpaintner, K; Ganten, D; Lehrach, H; Knoblauch, M

    2000-11-01

    We report the establishment of a hybridization-based marker system for the rat genome based on the PCR amplification of interspersed repetitive sequences (IRS). Overall, 351 IRS markers were mapped within the rat genome. The IRS marker panel consists of 210 nonpolymorphic and 141 polymorphic markers that were screened for presence/absence polymorphism patterns in 38 different rat strains and substrains that are commonly used in biomedical research. The IRS marker panel was demonstrated to be useful for rapid genome screening in experimental rat crosses and high-throughput characterization of large-insert genomic library clones. Information on corresponding YAC clones is made available for this IRS marker set distributed over the whole rat genome. The two existing rat radiation hybrid maps were integrated by placing the IRS markers in both maps. The genetic and physical mapping data presented provide substantial information for ongoing positional cloning projects in the rat. Copyright 2000 Academic Press.

  5. Chromosome number9 specific repetitive DNA sequence

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    Joste, N.E.; Cram, L.S.; Hildebrand, C.E.; Jones, M.; Longmire, J.; Robinson, T.; Moyzis, R.K.

    1986-05-01

    Human repetitive DNA libraries have been constructed and various recombinant DNA clones isolated that are likely candidates for chromosome specific sequences. The first clone tested (pHuR 98; plasmid human repeat 98) was biotinylated and hybridized to human chromosomes in situ. The hybridized recombinant probe was detected with fluoresceinated avidin, and chromosomes were counter-stained with either propidium iodide or distamycin-DAPI. Specific hybridization to chromosome band 9q1 was obtained. The localization was confirmed by hybridizing radiolabeled pHuR 98 DNA to human chromosomes sorted by flow cytometry. Various methods, including orthogonal field pulsed gel electrophoresis analysis indicate that 75 kilobase blocks of this sequence are interspersed with other repetitive DNA sequences in this chromosome band. This study is the first to report a human repetitive DNA sequence uniquely localized to a specific chromosome. This clone provides an easily detected and highly specific chromosomal marker for molecular cytogenetic analyses in numerous basic research and clinical studies.

  6. Effect of time sequences in scanning algorithms on the surface temperature during corneal laser surgery with high-repetition-rate excimer laser.

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    Mrochen, Michael; Schelling, Urs; Wuellner, Christian; Donitzky, Christof

    2009-04-01

    To investigate the influence of temporal and spatial spot sequences on the ocular surface temperature increase during corneal laser surgery with a high-repetition-rate excimer laser. Institute for Refractive and Ophthalmic Surgery, Zurich, Switzerland, and WaveLight AG, Erlangen, Germany. An argon-fluoride excimer laser system working at a repetition rate of 1050 Hz was used to photoablate bovine corneas with various myopic, hyperopic, and phototherapeutic ablation profiles. The temporal distribution of ablation profiles was modified by 4 spot sequences: line, circumferential, random, and an optimized scan algorithm. The increase in ocular surface temperature was measured using an infrared camera. The maximum and mean ocular surface temperature increases depended primarily on the spatial and temporal distribution of the spots during photoablation and the amount of refractive correction. The highest temperature increases were with the line and circumferential scan sequences. Significant lower temperature increases were found with the optimized and random scan algorithms. High-repetition-rate excimer laser systems require spot sequences with optimized temporal and spatial spot distribution to minimize the increase in ocular surface temperature. An ocular surface temperature increase will always occur depending on the amount of refractive correction, the type of ablation profile, the radiant exposure, and the repetition rate of the laser system.

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

    National Research Council Canada - National Science Library

    Novák, Petr; Neumann, Pavel; Macas, Jirí

    2010-01-01

    .... Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis...

  8. Evaluation of a High-Throughput Repetitive-Sequence-Based PCR System for DNA Fingerprinting of Mycobacterium tuberculosis and Mycobacterium avium Complex Strains

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    Cangelosi, Gerard A.; Freeman, Robert J.; Lewis, Kaeryn N.; Livingston-Rosanoff, Devon; Shah, Ketan S.; Milan, Sparrow Joy; Goldberg, Stefan V.

    2004-01-01

    Repetitive-sequence-based PCR (rep-PCR) is useful for generating DNA fingerprints of diverse bacterial and fungal species. Rep-PCR amplicon fingerprints represent genomic segments lying between repetitive sequences. A commercial system that electrophoretically separates rep-PCR amplicons on microfluidic chips, and provides computer-generated readouts of results has been adapted for use with Mycobacterium species. The ability of this system to type M. tuberculosis and M. avium complex (MAC) isolates was evaluated. M. tuberculosis strains (n = 56) were typed by spoligotyping with rep-PCR as a high-resolution adjunct. Results were compared with those generated by a standard approach of spoligotyping with IS6110-targeted restriction fragment length polymorphism (IS6110-RFLP) as the high-resolution adjunct. The sample included 11 epidemiologically and genotypically linked outbreak isolates and a population-based sample of 45 isolates from recent immigrants to Seattle, Wash., from the African Horn countries of Somalia, Eritrea, and Ethiopia. Twenty isolates exhibited unique spoligotypes and were not analyzed further. Of the 36 outbreak and African Horn isolates with nonunique spoligotypes, 23 fell into four clusters identified by IS6110-RFLP and rep-PCR, with 97% concordance observed between the two methods. Both approaches revealed extensive strain heterogeneity within the African Horn sample, consistent with a predominant pattern of reactivation of latent infections in this immigrant population. Rep-PCR exhibited 89% concordance with IS1245-RFLP typing of 28 M. avium subspecies avium strains. For M. tuberculosis as well as M. avium subspecies avium, the discriminative power of rep-PCR equaled or exceeded that of RFLP. Rep-PCR also generated DNA fingerprints from M. intracellulare (n = 8) and MACx (n = 2) strains. It shows promise as a fast, unified method for high-throughput genotypic fingerprinting of multiple Mycobacterium species. PMID:15184453

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

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    Novák, Petr; Neumann, Pavel; Macas, Jirí

    2010-07-15

    The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization. We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families. Repetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences.

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

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    Macas Jiří

    2010-07-01

    Full Text Available Abstract Background The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization. Results We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families. Conclusions Repetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences.

  11. Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.).

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    He, Qunyan; Cai, Zexi; Hu, Tianhua; Liu, Huijun; Bao, Chonglai; Mao, Weihai; Jin, Weiwei

    2015-04-18

    Radish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To date, studies about repetitive elements of radish are still limited. To better understand genome structure of radish, we undertook a study to evaluate the proportion of repetitive elements and their distribution in radish. We conducted genome-wide characterization of repetitive elements in radish with low coverage genome sequencing followed by similarity-based cluster analysis. Results showed that about 31% of the genome was composed of repetitive sequences. Satellite repeats were the most dominating elements of the genome. The distribution pattern of three satellite repeat sequences (CL1, CL25, and CL43) on radish chromosomes was characterized using fluorescence in situ hybridization (FISH). CL1 was predominantly located at the centromeric region of all chromosomes, CL25 located at the subtelomeric region, and CL43 was a telomeric satellite. FISH signals of two satellite repeats, CL1 and CL25, together with 5S rDNA and 45S rDNA, provide useful cytogenetic markers to identify each individual somatic metaphase chromosome. The centromere-specific histone H3 (CENH3) has been used as a marker to identify centromere DNA sequences. One putative CENH3 (RsCENH3) was characterized and cloned from radish. Its deduced amino acid sequence shares high similarities to those of the CENH3s in Brassica species. An antibody against B. rapa CENH3, specifically stained radish centromeres. Immunostaining and chromatin immunoprecipitation (ChIP) tests with anti-BrCENH3 antibody demonstrated that both the centromere-specific retrotransposon (CR-Radish) and satellite repeat (CL1) are directly associated with RsCENH3 in radish. Proportions

  12. Hebb repetition effects for non-verbal visual sequences: determinants of sequence acquisition.

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    Johnson, Andrew J; Dygacz, Artur; Miles, Christopher

    2017-10-01

    We report four experiments premised upon the work of Horton et al. [(2008). Hebb repetition effects in visual memory: The roles of verbal rehearsal and distinctiveness. Quarterly Journal of Experimental Psychology, 61(12), 1769-1777] and Page et al. [(2013). Repetition-spacing and item-overlap effects in the Hebb repetition task. Journal of Memory and Language, 69(4), 506-526], and explore conditions under which the visual Hebb repetition effect is observed. Experiment 1 showed that repetition learning is evident when the items comprising the non-repeated (filler) sequences and the repeated (Hebb) sequences are different (no-overlap). However, learning is abolished when the filler and Hebb sequences comprise the same items (full-overlap). Learning of the repeated sequence persisted when repetition spacing was increased to six trials (Experiment 2), consistent with that shown for verbal stimuli (Page et al., 2013). In Experiment 3, it was shown that learning for the repeated sequence is accentuated when the output motor response at test is also repeated for the Hebb sequence, but only under conditions of no-overlap. In Experiment 4, repetition spacing was re-examined with a repeated motor output response (a closer methodological analogue to Page et al., 2013). Under these conditions, the gradient of Hebb repetition learning for six trial repetition intervals was markedly similar to that for three trial intervals. These findings further support the universality of the Hebb repetition effect across memory and are discussed in terms of evidence for amodality within-sequence memory.

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

    DEFF Research Database (Denmark)

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

    1994-01-01

    over all chromosomes of H. vulgare and the wild barley species H. bulbosum, H. marinum and H. murinum. Southern blot hybridization revealed different levels of polymorphism among barley species and the RFLP data were used to generate a phylogenetic tree for the genus Hordeum. Our data are in a good......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...

  14. Genome sequence of the repetitive-sequence-rich Mycoplasma fermentans strain M64.

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    Shu, Hung-Wei; Liu, Tze-Tze; Chan, Huang-I; Liu, Yen-Ming; Wu, Keh-Ming; Shu, Hung-Yu; Tsai, Shih-Feng; Hsiao, Kwang-Jen; Hu, Wensi S; Ng, Wailap Victor

    2011-08-01

    Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich M. fermentans strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain.

  15. Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64▿

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    Shu, Hung-Wei; Liu, Tze-Tze; Chan, Huang-I; Liu, Yen-Ming; Wu, Keh-Ming; Shu, Hung-Yu; Tsai, Shih-Feng; Hsiao, Kwang-Jen; Hu, Wensi S.; Ng, Wailap Victor

    2011-01-01

    Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich M. fermentans strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain. PMID:21642450

  16. Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome.

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    Zhuang, Xuan; Yang, Chun; Fevolden, Svein-Erik; Cheng, C-H Christina

    2012-07-02

    Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. We

  17. Parallelism in evolution of highly repetitive DNAs in sibling species.

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    Mravinac, Brankica; Plohl, Miroslav

    2010-08-01

    Characterization of heterochromatin in the flour beetle Tribolium audax revealed two highly repetitive DNA families, named TAUD1 and TAUD2, which together constitute almost 60% of the whole genome. Both families originated from a common ancestral approximately 110-bp repeating unit. Tandem arrangement of these elements in TAUD1 is typical for satellite DNAs, whereas TAUD2 represents a dispersed family based on 1412-bp complex higher-order repeats composed of inversely oriented approximately 110 bp units. Comparison with repetitive DNAs in the sibling species Tribolium madens showed similarities in nucleotide sequence and length of basic repeating units and also revealed structural and organizational parallelism in tandem and dispersed families assembled from these elements. In both Tribolium species, one tandem and one dispersed family build equivalent distribution patterns in the pericentromeric heterochromatin of all chromosomes including supernumeraries. Differences in the nucleotide sequence and in the complexity of higher-order structures between families of the same type suggest a scenario according to which rearranged variants of the corresponding ancestral families were formed and distributed in genomes during or after the speciation event, following the same principles independently in each descendant species. We assume that random effects of sequence dynamics should be constrained by organizational and structural features of repeating units and possible requirements for spatial distribution of particular sequence elements. An interspersed pattern of repetitive families also points to the intensive recombination events in heterochromatin. Synergy between the meiotic bouquet stage and satellite DNA sequence dynamics could make a positive feedback loop that promotes the observed genome-wide distribution. At the same time, considering the abundance of these DNAs in heterochromatin spanning the (peri)centromeric chromosomal segments, we speculate that diverged

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

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    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

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

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    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

  20. 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.

  1. Photocathodes for High Repetition Rate Light Sources

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    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. Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region.

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    Sindičić, Magda; Gomerčić, Tomislav; Galov, Ana; Polanc, Primož; Huber, Duro; Slavica, Alen

    2012-06-01

    Mitochondrial DNA (mtDNA) control region (CR) of numerous species is known to include up to five different repetitive sequences (RS1-RS5) that are found at various locations, involving motifs of different length and extensive length heteroplasmy. Two repetitive sequences (RS2 and RS3) on opposite sides of mtDNA central conserved region have been described in domestic cat (Felis catus) and some other felid species. However, the presence of repetitive sequence RS3 has not been detected in Eurasian lynx (Lynx lynx) yet. We analyzed mtDNA CR of 35 Eurasian lynx (L. lynx L.) samples to characterize repetitive sequences and to compare them with those found in other felid species. We confirmed the presence of 80 base pairs (bp) repetitive sequence (RS2) at the 5' end of the Eurasian lynx mtDNA CR L strand and for the first time we described RS3 repetitive sequence at its 3' end, consisting of an array of tandem repeats five to ten bp long. We found that felid species share similar RS3 repetitive pattern and fundamental repeat motif TACAC.

  3. A dispersion-balanced Discrete Fourier Transform of repetitive pulse sequences using temporal Talbot effect

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    Fernández-Pousa, Carlos R.

    2017-11-01

    We propose a processor based on the concatenation of two fractional temporal Talbot dispersive lines with balanced dispersion to perform the DFT of a repetitive electrical sequence, for its use as a controlled source of optical pulse sequences. The electrical sequence is used to impart the amplitude and phase of a coherent train of optical pulses by use of a modulator placed between the two Talbot lines. The proposal has been built on a representation of the action of fractional Talbot effect on repetitive pulse sequences and a comparison with related results and proposals. It is shown that the proposed system is reconfigurable within a few repetition periods, has the same processing rate as the input optical pulse train, and requires the same technical complexity in terms of dispersion and pulse width as the standard, passive pulse-repetition rate multipliers based on fractional Talbot effect.

  4. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.

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    Versalovic, J; Koeuth, T; Lupski, J R

    1991-12-25

    Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.

  5. Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

    Science.gov (United States)

    Chen, Z Q; Ritzel, R G; Lin, C C; Hodgetts, R B

    1991-07-01

    CR1 is a short interspersed repetitive DNA element originally identified in the domestic chicken (Gallus gallus). However, unlike virtually all other such sequences described to date, CR1 is not confined to one or a few closely related species. It is probably a ubiquitous component of the avian genome, having been detected in representatives of nine orders encompassing a wide spectrum of the class Aves. This identification was made possible by using the polymerase chain reaction (PCR), which revealed interspecific similarities not detected by conventional Southern analysis. DNA sequence comparisons between a CR1 element isolated from a sarus crane (Grus antigone) and those isolated from an emu (Dromaius novaehollandiae) showed that two short highly conserved regions are present. These are included within two regions previously characterized in the CR1 units of domestic fowl. One of these behaves as a transcriptional silencer and the other is a binding site for a nuclear protein. Our observations suggest that CR1 has evolved under functional constraints and that interspersed repetitive sequences as a class may constitute a more significant component of the eukaryotic genome than is generally acknowledged.

  6. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal.

    Science.gov (United States)

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-02-04

    Genomic diversity of Portuguese accessions of Avena species--diploid A. strigosa and hexaploids A. sativa and A. sterilis--was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species--rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies--IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)--were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs.

  7. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

    Science.gov (United States)

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  8. Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

    Directory of Open Access Journals (Sweden)

    Brad S. Coates

    2012-01-01

    Full Text Available Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104±34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs. Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.

  9. A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes

    Science.gov (United States)

    Devine, Scott E.; Chissoe, Stephanie L.; Eby, Yolanda; Wilson, Richard K.; Boeke, Jef D.

    1997-01-01

    Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3–140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http://www.welch.jhu.edu/~devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans. [The sequences reported in this paper have been deposited in GenBank under accession nos. U53139 and U86946–U86951.] PMID:9149950

  10. High voltage high repetition rate pulse using Marx topology

    Science.gov (United States)

    Hakki, A.; Kashapov, N.

    2015-06-01

    The paper describes Marx topology using MOSFET transistors. Marx circuit with 10 stages has been done, to obtain pulses about 5.5KV amplitude, and the width of the pulses was about 30μsec with a high repetition rate (PPS > 100), Vdc = 535VDC is the input voltage for supplying the Marx circuit. Two Ferrite ring core transformers were used to control the MOSFET transistors of the Marx circuit (the first transformer to control the charging MOSFET transistors, the second transformer to control the discharging MOSFET transistors).

  11. Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae)

    Science.gov (United States)

    Ishijima, Junko; Uno, Yoshinobu; Nunome, Mitsuo; Nishida, Chizuko; Kuraku, Shigehiro

    2017-01-01

    Abstract All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S–28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of repetitive sequences were detected; a 200-bp AT-rich repetitive sequence, LCA-EcoRIa that co-localized with the 18S–28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three repetitive sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI). PMID:28025319

  12. Is the Hebb repetition task a reliable measure of individual differences in sequence learning?

    Science.gov (United States)

    Bogaerts, Louisa; Siegelman, Noam; Ben-Porat, Tali; Frost, Ram

    2017-03-20

    The Hebb repetition task, an operationalization of long-term sequence learning through repetition, is the focus of renewed interest, as it is taken to provide a laboratory analogue for naturalistic vocabulary acquisition. Indeed, recent studies have consistently related performance in the Hebb repetition task with a range of linguistic (dis)abilities. However, in spite of the growing interest in the Hebb repetition effect as a theoretical construct, no previous research has ever tested whether the task used to assess Hebb learning offers a stable and reliable measure of individual performance in sequence learning. Since reliability is a necessary condition to predictive validity, in the present work we tested whether individual ability in visual verbal Hebb repetition learning displays basic test-retest reliability. In a first experiment Hebrew-English bilinguals performed two verbal Hebb tasks, one with English and one with Hebrew consonant letters. They were retested on the same Hebb tasks after a period of about six months. Overall serial recall performance proved to be a stable and reliable capacity of an individual. By contrast, the test-retest reliability of individual learning performance in our Hebb task was close to zero. A second experiment with French speakers replicated these results and demonstrated that the concurrent learning of two repeated Hebb sequences within the same task minimally improves the reliability scores. Taken together, our results raise concerns regarding the usefulness of at least some current Hebb learning tasks, in predicting linguistic (dis)abilities. The theoretical implications are discussed.

  13. 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.

  14. Evidence of Anticipatory Eye Movements in the Spatial Hebb Repetition Effect: Insights for Modeling Sequence Learning

    Science.gov (United States)

    Tremblay, Sebastien; Saint-Aubin, Jean

    2009-01-01

    In the present study, the authors offer a window onto the mechanisms that drive the Hebb repetition effect through the analysis of eye movement and recall performance. In a spatial serial recall task in which sequences of dots are to be remembered in order, when one particular series is repeated every 4 trials, memory performance markedly improves…

  15. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.

    Science.gov (United States)

    Gilbert, Gwendolyn L; Sintchenko, Vitali

    2013-07-01

    Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.

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

    Indian Academy of Sciences (India)

    Theoretical and experimental studies of temporal dynamics of grazing incidence grating (GIG) cavity, single-mode dye laser pumped by high repetition rate copper vapour laser (CVL) are presented. Spectral chirp of the dye laser as they evolve in the cavity due to transient phase dynamics of the amplifier gain medium is ...

  17. The Ubiquitous Nature of the Hebb Repetition Effect: Error Learning Mistaken for the Absence of Sequence Learning

    Science.gov (United States)

    Lafond, Daniel; Tremblay, Sebastien; Parmentier, Fabrice

    2010-01-01

    Sequence learning is essential in cognition and underpins activities such as language and skill acquisition. One classical demonstration of sequence learning is that of the Hebb repetition effect, whereby serial recall improves over repetitions on a repeated list relative to random lists. When addressing the question of which mechanism underlies…

  18. Distribution of Repetitive and Nonrepetitive Sequence Transcripts in HeLa mRNA

    Science.gov (United States)

    Klein, William H.; Murphy, William; Attardi, Giuseppe; Britten, Roy J.; Davidson, Eric H.

    1974-01-01

    Polyadenylated messenger RNA extracted from HeLa cells was hybridized with a mass excess of HeLa DNA. The kinetics of the hybridization reaction demonstrated that most of the messenger RNA is transcribed from nonrepetitive DNA. The amount of messenger RNA hybridized to DNA was measured both with and without prior RNase treatment. Comparison of the results indicates that within the limits of detection, HeLa messenger RNA does not contain repetitive sequence elements covalently linked to nonrepetitive sequence transcripts. However, a small fraction of the HeLa messenger RNA preparation is transcribed entirely from repetitive DNA sequences. This fraction represents about 6% of the total polyadenylated messenger RNA preparation. PMID:4525461

  19. Stem-loop structures of the repetitive DNA sequences located at human centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.; Garcia, A.E.; Ratliff, R.; Moyzis, R.K. [Los Alamos National Lab., NM (United States); Catasti, P.; Hong, Lin; Yau, P. [California Univ., Davis, CA (United States). Dept. of Biological Chemistry; Bradbury, E.M. [Los Alamos National Lab., NM (United States)]|[California Univ., Davis, CA (United States). Dept. of Biological Chemistry

    1993-09-01

    The presence of the highly conserved repetitive DNA sequences in the human centromeres argues for a special role of these sequences in their biological functions - most likely achieved by the formation of unusual structures. This prompted us to carry out quantitative one- and two-dimensional nuclear magnetic resonance (lD/2D NMR) spectroscopy to determine the structural properties of the human centromeric repeats, d(AATGG){sub n.d}(CCATT){sub n}. The studies on centromeric DNAs reveal that the complementary sequence, d(AATGG){sub n.d}(CCATT){sub n}, adopts the usual Watson-Crick B-DNA duplex and the pyrimidine-rich d(CCATT){sub n} strand is essentially a random coil. However, the purine-rich d(AATGG){sub n} strand is shown to adopt unusual stem-loop structures for repeat lengths, n=2,3,4, and 6. In addition to normal Watson-Crick A{center_dot}T pairs, the stem-loop structures are stabilized by mismatch A{center_dot}G and G{center_dot}G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies. Thermal melting studies show that the DNA repeats, d(AATGG){sub n}, are as stable as the corresponding Watson-Crick duplex d(AATGG){sub n.d}(CCATT){sub n}. Therefore, the sequence d(AATGG){sub n} can, indeed, nucleate a stem-loop structure at little free-energy cost and if, during mitosis, they are located on the chromosome surface they can provide specific recognition sites for kinetochore function.

  20. An RB-EZH2 Complex Mediates Silencing of Repetitive DNA Sequences.

    Science.gov (United States)

    Ishak, Charles A; Marshall, Aren E; Passos, Daniel T; White, Carlee R; Kim, Seung J; Cecchini, Matthew J; Ferwati, Sara; MacDonald, William A; Howlett, Christopher J; Welch, Ian D; Rubin, Seth M; Mann, Mellissa R W; Dick, Frederick A

    2016-12-15

    Repetitive genomic regions include tandem sequence repeats and interspersed repeats, such as endogenous retroviruses and LINE-1 elements. Repressive heterochromatin domains silence expression of these sequences through mechanisms that remain poorly understood. Here, we present evidence that the retinoblastoma protein (pRB) utilizes a cell-cycle-independent interaction with E2F1 to recruit enhancer of zeste homolog 2 (EZH2) to diverse repeat sequences. These include simple repeats, satellites, LINEs, and endogenous retroviruses as well as transposon fragments. We generated a mutant mouse strain carrying an F832A mutation in Rb1 that is defective for recruitment to repetitive sequences. Loss of pRB-EZH2 complexes from repeats disperses H3K27me3 from these genomic locations and permits repeat expression. Consistent with maintenance of H3K27me3 at the Hox clusters, these mice are developmentally normal. However, susceptibility to lymphoma suggests that pRB-EZH2 recruitment to repetitive elements may be cancer relevant. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Identification of hornet silk gene with a characteristic repetitive sequence in Vespa simillima xanthoptera.

    Science.gov (United States)

    Kameda, Tsunenori; Kojima, Katsura; Zhang, Qiang; Sezutsu, Hideki

    2012-01-01

    Vssilk 5 is a gene encoding a component protein of the silk produced by the larvae of the yellow hornet (Vespa simillima, Vespinae, Vespidae). In this study, we deduced the complete cDNA sequence of Vssilk 5. It was found that 2 silk proteins, Vssilk 5 N and Vssilk 5 C, in the cocoon of the yellow hornet are both encoded by the Vssilk 5 gene. Vssilk 5 N and 5 C are the N- and C-terminal regions, respectively, of the Vssilk 5 pro-protein (Vssilk 5p). The complete amino acid sequences of Vssilk 5 N and Vssilk 5 C were deduced. Although a non-repetitive amino acid sequence and coiled-coil structure are properties common to the major components of silk proteins produced by the larvae of the social superfamilies Apoidea and Vespoidea of the Apocrita, nearly the entire sequence of Vssilk 5 C consisted of a repeated sequence of amino acids, and the calculated coiled-coil probability for this protein was low. Vssilk 5 N is a protein without a repetitive amino acid sequence and has a low coiled-coil probability. Moreover, we found a water soluble protein, Vssilk 5S that is likely segmented from Vssilk 5 C and contains an N-terminal sequence identical to that of Vssilk 5 C. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. 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.

  3. 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.

  4. 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.

  5. Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet’s Disease Patients

    Directory of Open Access Journals (Sweden)

    Şahru Yüksel

    2016-01-01

    Full Text Available Behcet’s Disease (BD is a multisystem chronic inflammatory disease. The pathology is believed to involve both genetic susceptibility and environmental factors. Hypomethylation leading to activation of interspersed repetitive sequences (IRSs such as LINE-1 and Alu contributes to the pathologies of autoimmune diseases and cancer. Herein, the epigenetic changes of IRSs in BD were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences (COBRA-IRS. DNA from neutrophils and peripheral blood mononuclear cells (PBMCs of BD patients with ocular involvement that were in active or inactive states and healthy controls were used to analyze LINE-1 and Alu methylation levels. For Alu sequences, significant differences were observed in the frequency of CuCu alleles between PBMCs of patients and controls (p=0.03, and between inactive patients and controls (p=0.03. For neutrophils, the frequency of CuCu was significantly higher between patients and controls (p=0.006 and between inactive patients and controls (p=0.002. The partial methylation (CuCm+CmCu frequencies of Alu between inactive patients and control samples also differed (p=0.02. No statistically significant differences for LINE-1 were detected. Thus, changes in the methylation level of IRS elements might contribute to the pathogenesis of BD. The role of Alu transcripts in BD should be investigated further.

  6. 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

  7. Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida

    Science.gov (United States)

    Aranda-Olmedo, Isabel; Tobes, Raquel; Manzanera, Maximino; Ramos, Juan L.; Marqués, Silvia

    2002-01-01

    Pseudomonas putida KT2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. Its genome has recently been sequenced. We describe that a 35 bp sequence with the structure of an imperfect palindrome, originally found repeated three times downstream of the rpoH gene terminator, is detected more than 800 times in the chromosome of this strain. The structure of this DNA segment is analogous to that of the so-called enterobacteriaceae repetitive extragenic palindromic (REP) sequences, although its sequence is different. Computer-assisted analysis of the presence and distribution of this repeated sequence in the P.putida chromosome revealed that in at least 80% of the cases the sequence is extragenic, and in 82% of the cases the distance of this extragenic element to the end of one of the neighbouring genes was <100 bp. This 35 bp element can be found either as a single element, as pairs of elements, or sometimes forming clusters of up to five elements in which they alternate orientation. PCR scanning of chromosomes from different isolates of Pseudomonas sp. strains using oligonucleotides complementary to the most conserved region of this sequence shows that it is only present in isolates of the species P.putida. For this reason we suggest that the P.putida 35 bp element is a distinctive REP sequence in P.putida. This is the first time that REP sequences have been described and characterised in a group of non-enterobacteriaceae. PMID:11937637

  8. 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

  9. The effects of high resistance-few repetitions and low resistance-high repetitions resistance training on climbing performance.

    Science.gov (United States)

    Hermans, Espen; Andersen, Vidar; Saeterbakken, Atle Hole

    2017-05-01

    The aim of the study was to compare the effects of different strength training intensities on climbing performance, climbing-specific tests and a general strength test. Thirty lower grade and intermediate-level climbers participated in a 10-week training programme. The participants were randomized into three groups: high resistance-few repetitions training groups (HR-FR), low resistance-high repetitions training groups (LR-HR) and a control group (CON) which continued climbing/training as usual. Post-testing results demonstrated statistical tendencies for climbing performance improvements in the HR-FR and LR-HR (p = 0.088-0.090, effect size = 0.55-0.73), but no differences were observed between the groups (p = 0.950). For the climbing-specific tests, no differences were observed between the groups (p = 0.507-1.000), but the HR-FR and LR-HR improved their time in both Dead-hang (p = 0.004-0.026) and Bent-arm hang (p climbing sessions during the intervention compared to the CON group (p = 0.057-0.074). In conclusion, HR-FR and LR-HR training programmes demonstrated an 11% and 12% non-significant improvement in climbing performance despite a 50% reduction in climbing sessions, but improved the results in strength and climbing-specific tests. None of the training intensities was superior compared to the others.

  10. 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

  11. CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing

    Science.gov (United States)

    Lambirth, Kevin C.; Whaley, Adam M.; Schlueter, Jessica A.; Bost, Kenneth L.; Piller, Kenneth J.

    2015-01-01

    Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. PMID:26697366

  12. Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere.

    Science.gov (United States)

    Méndez-Lago, María; Wild, Jadwiga; Whitehead, Siobhan L; Tracey, Alan; de Pablos, Beatriz; Rogers, Jane; Szybalski, Waclaw; Villasante, Alfredo

    2009-04-01

    The centromeric and telomeric heterochromatin of eukaryotic chromosomes is mainly composed of middle-repetitive elements, such as transposable elements and tandemly repeated DNA sequences. Because of this repetitive nature, Whole Genome Shotgun Projects have failed in sequencing these regions. We describe a novel kind of transposon-based approach for sequencing highly repetitive DNA sequences in BAC clones. The key to this strategy relies on physical mapping the precise position of the transposon insertion, which enables the correct assembly of the repeated DNA. We have applied this strategy to a clone from the centromeric region of the Y chromosome of Drosophila melanogaster. The analysis of the complete sequence of this clone has allowed us to prove that this centromeric region evolved from a telomere, possibly after a pericentric inversion of an ancestral telocentric chromosome. Our results confirm that the use of transposon-mediated sequencing, including positional mapping information, improves current finishing strategies. The strategy we describe could be a universal approach to resolving the heterochromatic regions of eukaryotic genomes.

  13. Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9.

    Science.gov (United States)

    Magnusson, Mattias; Tobes, Raquel; Sancho, Jaime; Pareja, Eduardo

    2007-07-01

    Bacterial DNA exerts immunostimulatory effects on mammalian cells via the intracellular TLR9. Although broad analysis of TLR9-mediated immunostimulatory potential of synthetic oligonucleotides has been developed, which kinds of natural bacterial DNA sequences are responsible for immunostimulation are not known. This work provides evidence that the natural DNA sequences named repetitive extragenic palindromic (REPs) sequences present in Gram-negative bacteria are able to produce innate immune system stimulation via TLR9. A strong induction of IFN-alpha production by REPs from Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, and Neisseria meningitidis was detected in splenocytes from 129 mice. In addition, the involvement of TLR9 in immune stimulation by REPs was confirmed using B6.129P2-Tlr9(tm1Aki) knockout mice. Considering the involvement of TLRs in Gram-negative septic shock, it is conceivable that REPs play a role in its pathogenesis. This study highlights REPs as a potential novel target in septic shock treatment.

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

    Directory of Open Access Journals (Sweden)

    Hřibová Eva

    2010-09-01

    Full Text Available Abstract Background 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. Results 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. Conclusion 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

  15. Sequence comparison of the dopamine receptor D4 exon III repetitive region in several species of the order Carnivora.

    Science.gov (United States)

    Inoue-Murayama, Miho; Matsuura, Naoto; Murayama, Yuichi; Tsubota, Toshio; Iwasaki, Toshiroh; Kitagawa, Hitoshi; Ito, Shin'ichi

    2002-08-01

    It was previously demonstrated that the dog dopamine receptor D4 (DRD4) gene is polymorphic in terms of the repeat number and/or order of 39- and 12-bp sequences located in the third exon. To examine whether or not the repetitive region is present in other species of the order Carnivora, the homologous region of DRD4 genes were sequenced in the gray wolf, raccoon dog, Asiatic black bear, common raccoon and domestic cat. In the family Canidae, the wolf had an identical sequence to that of the dog 447b allele, and a repetitive sequence similar to the dog DRD4 was also recognized in the raccoon dog. On the other hand, no obvious repeated structure was observed in the sequences of the bear, raccoon and cat.

  16. The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome

    Science.gov (United States)

    Bertioli, David J.; Vidigal, Bruna; Nielen, Stephan; Ratnaparkhe, Milind B.; Lee, Tae-Ho; Leal-Bertioli, Soraya C. M.; Kim, Changsoo; Guimarães, Patricia M.; Seijo, Guillermo; Schwarzacher, Trude; Paterson, Andrew H.; Heslop-Harrison, Pat; Araujo, Ana C. G.

    2013-01-01

    Background and Aims Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes. Methods The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues. Key Results BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity. Conclusions A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes. PMID

  17. Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences.

    Science.gov (United States)

    Palacios-Gimenez, Octavio M; Castillo, Elio R; Martí, Dardo A; Cabral-de-Mello, Diogo C

    2013-08-09

    The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C0t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers.

  18. Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs.

    Science.gov (United States)

    Renny-Byfield, Simon; Chester, Michael; Kovařík, Ales; Le Comber, Steven C; Grandbastien, Marie-Angèle; Deloger, Marc; Nichols, Richard A; Macas, Jiri; Novák, Petr; Chase, Mark W; Leitch, Andrew R

    2011-10-01

    We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (downsizing and sequences loss across most repeat types. This is particularly evident amongst the Ty3-gypsy retroelements in which all families identified are underrepresented in N. tabacum, as is 35S ribosomal DNA. Analysis of all repetitive DNA sequences indicates the T-genome of N. tabacum has experienced greater sequence loss than the S-genome, revealing preferential loss of paternally derived repetitive DNAs at a genome-wide level. Thus, the three genomes of N. sylvestris, N. tomentosiformis, and N. tabacum have experienced different evolutionary trajectories, with genomes that are dynamic, stable, and downsized, respectively.

  19. Highly repetitive tRNA(Pro)-tRNA(His) gene cluster from Photobacterium phosphoreum.

    Science.gov (United States)

    Giroux, S; Beaudet, J; Cedergren, R

    1988-01-01

    A DNA fragment comprising the four tRNA gene sequences of the Escherichia coli argT locus hybridized with two Sau3A-generated DNA fragments from the vibrio Photobacterium phosphoreum (ATCC 11040). Detailed sequence analysis of the longer fragment shows the following gene organization: 5'-promoter-tRNA(Pro)-tRNAPro-tRNA(Pro)-tRNA(His)-tRNA(Pro)-tRNA(Pro)- tRNA(His)-tRNA(Pro)-five pseudogenes derived from the upstream tRNAPro interspersed by putative Rho-independent terminators. This sequence demonstrates the presence of highly repetitive, tandem tRNA genes in a bacterial genome. Furthermore, a stretch of 304 nucleotides from this cluster was found virtually unchanged in the other (shorter) fragment which was previously sequenced. The two clusters together contain eight tRNA(Pro) pseudogenes and eight fully intact tRNA(Pro) genes, an unusually high number for a single eubacterial isoacceptor tRNA. These results show that the organization of some tRNA operons is highly variable in eubacteria. Images PMID:3056906

  20. Repetitive sequence analysis and karyotyping reveal different genome evolution and speciation of diploid and tetraploid Tripsacum dactyloides

    Directory of Open Access Journals (Sweden)

    Qilin Zhu

    2016-08-01

    Full Text Available In the subtribe Maydeae, Tripsacum and Zea are closely related genera. Tripsacum is a horticultural crop widely used as pasture forage. Previous studies suggested that Tripsacum might play an important role in maize origin and evolution. However, our understanding of the genomics and the evolution of Tripsacum remains limited. In this study, two diploids, T. dactyloides var. meridionale (2n = 36, MR and T. dactyloides (2n = 36, DD, and one tetraploid, T. dactyloides (2n = 72, DL were sequenced by low-coverage genome sequencing followed by graph-based cluster analysis. The results showed that 63.23%, 59.20%, and 61.57% of the respective genome of MR, DD, and DL were repetitive DNA sequence. The proportions of different repetitive sequences varied greatly among the three species. Fluorescence in situ hybridization (FISH analysis of mitotic metaphase chromosomes with satellite repeats as the probes showed that the FISH signal patterns of DL were more similar to that of DD than to that of MR. Comparative analysis of the repeats also showed that DL shared more common repeat families with DD than with MR. Phylogenetic analysis of internal transcribed spacer region sequences further supported the evolutionary relationship among the three species. Repetitive sequences comparison showed that Tripsacum shared more repeat families with Zea than with Coix and Sorghum. Our study sheds new light on the genomics of Tripsacum and differential speciation in the Poaceae family.

  1. Fast and Non-Toxic In Situ Hybridization without Blocking of Repetitive Sequences

    Science.gov (United States)

    Matthiesen, Steen H.; Hansen, Charles M.

    2012-01-01

    Formamide is the preferred solvent to lower the melting point and annealing temperature of nucleic acid strands in in situ hybridization (ISH). A key benefit of formamide is better preservation of morphology due to a lower incubation temperature. However, in fluorescence in situ hybridization (FISH), against unique DNA targets in tissue sections, an overnight hybridization is required to obtain sufficient signal intensity. Here, we identified alternative solvents and developed a new hybridization buffer that reduces the required hybridization time to one hour (IQFISH method). Remarkably, denaturation and blocking against repetitive DNA sequences to prevent non-specific binding is not required. Furthermore, the new hybridization buffer is less hazardous than formamide containing buffers. The results demonstrate a significant increased hybridization rate at a lowered denaturation and hybridization temperature for both DNA and PNA (peptide nucleic acid) probes. We anticipate that these formamide substituting solvents will become the foundation for changes in the understanding and performance of denaturation and hybridization of nucleic acids. For example, the process time for tissue-based ISH for gene aberration tests in cancer diagnostics can be reduced from days to a few hours. Furthermore, the understanding of the interactions and duplex formation of nucleic acid strands may benefit from the properties of these solvents. PMID:22911704

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

    Directory of Open Access Journals (Sweden)

    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. Changes in DNA methylation patterns and repetitive sequences in blood lymphocytes of aged horses.

    Science.gov (United States)

    Wnuk, Maciej; Lewinska, Anna; Gurgul, Artur; Zabek, Tomasz; Potocki, Leszek; Oklejewicz, Bernadetta; Bugno-Poniewierska, Monika; Wegrzyn, Magdalena; Slota, Ewa

    2014-02-01

    It is known that aged organisms have modified epigenomes. Epigenetic modifications, such as changes in global and locus-specific DNA methylation, and histone modifications are suspected to play an important role in cancer development and aging. In the present study, with the well-established horse aging model, we showed the global loss of DNA methylation in blood lymphocytes during juvenile-to-aged period. Additionally, we tested a pattern of DNA methylation of ribosomal DNA and selected genes such as IGF2 and found no significant changes during development and aging. We asked if genetic components such as polymorphisms within DNA methyltransferase genes, DNMT1, DNMT3a, and DNMT3b, may contribute to observed changes in global DNA methylation status. The analysis of seven intragenic polymorphisms did not reveal any significant association with changes in global DNA methylation. Telomere shortage and a loss of pericentromeric heterochromatin during juvenile-to-aged period were also observed. Transcriptional rDNA activity, assessed as the number and size of nucleolar organizer regions, reflecting physiological state of the cell, and mitotic index were decreased with increasing horse donor age. Moreover, changes during juvenile-to-aged period and adult-to-aged period were compared and discussed. Taken together, changes in global DNA methylation status originating in development and affecting the stability of repetitive sequences may be associated with previously reported genomic instability during horse aging.

  4. Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea.

    Science.gov (United States)

    Schmid, Max; Csencsics, Daniela; Gugerli, Felix

    2016-11-01

    Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages repark and repeatmasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development. © 2016 John Wiley & Sons Ltd.

  5. Safety and efficacy of low fluence, high repetition rate versus high fluence, low repetition rate 810-nm diode laser for axillary hair removal in Chinese women.

    Science.gov (United States)

    Li, Wenhai; Liu, Chengyi; Chen, Zhou; Cai, Lin; Zhou, Cheng; Xu, Qianxi; Li, Houmin; Zhang, Jianzhong

    2016-11-01

    High-fluence diode lasers with contact cooling have emerged as the gold standard to remove unwanted hair. Lowering the energy should result in less pain and could theoretically affect the efficacy of the therapy. To compare the safety and efficacy of a low fluence high repetition rate 810-nm diode laser to those of a high fluence, low repetition rate diode laser for permanent axillary hair removal in Chinese women. Ninety-two Chinese women received four axillae laser hair removal treatments at 4-week intervals using the low fluence, high repetition rate 810-nm diode laser in super hair removal (SHR) mode on one side and the high fluence, low repetition rate diode laser in hair removal (HR) mode on the other side. Hair counts were done at each follow-up visit and 6-month follow-up after the final laser treatment using a "Hi Quality Hair Analysis Program System"; the immediate pain score after each treatment session was recorded by a visual analog scale. The overall median reduction of hair was 90.2% with the 810-nm diode laser in SHR mode and 87% with the same laser in HR mode at 6-month follow-up. The median pain scores in SHR mode and in HR mode were 2.75 and 6.75, respectively. Low fluence, high repetition rate diode laser can efficiently remove unwanted hair but also significantly improve tolerability and reduce adverse events during the course of treatment.

  6. High repetition rate tunable femtosecond pulses and broadband amplification from fiber laser pumped parametric amplifier.

    Science.gov (United States)

    Andersen, T V; Schmidt, O; Bruchmann, C; Limpert, J; Aguergaray, C; Cormier, E; Tünnermann, A

    2006-05-29

    We report on the generation of high energy femtosecond pulses at 1 MHz repetition rate from a fiber laser pumped optical parametric amplifier (OPA). Nonlinear bandwidth enhancement in fibers provides the intrinsically synchronized signal for the parametric amplifier. We demonstrate large tunability extending from 700 nm to 1500 nm of femtosecond pulses with pulse energies as high as 1.2 muJ when the OPA is seeded by a supercontinuum generated in a photonic crystal fiber. Broadband amplification over more than 85 nm is achieved at a fixed wavelength. Subsequent compression in a prism sequence resulted in 46 fs pulses. With an average power of 0.5 W these pulses have a peak-power above 10 MW. In particular, the average power and pulse energy scalability of both involved concepts, the fiber laser and the parametric amplifier, will enable easy up-scaling to higher powers.

  7. Mode locking of fiber lasers at high repetition rates

    Science.gov (United States)

    Usechak, Nicholas G.

    Mode-locked fiber lasers have become indispensable tools in many fields as their use is no longer relegated to the optics community. In the future, their size will decrease and their applications will become far more prevalent than they are today. At present, the field is undergoing a cardinal shift as these devices have become commercially available in the last decade. This has put an emphasis on long-term performance and reliability as these devices are beginning to be integrated into complex systems in areas as diverse as medical optics, micro-machining, forensics, and tracking as well as their obvious use as laboratory tools or sources in telecommunications. This is also resulting in a transition from research to engineering. Since the field of mode-locked lasers has been extensively studied for over forty years, one may expect that little has been overlooked. However, since the mode-locking phenomena is governed by nonlinear partial differential equations, a rich degree of effects exist and the field has not yet been exhausted. During the past two decades, the main emphasis has been on short-pulse generation; however, the main thrust of research is likely to change to producing high-power devices, which will result in limiting effects and thermal issues that are currently ignored for low-power sources. Finally, detailed studies have generally been performed numerically as analytic solutions only exist in limiting cases. In this thesis, mode-locked fiber lasers are studied experimentally, numerically, and theoretically. The experimental work focuses on high-repetition rate, mode-locked cavities, which are then modeled numerically. A semi-analytic tool, which goes beyond the prior theories and includes all of the effects experienced by steady-state, mode-locked pulses as they propagate in a laser cavity, is also derived. The only caveats to this approach are an assumption of the pulse shape and the requirement that it not change during propagation through the

  8. 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

  9. High-order harmonic generation using a high-repetition-rate turnkey laser

    CERN Document Server

    Lorek, Eleonora; Heyl, Christoph Michael; Carlström, Stefanos; Paleček, David; Zigmantas, Donatas; Mauritsson, Johan

    2014-01-01

    We generate high-order harmonics at high pulse repetition rates using a turnkey laser. High-order harmonics at 400 kHz are observed when argon is used as target gas. In neon we achieve generation of photons with energies exceeding 90 eV ($\\sim$13 nm) at 20 kHz. We measure a photon flux of 4.4$\\cdot10^{10}$ photons per second per harmonic in argon at 100 kHz. Many experiments employing high-order harmonics would benefit from higher repetition rates, and the user-friendly operation opens up for applications of coherent extreme ultra-violet pulses in new research areas.

  10. A comparison of repetitive behaviors in Aspergers Disorder and high functioning autism.

    Science.gov (United States)

    Cuccaro, Michael L; Nations, Laura; Brinkley, Jason; Abramson, Ruth K; Wright, Harry H; Hall, Alicia; Gilbert, John; Pericak-Vance, Margaret A

    2007-04-01

    In this study we compared 33 IQ and age matched pairs of individuals with Aspergers Disorder (ASP) and high functioning autism (HFA) on measures of repetitive behavior. On the Repetitive Behavior Scale-Revised (RBS-R), the ASP and HFA groups showed no differences in RBS-R Intensity score (severity) score or Frequency score (number of problems present). This suggests that the two groups are similar with respect to the intensity or severity of repetitive behaviors and the presence of repetitive behaviors. At the item level there were no differences on scales typically associated with autism (Stereotyped Behavior) and ASP (Restricted Interests). Similarly, there were no differences between the groups on the Aberrant Behavior Checklist Stereotypy scale. These findings add to the body of literature showing that HFA and ASP fail to differ with respect to repetitive behaviors. The implications of the findings for neurobiologic and genetic studies are discussed.

  11. The history of mutation pattern in human: A statistical analysis of repetitive sequences

    Science.gov (United States)

    Arndt, Peter

    2003-03-01

    Different regions of the human genome show large variation in GC-content (from 30% to 60%) at scales exceeding hundreds of kilobases. The origin, timing and implications of this so called ``human isochore structure'' is still controversial, primarily due to a number of technical issues that have made it difficult to reconstruct the history of the substitutional process. To gain more insight into these questions, we utilize the vast amount of repetitive elements in the human genome to estimate substitution patterns at different evolutionary times going back approximately 250 Myr. We demonstrate that the large-scale variation in GC-content in the human genome has been generated through substitutional biases prior to the radiation of eutherian mammals. While the eutherian substitution pattern allows the formation and maintenance of isochores, the substitution patterns changed abruptly at approximately the time of the mammalian radiation. The newly evolved mammalian pattern of substitution is expected to largely homogenize GC content across the human genome over time. Eutherian mammals are also predicted to share a newly evolved high rate of methylation-induced cytosine transition in CpG pairs, with a 4- to 8-fold increase in rate compared to that of the reptilian ancestor.

  12. High Energy Single Frequency Fiber Laser at Low Repetition Rate Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR phase II project proposes a single frequency high energy fiber laser system operating at low repetition rate of 10 Hz to 1 kHz for coherent Lidar systems...

  13. DC high voltage to drive helium plasma jet comprised of repetitive streamer breakdowns

    CERN Document Server

    Wang, Xingxing

    2016-01-01

    This paper demonstrates and studies helium atmospheric pressure plasma jet comprised of series of repetitive streamer breakdowns, which is driven by a pure DC high voltage (auto-oscillations). Repetition frequency of the breakdowns is governed by the geometry of discharge electrodes/surroundings and gas flow rate. Each next streamer is initiated when the electric field on the anode tip recovers after the previous breakdown and reaches the breakdown threshold value of about 2.5 kV/cm. Repetition frequency of the streamer breakdowns excited using this principle can be simply tuned by reconfiguring the discharge electrode geometry. This custom-designed type of the helium plasma jet, which operates on the DC high voltage and is comprised of the series of the repetitive streamer breakdowns at frequency about 13 kHz, is demonstrated.

  14. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

    Science.gov (United States)

    Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

    2016-08-02

    The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  15. Comparison of multilocus sequence typing (MLST) and repetitive sequence-based PCR (rep-PCR) fingerprinting for differentiation of Campylobacter jejuni isolated from broiler in Chiang Mai, Thailand.

    Science.gov (United States)

    Patchanee, Prapas; Chokboonmongkol, Chomporn; Zessin, Karl-Hans; Alter, Thomas; Pornaem, Sarinya; Chokesajjawatee, Nipa

    2012-11-01

    We compared rapid fingerprinting using repetitive sequence-based PCR (rep-PCR) for subtyping Campylobacter jejuni isolates to the widely used multilocus sequence typing (MLST). Representative C. jejuni isolates (n = 16) from broilers were analyzed using MLST and rep-PCR. Both techniques demonstrated an equal discriminatory power of 0.8917, and 9 subgroups were identified. Clonal identification of all 16 isolates was identical for both techniques. The rep-PCR as described in this study may be used as a rapid and cost-effective alternative for subtyping of C. jejuni isolates, or as an effective screening tool in large epidemiological studies.

  16. Relationships among Repetitive Behaviors, Sensory Features, and Executive Functions in High Functioning Autism

    OpenAIRE

    Boyd, Brian A.; McBee, Matthew; Holtzclaw, Tia; Baranek, Grace T.; Bodfish, James W.

    2009-01-01

    This study examined the relationship between repetitive behaviors and sensory processing issues in school-aged children with high functioning autism (HFA). Children with HFA (N = 61) were compared to healthy, typical controls (N = 64) to determine the relationship between these behavioral classes and to examine whether executive dysfunction explained any relationship between the variables. Particular types of repetitive behavior (i.e., stereotypy and compulsions) were related to sensory featu...

  17. High energy high repetition-rate thin-disk amplifier for OPCPA pumping

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, Michael

    2013-08-15

    The development of a pump laser system for a high power and high repetition rate optical parametric chirped-pulse amplification (OPCPA) is presented in this thesis. The OPCPA system requires pump pulse energies in the range of tens of millijoules at high repetition rates with sub-picosecond pulse durations. This can be achieved to some extend with Innoslab amplifier technology. However, scaling to higher pulse energies at high repetition rates may be problematic. With the thin-disk amplifier presented in this thesis, output energies of 140 mJ at 100 kHz repetition rate could be achieved in burst-mode operation, which is a world record for this type of laser amplifier. Due to its material and spectral properties, ytterbium doped YAG (Yb:YAG) is used as a gain medium for the high power amplifier stages. The low quantum defect and the comparatively large emission bandwidth makes this material the choice for high power operation and sub-picosecond compressed pulse durations. The output beam profile as well as the shape of the output bursts is ideal to pump an OPCPA system. An OPCPA output energy in the millijoule range with repetition rates of 100 kHz to 1 MHz is needed to generate seed pulses for the FEL and for the application as pump-probe laser at the FEL facility. Since the development of this laser system needs to meet requirements set by the Free-Electron Laser in Hamburg (FLASH), the amplifier is conceived for burst-mode operation. The main requirement is a high intra-burst pulse repetition rate of more than 100 kHz and a uniform pulse train (burst) with equal properties for every pulse. The burst-mode is an operation mode where the laser never reaches a lasing equilibrium, which means that the behavior of the amplifier is similar to a switch-on of the laser system for every burst. This makes the development of the amplifier system difficult. Therefore, an analytical model has been developed to study the amplification process during the burst. This includes the

  18. Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion

    Science.gov (United States)

    Wang, Dapeng; Su, Yao; Wang, Xumin; Lei, Hongxing; Yu, Jun

    2012-01-01

    Background Repetitive sequences (RSs) are redundant, complex at times, and often lineage-specific, representing significant “building” materials for genes and genomes. According to their origins, sequence characteristics, and ways of propagation, repetitive sequences are divided into transposable elements (TEs) and satellite sequences (SSs) as well as related subfamilies and subgroups hierarchically. The combined changes attributable to the repetitive sequences alter gene and genome architectures, such as the expansion of exonic, intronic, and intergenic sequences, and most of them propagate in a seemingly random fashion and contribute very significantly to the entire mutation spectrum of mammalian genomes. Principal findings Our analysis is focused on evolutional features of TEs and SSs in the intronic sequence of twelve selected mammalian genomes. We divided them into four groups—primates, large mammals, rodents, and primary mammals—and used four non-mammalian vertebrate species as the out-group. After classifying intron size variation in an intron-centric way based on RS-dominance (TE-dominant or SS-dominant intron expansions), we observed several distinct profiles in intron length and positioning in different vertebrate lineages, such as retrotransposon-dominance in mammals and DNA transposon-dominance in the lower vertebrates, amphibians and fishes. The RS patterns of mouse and rat genes are most striking, which are not only distinct from those of other mammals but also different from that of the third rodent species analyzed in this study—guinea pig. Looking into the biological functions of relevant genes, we observed a two-dimensional divergence; in particular, genes that possess SS-dominant and/or RS-free introns are enriched in tissue-specific development and transcription regulation in all mammalian lineages. In addition, we found that the tendency of transposons in increasing intron size is much stronger than that of satellites, and the

  19. Investigation of a reacting jet injected into vitiated crossflow using CARS, high repetition rate OH-PLIF, and high repetition rate PIV

    Science.gov (United States)

    Roa, Mario

    The proposed PhD thesis research program will be carried out in a staged combustion test rig developed with funding from Siemens Power Generation Inc. and the United States Department of Energy. This research program will study the reacting flow field created by an injector that is axially distributed along the combustor with use the laser diagnostics methods: Coherent Anti-Stokes Raman Spectroscopy (CARS), high repetition rate OH Planar Laser Induced Florescence (OHPLIF), and high repetition rate Particle Image Velocimetry (PIV), to determine why certain conditions result in low NOx emissions. This data will be used to validated the development of more precise computer models. These laser diagnostic techniques will be applied to the reacting jet produced using an extended, premixed 10 mm injector using both natural gas (NG) and hydrogen (H2) as fuels. The objective of this thesis research is to use advance laser diagnostics to gain insight into the reacting flow field resulting form transverse injection into a vitiated cross flow. The advance laser diagnostics will also provide insight into pollution formation mechanisms and will be used for validating CFD models of the transverse jet injection. The following measurements will be performed: (1) dual pump nitrogen/hydrogen (H2/ N2) CARS at the midplane of the extended 10 mm nozzle, (2) high repetition rate OH-PLIF and emission sampling for the same extended nozzle using NG and H2 as secondary fuel, (3) and combing both high repetition OH-PLIF and high repetition rate PIV for extended 10 mm nozzle for both NG and H2 secondary fuel. The PIV measurements will be combined with OH-PLIF in a simultaneous manner, with the OH fluorescence centered between the two PIV laser pulses. The dual pump H2/N2 CARS system will be used to measure both temperature of the reacting jet and the species concentration ratio of H2/ N2. The high repetition rate OH-PLIF, conducted with a 5 kHz, dual cavity Nd:YAG laser that optically pumps a

  20. Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans.

    Science.gov (United States)

    Seo, Beomseok; Lee, Junho

    2016-08-04

    Telomere is a ribonucleoprotein structure that protects chromosomal ends from aberrant fusion and degradation. Telomere length is maintained by telomerase or an alternative pathway, known as alternative lengthening of telomeres (ALT)(1). Recently, C. elegans has emerged as a multicellular model organism for the study of telomere and ALT(2). Visualization of repetitive sequences in the genome is critical in understanding the biology of telomeres. While telomere length can be measured by telomere restriction fragment assay or quantitative PCR, these methods only provide the averaged telomere length. On the contrary, fluorescence in situ hybridization (FISH) can provide the information of the individual telomeres in cells. Here, we provide protocols and representative results of the method to determine telomere length of C. elegans by fluorescent in situ hybridization. This method provides a simple, but powerful, in situ procedure that does not cause noticeable damage to morphology. By using fluorescently labeled peptide nucleic acid (PNA) and digoxigenin-dUTP-labeled probe, we were able to visualize two different repetitive sequences: telomere repeats and template of ALT (TALT) in C. elegans embryos and gonads.

  1. Chromosomal organization of four classes of repetitive DNA sequences in killifish Orestias ascotanensis Parenti, 1984 (Cyprinodontiformes, Cyprinodontidae

    Directory of Open Access Journals (Sweden)

    Cristian Araya-Jaime

    2017-07-01

    Full Text Available Orestias Valenciennes, 1839 is a genus of freshwater fish endemic to the South American Altiplano. Cytogenetic studies of these species have focused on conventional karyotyping. The aim of this study was to use classical and molecular cytogenetic methods to identify the constitutive heterochromatin distribution and chromosome organization of four classes of repetitive DNA sequences (histone H3 DNA, U2 snRNA, 18S rDNA and 5S rDNA in the chromosomes of O. ascotanensis Parenti, 1984, an endemic species restricted to the Salar de Ascotán in the Chilean Altiplano. All individuals analyzed had a diploid number of 48 chromosomes. C-banding identified constitutive heterochromatin mainly in the pericentromeric region of most chromosomes, especially a GC-rich heterochromatic block of the short arm of pair 3. FISH assay with an 18S probe confirmed the location of the NOR in pair 3 and revealed that the minor rDNA cluster occurs interstitially on the long arm of pair 2. Dual FISH identified a single block of U2 snDNA sequences in the pericentromeric regions of a subtelocentric chromosome pair, while histone H3 sites were observed as small signals scattered in throughout the all chromosomes. This work represents the first effort to document the physical organization of the repetitive fraction of the Orestias genome. These data will improve our understanding of the chromosomal evolution of a genus facing serious conservation problems.

  2. Single Longitudinal Mode, High Repetition Rate, Q-switched Ho:YLF Laser for Remote Sensing

    Science.gov (United States)

    Bai, Yingxin; Yu, Jirong; Petzar, Paul; Petros, M.; Chen, Songsheng; Trieu, Bo; Lee, Nyung; Singh, U.

    2009-01-01

    Ho:YLF/LuLiF lasers have specific applications for remote sensing such as wind-speed measurement and carbon dioxide (CO2) concentration measurement in the atmosphere because the operating wavelength (around 2 m) is located in the eye-safe range and can be tuned to the characteristic lines of CO2 absorption and there is strong backward scattering signal from aerosol (Mie scattering). Experimentally, a diode pumped Ho:Tm:YLF laser has been successfully used as the transmitter of coherent differential absorption lidar for the measurement of with a repetition rate of 5 Hz and pulse energy of 75 mJ [1]. For highly precise CO2 measurements with coherent detection technique, a laser with high repetition rate is required to averaging out the speckle effect [2]. In addition, laser efficiency is critically important for the air/space borne lidar applications, because of the limited power supply. A diode pumped Ho:Tm:YLF laser is difficult to efficiently operate in high repetition rate due to the large heat loading and up-conversion. However, a Tm:fiber laser pumped Ho:YLF laser with low heat loading can be operated at high repetition rates efficiently [3]. No matter whether wind-speed or carbon dioxide (CO2) concentration measurement is the goal, a Ho:YLF/LuLiF laser as the transmitter should operate in a single longitudinal mode. Injection seeding is a valid technique for a Q-switched laser to obtain single longitudinal mode operation. In this paper, we will report the new results for a single longitudinal mode, high repetition rate, Q-switched Ho:YLF laser. In order to avoid spectral hole burning and make injection seeding easier, a four mirror ring cavity is designed for single longitudinal mode, high repetition rate Q-switched Ho:YLF laser. The ramp-fire technique is chosen for injection seeding.

  3. Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

    Science.gov (United States)

    Quinn, J S; Guglich, E; Seutin, G; Lau, R; Marsolais, J; Parna, L; Boag, P T; White, B N

    1992-02-01

    The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

  4. All solid-state high power microwave source with high repetition frequency

    Science.gov (United States)

    Bragg, J.-W. B.; Sullivan, W. W.; Mauch, D.; Neuber, A. A.; Dickens, J. C.

    2013-05-01

    An all solid-state, megawatt-class high power microwave system featuring a silicon carbide (SiC) photoconductive semiconductor switch (PCSS) and a ferrimagnetic-based, coaxial nonlinear transmission line (NLTL) is presented. A 1.62 cm2, 50 kV 4H-SiC PCSS is hard-switched to produce electrical pulses with 7 ns full width-half max (FWHM) pulse widths at 2 ns risetimes in single shot and burst-mode operation. The PCSS resistance drops to sub-ohm when illuminated with approximately 3 mJ of laser energy at 355 nm (tripled Nd:YAG) in a single pulse. Utilizing a fiber optic based optical delivery system, a laser pulse train of four 7 ns (FWHM) signals was generated at 65 MHz repetition frequency. The resulting electrical pulse train from the PCSS closely follows the optical input and is utilized to feed the NLTL generating microwave pulses with a base microwave-frequency of about 2.1 GHz at 65 MHz pulse repetition frequency (prf). Under typical experimental conditions, the NLTL produces sharpened output risetimes of 120 ps and microwave oscillations at 2-4 GHz that are generated due to damped gyromagnetic precession of the ferrimagnetic material's axially pre-biased magnetic moments. The complete system is discussed in detail with its output matched into 50 Ω, and results covering MHz-prf in burst-mode operation as well as frequency agility in single shot operation are discussed.

  5. Managing Problems of Acceptability through High Rise-Fall Repetitions

    Science.gov (United States)

    Benjamin, Trevor; Walker, Traci

    2013-01-01

    This article examines one of the ways in which matters of truth, appropriateness, and acceptability are raised and managed within the course of everyday conversation. Using the methodology of conversation analysis, we show that by repeating what another participant has said and doing so with a high rise-fall intonation contour, a speaker claims…

  6. Effects of inspiratory muscle training upon recovery time during high intensity, repetitive sprint activity.

    Science.gov (United States)

    Romer, L M; McConnell, A K; Jones, D A

    2002-07-01

    The present study examined the influence of specific inspiratory muscle training (IMT) upon recovery time during repetitive sprint activity, as well as the physiological and perceptual responses to fixed intensity shuttle running. Using a double-blind placebo-controlled design, 24 male repetitive sprint athletes were assigned randomly to either an IMT (n = 12) or placebo (n = 12) group. The self-selected recovery time during a repetitive sprint test and the physiological response to submaximal endurance exercise were determined. Following completion of baseline and pre-intervention measures, the IMT group performed 30 inspiratory efforts twice daily against a resistance equivalent to 50 % maximum inspiratory mouth pressure (MIP) for 6 wk. The placebo group performed 60 breaths once daily, for 6 wk, at a resistance equivalent to 15 % MIP, a load known to elicit negligible changes in respiratory muscle function. The IMT group improved total recovery time during the repetitive sprint test by 6.2 +/- 1.1 % (mean +/- SEM) above the changes noted for the placebo group (p = 0.006). Blood lactate and perceptual responses to submaximal exercise were also significantly attenuated following IMT (p lactate and perceptual responses to submaximal endurance exercise. In addition, the present study provides new evidence that IMT improves recovery time during high intensity, intermittent exercise in repetitive sprint athletes.

  7. High repetition rate multi-channel source of high-power rf-modulated pulses

    Science.gov (United States)

    Ulmaskulov, M. R.; Pedos, M. S.; Rukin, S. N.; Sharypov, K. A.; Shpak, V. G.; Shunailov, S. A.; Yalandin, M. I.; Romanchenko, I. V.; Rostov, V. V.

    2015-07-01

    This paper presents the results of testing a high voltage pulse generator based on parallel gyromagnetic nonlinear transmission lines filled with saturable ferrite. The generator is capable of producing almost identical stable rf-modulated nanosecond high voltage pulses in each of the two, or four, parallel output channels. The output voltage amplitude in each channel can reach -285 or -180 kV, respectively, with a rf modulation depth of up to 60%. Drive pulses were produced as the packets of duration 1-5 s at a pulse repetition frequency of 800 Hz using a driver equipped with all-solid-state switches. Splitting the driver pulse provided electric field strengths in the channels which were below the breakdown field strength of the transmission lines. As a result, the use of nonlinear transmission lines of reduced diameter made it possible to increase the center frequency of the excited rf oscillations to ˜2 GHz.

  8. High repetition rate multi-channel source of high-power rf-modulated pulses.

    Science.gov (United States)

    Ulmaskulov, M R; Pedos, M S; Rukin, S N; Sharypov, K A; Shpak, V G; Shunailov, S A; Yalandin, M I; Romanchenko, I V; Rostov, V V

    2015-07-01

    This paper presents the results of testing a high voltage pulse generator based on parallel gyromagnetic nonlinear transmission lines filled with saturable ferrite. The generator is capable of producing almost identical stable rf-modulated nanosecond high voltage pulses in each of the two, or four, parallel output channels. The output voltage amplitude in each channel can reach -285 or -180 kV, respectively, with a rf modulation depth of up to 60%. Drive pulses were produced as the packets of duration 1-5 s at a pulse repetition frequency of 800 Hz using a driver equipped with all-solid-state switches. Splitting the driver pulse provided electric field strengths in the channels which were below the breakdown field strength of the transmission lines. As a result, the use of nonlinear transmission lines of reduced diameter made it possible to increase the center frequency of the excited rf oscillations to ∼2 GHz.

  9. Advances in high repetition rate, ultra-short, gigawatt laser systems for time-resolved spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    DiMauro, L.F.

    1991-12-31

    The objective of this article is to emphasize the current advances in the development of high-repetition rate amplifier pumps. Although this review highlights amplifier pump development, any recent data from achieved outputs via the tunable amplifier section is also discussed. The first section describes desirable parameters attributable to the pump amplifier while the rest of the article deals with specific examples for various options. The pump amplifiers can be characterized into two distinct classes; those achieving operation in the hundred hertz regime and those performing at repetition rates {ge}1kHz. 23 refs., 4 figs.

  10. Advances in high repetition rate, ultra-short, gigawatt laser systems for time-resolved spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    DiMauro, L.F.

    1991-01-01

    The objective of this article is to emphasize the current advances in the development of high-repetition rate amplifier pumps. Although this review highlights amplifier pump development, any recent data from achieved outputs via the tunable amplifier section is also discussed. The first section describes desirable parameters attributable to the pump amplifier while the rest of the article deals with specific examples for various options. The pump amplifiers can be characterized into two distinct classes; those achieving operation in the hundred hertz regime and those performing at repetition rates {ge}1kHz. 23 refs., 4 figs.

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

    OpenAIRE

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

    2016-01-01

    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 la...

  12. Improvement of the repetitive sequence-based identification and genotyping of Candida albicans using ALT-specific primers.

    Science.gov (United States)

    Hattori, Hisao; Tanaka, Reiko; Chibana, Hiroji; Kawamoto, Fumihiko; Adachi, Hidesada; Shimizu, Kazue; Kanbe, Toshio

    2009-05-01

    The nucleotide sequences of the inner repeats of the repetitive sequence (RPS), termed ALTs, of Candida albicans and its related species C. albicans var. stellatoidea and C. dubliniensis, were analyzed. ALT sequences were grouped into 4 types for C. albicans (Aa, Ab, Ac and Ad) and C. albicans var. stellatoidea (Sa1, Sa2, Sb, Sc and Sd), and 3 types for C. dubliniensis (Da, Db and Dc). In addition to the primer set P-II (specific to RPS), 2 primer sets (AS-I and AiR-I) specific to the nucleotide sequences of C. albicans ALT were designed and tested for their potential for RPS-based identification/genotyping of C. albicans. PCRs using AS-I and AiR-I clearly distinguished C. albicans from both C. albicans var. stellatoidea and C. dubliniensis. Furthermore, the strains of C. albicans that showed similar electrophoretic patterns in the PCR using P-II were discriminated at the subtype level. These results indicate that the PCRs using RPS- and ALT-specific primer sets are useful as simple and rapid systems for the specific identification and genotyping of C. albicans.

  13. Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins

    Science.gov (United States)

    Lindhout, Beatrice I.; Fransz, Paul; Tessadori, Federico; Meckel, Tobias; Hooykaas, Paul J.J.; van der Zaal, Bert J.

    2007-01-01

    Several techniques are available to study chromosomes or chromosomal domains in nuclei of chemically fixed or living cells. Current methods to detect DNA sequences in vivo are limited to trans interactions between a DNA sequence and a transcription factor from natural systems. Here, we expand live cell imaging tools using a novel approach based on zinc finger-DNA recognition codes. We constructed several polydactyl zinc finger (PZF) DNA-binding domains aimed to recognize specific DNA sequences in Arabidopsis and mouse and fused these with GFP. Plants and mouse cells expressing PZF:GFP proteins were subsequently analyzed by confocal microscopy. For Arabidopsis, we designed a PZF:GFP protein aimed to specifically recognize a 9-bp sequence within centromeric 180-bp repeat and monitored centromeres in living roots. Similarly, in mouse cells a PZF:GFP protein was targeted to a 9-bp sequence in the major satellite repeat. Both PZF:GFP proteins localized in chromocenters which represent heterochromatin domains containing centromere and other tandem repeats. The number of PZF:GFP molecules per centromere in Arabidopsis, quantified with near single-molecule precision, approximated the number of expected binding sites. Our data demonstrate that live cell imaging of specific DNA sequences can be achieved with artificial zinc finger proteins in different organisms. PMID:17704126

  14. Repetitively Pulsed High Power RF Solid-State System

    Science.gov (United States)

    Bowman, Chris; Ziemba, Timothy; Miller, Kenneth E.; Prager, James; Quinley, Morgan

    2017-10-01

    Eagle Harbor Technologies, Inc. (EHT) is developing a low-cost, fully solid-state architecture for the generation of the RF frequencies and power levels necessary for plasma heating and diagnostic systems at validation platform experiments within the fusion science community. In Year 1 of this program, EHT has developed a solid-state RF system that combines an inductive adder, nonlinear transmission line (NLTL), and antenna into a single system that can be deployed at fusion science experiments. EHT has designed and optimized a lumped-element NLTL that will be suitable RF generation near the lower-hybrid frequency at the High Beta Tokamak (HBT) located at Columbia University. In Year 2, EHT will test this system at the Helicity Injected Torus at the University of Washington and HBT at Columbia. EHT will present results from Year 1 testing and optimization of the NLTL-based RF system. With support of DOE SBIR.

  15. The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharyya Madan K

    2008-03-01

    Full Text Available Abstract Background A series of Rps (resistance to Pytophthora sojae genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean. Results Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region 1 was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus. Conclusion These data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a

  16. Low load, high repetition resistance training program increases bone mineral density in untrained adults.

    Science.gov (United States)

    Petersen, Bailey A; Hastings, Bryce; Gottschall, Jinger S

    2017-01-01

    High load, low repetition resistance training increases BMD in untrained adults; however, many older and untrained adults cannot maintain this type of strenuous program. Our goal was to evaluate whether a low load, high repetition resistance training program would increase BMD in untrained adults. Twenty sedentary, but otherwise healthy, adults (6 men and 14 women, age 28-63 yrs) completed a 27-week group exercise program. The participants were randomly assigned to one of two strength groups: one group completed full body, low load, high repetition weight training classes (S-WEIGHT), while the other group completed core focused fusion classes (S-CORE). Both groups also completed indoor cycling classes for cardiovascular conditioning. After a 3-week familiarization period, all participants completed a 12-week block of 5 fitness classes per week (3 cycling + 2 strength) and concluded with another 12-week block of 6 classes per week (3 cycling + 3 strength). We completed iDXA scans at baseline (week 3) and final (week 28). Compared to baseline, BMD significantly increased for S-WEIGHT in the arms (+4%, Pload, high repetition resistance training program may be an effective method to improve bone mass in adults.

  17. Femtosecond Ti:sapphire cryogenic amplifier with high gain and MHz repetition rate

    DEFF Research Database (Denmark)

    Dantan, Aurelien Romain; Laurat, Julien; Ourjoumtsev, Alexei

    2007-01-01

    We demonstrate high gain amplification of 160-femtosecond pulses in a compact double-pass cryogenic Ti:sapphire amplifier. The setup involves a negative GVD mirrors recompression stage, and operates with a repetition rate between 0.2 and 4 MHz with a continuous pump laser. Amplification factors...

  18. Relationships among Repetitive Behaviors, Sensory Features, and Executive Functions in High Functioning Autism

    Science.gov (United States)

    Boyd, Brian A.; McBee, Matthew; Holtzclaw, Tia; Baranek, Grace T.; Bodfish, James W.

    2009-01-01

    This study examined the relationship between repetitive behaviors and sensory processing issues in school-aged children with high functioning autism (HFA). Children with HFA (N = 61) were compared to healthy, typical controls (N = 64) to determine the relationship between these behavioral classes and to examine whether executive dysfunction…

  19. Accelerated high-frequency repetitive transcranial magnetic stimulation enhances motor activity in rats

    NARCIS (Netherlands)

    El Arfani, Anissa; Parthoens, Joke; Demuyser, Thomas; Servaes, Stijn; De Coninck, Mattias; De Deyn, Peter Paul; Van Dam, Debby; Wyckhuys, Tine; Baeken, Chris; Smolders, Ilse; Staelens, Steven

    2017-01-01

    High-frequency repetitive transcranial magnetic stimulation (HF-rTMS) is currently accepted as an evidence-based treatment option for treatment-resistant depression (TRD). Additionally, HF-rTMS showed beneficial effects on psychomotor retardation in patients. The classical HF-rTMS paradigms however

  20. Development of a highly efficient, repetitive system of organogenesis in soybean (Glycine max (L.) Merr).

    NARCIS (Netherlands)

    Shan, Zhihui; Raemakers, C.J.J.M.; Tzitzikas, E.; Ma, Zhengqiang; Visser, R.G.F.

    2005-01-01

    A highly efficient, repetitive system of organogenesis was developed in soybean. Seeds of soybean cv. White hilum pretreated with TDZ formed multiple bud tissue(s) (MBT) at the cotyledonary nodes. MBT initiation occurred only if the axillary buds were not removed from the cotyledonary node. The best

  1. 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.

  2. 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.

  3. Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin.

    Directory of Open Access Journals (Sweden)

    Rodrigo S Lacruz

    2011-03-01

    Full Text Available Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL, the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates.

  4. Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC).

    Science.gov (United States)

    Lukinmaa-Åberg, Susanna; Horsma, Jenni; Pasanen, Tanja; Mero, Sointu; Aulu, Laura; Vaara, Martti; Siitonen, Anja; Antikainen, Jenni

    2013-07-01

    Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.

  5. Longitudinally excited CO2 laser with short laser pulse operating at high repetition rate

    Science.gov (United States)

    Li, Jianhui; Uno, Kazuyuki; Akitsu, Tetsuya; Jitsuno, Takahisa

    2016-11-01

    A short-pulse longitudinally excited CO2 laser operating at a high repetition rate was developed. The discharge tube was made of a 45 cm-long or 60 cm-long dielectric tube with an inner diameter of 16 mm and two metallic electrodes at the ends of the tube. The optical cavity was formed by a ZnSe output coupler with a reflectivity of 85% and a high-reflection mirror. Mixed gas (CO2:N2:He = 1:1:2) was flowed into the discharge tube. A high voltage of about 33 kV with a rise time of about 200 ns was applied to the discharge tube. At a repetition rate of 300 Hz and a gas pressure of 3.4 kPa, the 45 cm-long discharge tube produced a short laser pulse with a laser pulse energy of 17.5 mJ, a spike pulse energy of 0.2 mJ, a spike width of 153 ns, and a pulse tail length of 90 μs. The output power was 5.3 W. The laser pulse waveform did not depend on the repetition rate, but the laser beam profile did. At a low repetition rate of less than 50 Hz, the laser beam had a doughnut-like shape. However, at a high repetition rate of more than 150 Hz, the discharge concentrated at the center of the discharge tube, and the intensity at the center of the laser beam was higher. The laser beam profile depended on the distribution of the discharge. An output power of 7.0 W was achieved by using the 60 cm-long tube.

  6. 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

  7. Indirect high-bandwidth stabilization of carrier-envelope phase of a high-energy, low-repetition-rate laser.

    Science.gov (United States)

    Fu, Yuxi; Takahashi, Eiji J; Midorikawa, Katsumi

    2016-06-13

    We demonstrate a method of stabilizing the carrier-envelope phase (CEP) of low-repetition-rate, high-energy femtosecond laser systems such as TW-PW class lasers. A relatively weak high-repetition-rate (~1 kHz) reference pulse copropagates with a low-repetition-rate (10 Hz) high-energy pulse, which are s- and p-polarized, respectively. Using a Brewster angle window, the reference pulse is separated after the power amplifier and used for feedback to stabilize its CEP. The single-shot CEP of the high-energy pulse is indirectly stabilized to 550 mrad RMS, which is the highest CEP stability ever reported for a low-repetition-rate (10-Hz) high-energy laser system. In this novel method, the feedback frequency of the reference pulse from the front-end preamplifier can be almost preserved. Thus, higher CEP stability can be realized than for lower frequencies. Of course, a reference pulse with an even higher repetition rate (e.g., 10 kHz) can be easily employed to sample and feed back CEP jitter over a broader frequency bandwidth.

  8. Paleogenomics: Investigation of an ancient family of repetitive sequences present in great numbers in human genome

    Energy Technology Data Exchange (ETDEWEB)

    Zietkiewicz, E.; Labuda, D. [Universite de Montreal, Que (Canada); Jurka, J. [Linus Pauling Institute, Palo Alto, CA (United States)

    1994-09-01

    Paleogenomics is the research activity aiming to reconstruct ancient genetic events and/or structures from the {open_quotes}fossil{close_quotes} genomic record. With about 120,000 copies, mammalian interspersed repeats, MIRs, represent the second most abundant family of short interspersed repeats in human DNA, only outnumbered by Alu elements. MIR consensus sequence of 100 nucleotides was reconstructed from 455 mutated copies preserved in contemporary genome (GenBank release 69). As no division into subfamilies was observed, we assume that this consensus represents an ancestral MIR sequence. To find out how far MIRs can be traced down the phylogenetic tree, we examined their distribution in a variety of mammalian and non-mammalian DNAs. Oligonucleotide primers based on the MIR consensus were used, one at a time, for PCR amplification of the genomic fragments flanked by MIR repeats (inter-MIR-PCR). Significant amplification in DNA samples from a variety of placental orders as well as marsupials and monotremes indicates that MIRs originated in early mammals. Sequence analysis is consistent with their proliferation during the Mesozoic era. Electrophoretic profiles of inter-MIR-PCR products are distinct among different species. Intra-species comparison of multiple human samples reveals polymorphic bands segregating as Mendelian traits which can be used as genetic markers in both mapping and fingerprinting.

  9. High-Repetition-Rate Laser for Thomson Scattering on the MST Reversed-Field Pinch

    Science.gov (United States)

    Young, William C.; Morton, L. A.; Parke, E.; den Hartog, D. J.; MST Team

    2013-10-01

    The MST Thomson scattering diagnostic has operated with a new, high-repetition-rate laser system, demonstrating 2 J pulses at repetition rates up to 50 kHz. The pulse repetition rate can maintain 2 J pulses for bursts of 5 kHz (sustained for 5 ms), to 50 kHz (for 10 bursts of 240 μs each). The 1064 nm laser currently employs a q-switched, diode pumped Nd:YVO4 master oscillator, four Nd:YAG amplifier stages, and a Nd:glass amplifier. The future implementation of the full laser as designed, including a second Nd:glass amplifier, is expected to produce bursts of 2 J pulses at a repetition rate of at least 250 kHz. The new laser integrates with the same collection optics and detectors as used by the present MST Thomson scattering system: 21 spatial points across the MST minor radius with sensitivity over a 10 eV-5 keV range. Initial results will be presented from application of this diagnostic to parametric scans of MST plasmas, evolution of energy confinement during spontaneous enhanced confinement periods, and non-Maxwellian electron distributions. Work Supported by the U. S. Department of Energy and National Science Foundation.

  10. A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.

    Science.gov (United States)

    Young, R J; Francis, D M; St Clair, D A; Taylor, B H

    1994-06-01

    A segment of DNA 5' to the transcribed region of an auxin-regulated gene, ARPI, from Lycopersicon esculentum Mill. cv. VFN8 contains a sequence with the structural characteristics of a transposable element. The putative element (Lyt1) is 1340 bp long, has terminal inverted repeats of approximately 235 bp and is flanked by 9-bp direct repeats. Lyt1 has a structure similar to the Robertson's Mutator (Mu) family from maize. The terminal inverted repeats are 80% AT-rich, are 96.6% identical, and define a larger family of repetitive elements. Southern analysis and genomic dot-blot reconstructions detected at least 41 copies of Lyt1-hybridizing sequences in red-fruited Lycopersicon spp. (L. esculentum, L. pimpinellifolium and L. cheesmanii), and 2-8 copies in the green-fruited species (L. hirsutum, L. pennellii, L. peruvianum, L. chilense and L. chmielewskii). There were two to four copies in the Solanum spp. closely allied with the genus Lycopersicon (S. lycopersicoides, S. ochranthum and S. juglandifolium), while the more distantly related Solanum spp. showed little (one to two copies in S. tuberosum) to no (S. quitoense) detectable hybridization under stringent conditions. Linkage analysis in the F2 progeny of a cross between L. esculentum and L. cheesmanii indicated that at least six loci that hybridize to the Lyt1 sequence are dispersed in the genome. Polymerase chain reaction and Southern analyses revealed that some red-fruited accessions and L. chmielewskii lacked Lyt1 5' to the transcribed region of ARPI. Subsequent sequence analysis indicated that only one copy of the 9-bp direct repeat (target site) was present, suggesting that transposition of the element into the ARPI gene occurred after the divergence of the red-fruited and green-fruited Lycopersicon species.

  11. Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR

    Energy Technology Data Exchange (ETDEWEB)

    Louws, F.J.; Stephens, C.T.; Fulbright, D.W. [Michigan State Univ., East Lansing, MI (United States)] [and others

    1994-07-01

    DNA primers corresponding to conserved motifs in bacterial repetitive (REP, ERIC, and BOX) elements and PCR were used to show that REP-, ERIC-, and BOX-like DNA sequences are widely distributed in phytopathogenic Xanthomonas and Pseudomonas strains. REP-, ERIC-, and BOX-PCR (collectively known as rep-PCR) were used to generate genomic fingerprints of a variety of Xanthomonas and Pseudomonas isolates and to to identify pathovars and strains that were previously not distinguishable by other classification methods. Analogous rep-PCR-derived genomic fingerprints were generated from purified genomic DNA, colonies on agar plates, liquid cultures, and directly from lesions on infected plants. REP-, ERIC-, and BOX-PCR-generated fingerprints of specific Xanthomonas and Pseudomonas strains were found to yield similar conclusions with regard to the identity of and relationship between these strains. This suggests that the distribution of REP-, ERIC-, and BOX-like sequences in these strains is a reflection of their genomic structure. Thus, the rep-PCR technique appears to be a rapid, simple, and reproducible method to identify and classify Xanthomonas and Pseudomonas strains, and it may be a useful diagnostic tool for these important plant pathogens. 70 refs., 5 figs., 1 tab.

  12. High-power, high repetition rate, tunable, ultrafast vortex beam in the near-infrared

    Science.gov (United States)

    Aadhi, A.; Samanta, G. K.

    2018-01-01

    We report on experimental demonstration of high power, ultrafast, high repetition rate (RR) vortex beam source tunable in the near-IR wavelength range. Based on single-pass optical parametric generation of Yb-fiber laser of vortex order l p = 1 in a 50 mm long MgO doped periodically poled LiNbO3 crystal, the source produces signal beam in vortex profile of order l s = 1 across 1433–1553 nm. Additionally, the source produces broadband idler radiation tunable across 3379–4132 nm in the Gaussian beam profile. We observed that the vortex profile of the pump beam is always transferred to the signal beam due to the highest overlapping integral among the interacting beams and the idler maintains a Gaussian spatial profile owing to the conservation of orbital angular momentum in optical parametric processes. For a pump power of 4.72 W, the signal and idler beams have a maximum power of 1.7 W at 1509 nm and 0.48 W at 3625 nm respectively. The signal vortex beam has output pulses of width ∼637 fs at a RR of 78 MHz. The signal (idler) has a spectral width of 4.3 nm (129.5 nm) and a passive peak-to-peak power fluctuation better than 3% (1.1%) over 30 min, respectively.

  13. Design of high gradient, high repetition rate damped C -band rf structures

    Science.gov (United States)

    Alesini, David; Bellaveglia, Marco; Bini, Simone; Gallo, Alessandro; Lollo, Valerio; Pellegrino, Luigi; Piersanti, Luca; Cardelli, Fabio; Migliorati, Mauro; Mostacci, Andrea; Palumbo, Luigi; Tocci, Simone; Ficcadenti, Luca; Pettinacci, Valerio

    2017-03-01

    The gamma beam system of the European Extreme Light Infrastructure-Nuclear Physics project foresees the use of a multibunch train colliding with a high intensity recirculated laser pulse. The linac energy booster is composed of 12 traveling wave C -band structures, 1.8 m long with a field phase advance per cell of 2 π /3 and a repetition rate of 100 Hz. Because of the multibunch operation, the structures have been designed with a dipole higher order mode (HOM) damping system to avoid beam breakup (BBU). They are quasiconstant gradient structures with symmetric input couplers and a very effective damping of the HOMs in each cell based on silicon carbide (SiC) rf absorbers coupled to each cell through waveguides. An optimization of the electromagnetic and mechanical design has been done to simplify the fabrication and to reduce the cost of the structures. In the paper, after a review of the beam dynamics issues related to the BBU effects, we discuss the electromagnetic and thermomechanic design criteria of the structures. We also illustrate the criteria to compensate the beam loading and the rf measurements that show the effectiveness of the HOM damping.

  14. Design of high gradient, high repetition rate damped C-band rf structures

    Directory of Open Access Journals (Sweden)

    David Alesini

    2017-03-01

    Full Text Available The gamma beam system of the European Extreme Light Infrastructure–Nuclear Physics project foresees the use of a multibunch train colliding with a high intensity recirculated laser pulse. The linac energy booster is composed of 12 traveling wave C-band structures, 1.8 m long with a field phase advance per cell of 2π/3 and a repetition rate of 100 Hz. Because of the multibunch operation, the structures have been designed with a dipole higher order mode (HOM damping system to avoid beam breakup (BBU. They are quasiconstant gradient structures with symmetric input couplers and a very effective damping of the HOMs in each cell based on silicon carbide (SiC rf absorbers coupled to each cell through waveguides. An optimization of the electromagnetic and mechanical design has been done to simplify the fabrication and to reduce the cost of the structures. In the paper, after a review of the beam dynamics issues related to the BBU effects, we discuss the electromagnetic and thermomechanic design criteria of the structures. We also illustrate the criteria to compensate the beam loading and the rf measurements that show the effectiveness of the HOM damping.

  15. Odd harmonic high order repetitive control of single-phase pmw rectifiers: varying frequency operation

    Directory of Open Access Journals (Sweden)

    Germán A. Ramos-Fuentes

    2016-01-01

    Full Text Available Controlled rectifiers are electronic power devices aimed at reducing the harmonic pollution in electrical networks caused by the power conversion process. The main goal is to obtain a sinusoidal shape current in phase with the voltage network. Although Proportional Integral controllers are widely used for the current control loop, they do not provide high performance results. On the contrary, Resonant and Repetitive Control are techniques with remarkable results on this area. However, their main drawback is the lost of performance due to frequency changes in the exogenous signal. In this work, the implementation of an Odd Harmonic High Order Repetitive Controller is proposed for the rectifier current loop. The odd harmonic characteristic of this compensator makes possible to obtain a computational burden that is very similar to the one obtained by conventional repetitive controllers with the advantage of increase the robustness against frequency variations. Experimental results show the high performance obtained even when the network frequency does not match the designed nominal frequency

  16. Karyotypic Evolution and Chromosomal Organization of Repetitive DNA Sequences in Species of Panaque, Panaqolus, and Scobinancistrus (Siluriformes and Loricariidae) from the Amazon Basin.

    Science.gov (United States)

    Ayres-Alves, Thayana; Cardoso, Adauto Lima; Nagamachi, Cleusa Yoshiko; Sousa, Leandro Melo de; Pieczarka, Julio Cesar; Noronha, Renata Coelho Rodrigues

    2017-06-01

    Loricariidae family comprises the greatest variability of Neotropical catfish species, with more than 800 valid species. This family shows significant chromosomal diversity. Mapping of repetitive DNA sequences can be very useful in exploring such diversity, especially among groups that appear to share a preserved karyotypic macrostructure. We describe the karyotypes of Panaque armbrusteri and Panaqolus sp., as assessed using classical cytogenetic methods. Moreover, we offer a map of their repetitive sequences, including 18S and 5S ribosomal DNAs, the Rex1 and Rex3 retrotransposons, and the Tc1-mariner transposon in P. armbrusteri, Panaqolus sp., Scobinancistrus aureatus, and Scobinancistrus pariolispos. Those species share chromosome numbers of 2n = 52, but are divergent in their chromosome structures and the distributions of their repetitive DNA sequences. In situ hybridization with 18S and 5S rDNA probes confirms chromosome location in different pairs; in Panaqolus sp. these sites are in synteny. This multigene family organization can be explained by the occurrence of chromosome rearrangements, and possible events, such as transposition and unequal crossing-over. Rex1 and Rex3 retrotransposons and the Tc1-mariner transposon appeared predominantly dispersed and in small clusters in some chromosome regions. These data emphasize the importance of repetitive sequences in promoting the karyotypic evolution of these species.

  17. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

    Directory of Open Access Journals (Sweden)

    Halder Georg

    2008-07-01

    Full Text Available Abstract Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC and H. melpomene (Yb-linked BAC revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved

  18. CA88, a nuclear repetitive DNA sequence identified in Schistosoma mansoni, aids in the genotyping of nine Schistosoma species of medical and veterinary importance

    OpenAIRE

    Diana Bahia; Rodrigues,Nilton B; Araújo,Flávio Marcos G; Álvaro José Romanha; Ruiz, Jerônimo C.; Johnston, David A.; Guilherme Oliveira

    2010-01-01

    CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma mansoni. The assembled S. mansoni sequence, which contains the CA88 repeat, has 8,887 nucleotides and at least three repeat units of approximately 360 bp. In addition, CA88 also possesses an internal CA microsatellite, identified as SmBr18. Both PCR and BLAST analysis have been used to analyse and confirm the CA88 sequence in other S. mansoni sequences in the public database. PCR-acquired nuclear...

  19. Optimization of graffiti removal on natural stone by means of high repetition rate UV laser

    Energy Technology Data Exchange (ETDEWEB)

    Fiorucci, M.P., E-mail: m.p.fiorucci@udc.es [Centro de Investigacións Tecnolóxicas, Universidade da Coruña, 15403 Ferrol (Spain); Dpto. Enxeñaría dos Recursos Naturais e Medio Ambiente, E.T.S.E. Minas, Universidade de Vigo, 36200 Vigo (Spain); López, A.J., E-mail: ana.xesus.lopez@udc.es [Centro de Investigacións Tecnolóxicas, Universidade da Coruña, 15403 Ferrol (Spain); Ramil, A., E-mail: alberto.ramil@udc.es [Centro de Investigacións Tecnolóxicas, Universidade da Coruña, 15403 Ferrol (Spain); Pozo, S., E-mail: ipozo@uvigo.es [Dpto. Enxeñaría dos Recursos Naturais e Medio Ambiente, E.T.S.E. Minas, Universidade de Vigo, 36200 Vigo (Spain); Rivas, T., E-mail: trivas@uvigo.es [Dpto. Enxeñaría dos Recursos Naturais e Medio Ambiente, E.T.S.E. Minas, Universidade de Vigo, 36200 Vigo (Spain)

    2013-08-01

    The use of laser for graffiti removal is a promising alternative to conventional cleaning methods, though irradiation parameters must be carefully selected in order to achieve the effective cleaning without damaging the substrate, especially when referring to natural stone. From a practical point of view, once a safe working window is selected, it is necessary to determine the irradiation conditions to remove large paint areas, with minimal time consumption. The aim of this paper is to present a systematic procedure to select the optimum parameters for graffiti removal by means of the 3rd harmonic of a high repetition rate nanosecond Nd:YVO{sub 4} laser. Ablation thresholds of four spray paint colors were determined and the effect of pulse repetition frequency, beam diameter and line scan separation was analyzed, obtaining a set of values which optimize the ablation process.

  20. High Repetition Rate, LINAC-Based Nuclear Resonance Fluorescence FY 2008 Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Scott M Watson; Mathew T Kinlaw; James L Jones; Alan W. Hunt; Glen A. Warren

    2008-12-01

    This summarizes the first year of a multi-laboratory/university, multi-year effort focusing on high repetition rate, pulsed LINAC-based nuclear resonance fluorescence (NRF) measurements. Specifically, this FY2008 effort centered on experimentally assessing NRF measurements using pulsed linear electron accelerators, operated at various repetition rates, and identifying specific detection requirements to optimize such measurements. Traditionally, interest in NRF as a detection technology, which continues to receive funding from DHS and DOE/NA-22, has been driven by continuous-wave (CW), Van de Graff-based bremsstrahlung sources. However, in addition to the relatively sparse present-day use of Van de Graff sources, only limited NRF data from special nuclear materials has been presented; there is even less data available regarding shielding effects and photon source optimization for NRF measurements on selected nuclear materials.

  1. Optimization of graffiti removal on natural stone by means of high repetition rate UV laser

    Science.gov (United States)

    Fiorucci, M. P.; López, A. J.; Ramil, A.; Pozo, S.; Rivas, T.

    2013-08-01

    The use of laser for graffiti removal is a promising alternative to conventional cleaning methods, though irradiation parameters must be carefully selected in order to achieve the effective cleaning without damaging the substrate, especially when referring to natural stone. From a practical point of view, once a safe working window is selected, it is necessary to determine the irradiation conditions to remove large paint areas, with minimal time consumption. The aim of this paper is to present a systematic procedure to select the optimum parameters for graffiti removal by means of the 3rd harmonic of a high repetition rate nanosecond Nd:YVO4 laser. Ablation thresholds of four spray paint colors were determined and the effect of pulse repetition frequency, beam diameter and line scan separation was analyzed, obtaining a set of values which optimize the ablation process.

  2. Group velocity locked vector dissipative solitons in a high repetition rate fiber laser

    CERN Document Server

    Luo, Yiyang; Li, Lei; Sun, Qizhen; Wu, Zhichao; Xu, Zhilin; Fu, Songnian; Zhao, Luming

    2016-01-01

    Vectorial nature of dissipative solitons (DSs) with high repetition rates is studied for the first time in a normal-dispersion fiber laser. Despite the fact that the formed DSs are strongly chirped and the repetition rate is greater than 100 MHz, polarization locked and polarization rotating group velocity locked vector DSs can be formed under 129.3 MHz fundamental mode-locking and 258.6 MHz harmonic mode-locking of the fiber laser, respectively. The two orthogonally polarized components of these vector DSs possess distinctly different central wavelengths and travel together at the same group velocity in the laser cavity, resulting in a gradual spectral edge and small steps on the optical spectra, which can be considered as an auxiliary indicator of the group velocity locked vector DSs.

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

    CERN Document Server

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

    2016-01-01

    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%.

  4. High repetition rate laser-driven MeV ion acceleration at variable background pressures

    Science.gov (United States)

    Snyder, Joseph; Ngirmang, Gregory; Orban, Chris; Feister, Scott; Morrison, John; Frische, Kyle; Chowdhury, Enam; Roquemore, W. M.

    2017-10-01

    Ultra-intense laser-plasma interactions (LPI) can produce highly energetic photons, electrons, and ions with numerous potential real-world applications. Many of these applications will require repeatable, high repetition targets that are suitable for LPI experiments. Liquid targets can meet many of these needs, but they typically require higher chamber pressure than is used for many low repetition rate experiments. The effect of background pressure on the LPI has not been thoroughly studied. With this in mind, the Extreme Light group at the Air Force Research Lab has carried out MeV ion and electron acceleration experiments at kHz repetition rate with background pressures ranging from 30 mTorr to >1 Torr using a submicron ethylene glycol liquid sheet target. We present these results and provide two-dimensional particle-in-cell simulation results that offer insight on the thresholds for the efficient acceleration of electrons and ions. This research is supported by the Air Force Office of Scientific Research under LRIR Project 17RQCOR504 under the management of Dr. Riq Parra and Dr. Jean-Luc Cambier. Support was also provided by the DOD HPCMP Internship Program.

  5. High microbial production and characterization of strictly periodic polymers modelled on the repetitive domain of wheat gliadins.

    Science.gov (United States)

    Sourice, Sophie; Nisole, Audrey; Guéguen, Jacques; Popineau, Yves; Elmorjani, Khalil

    2003-12-26

    Primary structures of wheat prolamins contain repetitive domains involved in the mechanical properties of gluten. In order to experience the ability of recombinant strictly periodic polypeptides, modelled on a consensus sequence of wheat gliadins (PQQPY)(8) and (PQQPY)(17) (SPR8 and SPR17 polypeptides, respectively), to be formulated in film solutions, their heterologous expression conditions, in batch culture and low cell densities, were optimized to match the high requirements of this process. A convenient and general purification procedure was also devised. Moreover, FTIR-ATR characterizations indicated that these periodic polypeptides prepared as hydrated doughy state and dried have the tendency to form a protein network through intermolecular beta-sheets, strongly maintained by hydrogen bonds. Accordingly, these recombinant polypeptides are assumed to be a suitable candidate for potential application.

  6. Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

    Science.gov (United States)

    Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

    2000-01-01

    Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint patterns were detected in the H. influenzae strains. Isolates from patients with different diseases were represented by a variety of patterns, which clustered into two major groups. Of the 37 strains isolated from cases of meningitis, 24 shared patterns and were clustered into five groups within a similarity level of 1.0. One fragment of 1.25 kb was common to all meningitis strains. H. influenzae strains from healthy carriers presented fingerprint patterns different from those found in strains from sick children. Isolates from healthy individuals were more variable and were distributed differently from those from patients. The results show that ERIC-PCR provides a powerful tool for the determination of the distinctive pathogenicity potentials of H. influenzae strains and encourage its use for molecular epidemiology investigations. PMID:10878033

  7. Two-dimensional agarose gel electrophoresis as a tool to isolate genus- and species-specific repetitive DNA sequences.

    Science.gov (United States)

    Harms, C; Klarholz, I; Hildebrandt, A

    2000-08-15

    Two-dimensional electrophoresis in agarose gels separates DNA-restriction fragments not only by molecular weight but also according to their AT-cluster content. The method produced genus-specific spot patterns of multicopy DNA fragments of grains as well as spot patterns of highly repetitive DNA fragments of ciliates, demonstrated for barley, spelt, and Tetrahymena. Further investigations in regard to their specificity by hybridization with three other grain species (wheat, oat, and rye) and three ciliate species (Tetrahymena thermophila, Tetrahymena pigmentosa, and Tetrahymena borealis) were performed. The DNA samples from spelt and Tetrahymena were demonstrated to be genus specific for Triticum and species specific for Tetrahymena pyriformis, respectively. Copyright 2000 Academic Press.

  8. High power and high repetition solid state laser for EUV lithography

    Energy Technology Data Exchange (ETDEWEB)

    Fujita, H.; Mitra, A.; Wang, T. and the others [Osaka Univ., Osaka (Japan)

    2004-07-01

    We have been developing a high repetition (5 kHz) and high power (5kW) Nd:YAG laser system for EUV lithography. Key subjects are (1) reliable front-end, (2) uniform and high density pumping of main amplifier rods, and (3) compensation of thermal effects. A stable and reliable front-end based on fiber lasers has been developed. As a cw oscillator using Yb-doped silica fiber operates single longitudinal mode at 1030 nm to 1080nm, various laser materials (Yb:YAG, Nd:YLF, Nd:YAG, Nd:YAP, etc) can be used as main laser medium. A fast LN EO modulator switches out arbitrary pulse shape with response time of 100 ps. Laser pulses from the modulator are amplified by 3 stage fiber amplifiers up to 1 J. We will focus our efforts to attain 1 mJ output from the fiber front-end. Output pulses from the front-end are amplified to 100 mJ level by two 4-mm rod amplifiers (Nd:YAG) and two 6-mm rod amplifiers. Main amplifier chain consists of eight 12-mm rod amplifiers pumped by cw laser diodes. Total output power of the laser diodes is 28.8 kW. Double pass geometry is required to get enough gain and to compensate thermal effects. Spatial filters are installed to adjust thermal lens in the amplifiers and to send an image into just the center of the amplifiers. Ninty degree rotators and faraday rotators are installed in order to compensate thermal birefringence. A test amplifier module was made for investigation on uniform pumping, thermal effects, gain properties, and so on. Six laser diode modules with 4.5 kW total output power are installed in symmetric configuration. Active medium is Nd:YAG rod with 0.6% doping. Diameter and length of the rod are 12 mm and 150 mm, respectively. Peak gain of 1.67 was obtained at 4.2 kW pumping power and 200s pumping duration. Pumping uniformity was measured by both gain distribution and spontaneous emission from the laser rod. Fairly good uniformity was achieved by adjusting pumping geometry. Detail system analysis suggests that 8 amplifier modules

  9. CA88, a nuclear repetitive DNA sequence identified in Schistosoma mansoni, aids in the genotyping of nine Schistosoma species of medical and veterinary importance.

    Science.gov (United States)

    Bahia, Diana; Rodrigues, Nilton B; Araújo, Flávio Marcos G; Romanha, Alvaro José; Ruiz, Jerônimo C; Johnston, David A; Oliveira, Guilherme

    2010-07-01

    CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma mansoni. The assembled S. mansoni sequence, which contains the CA88 repeat, has 8,887 nucleotides and at least three repeat units of approximately 360 bp. In addition, CA88 also possesses an internal CA microsatellite, identified as SmBr18. Both PCR and BLAST analysis have been used to analyse and confirm the CA88 sequence in other S. mansoni sequences in the public database. PCR-acquired nuclear repetitive DNA sequence profiles from nine Schistosoma species were used to classify this organism into four genotypes. Included among the nine species analysed were five sequences of both African and Asian lineages that are known to infect humans. Within these genotypes, three of them refer to recognised species groups. A panel of four microsatellite loci, including SmBr18 and three previously published loci, has been used to characterise the nine Schistosoma species. Each species has been identified and classified based on its CA88 DNA fingerprint profile. Furthermore, microsatellite sequences and intra-specific variation have also been observed within the nine Schistosoma species sequences. Taken together, these results support the use of these markers in studying the population dynamics of Schistosoma isolates from endemic areas and also provide new methods for investigating the relationships between different populations of parasites. In addition, these data also indicate that Schistosoma magrebowiei is not a sister taxon to Schistosoma mattheei, prompting a new designation to a basal clade.

  10. Asynchronous single-shot characterization of high-repetition-rate ultrafast waveforms using a time-lens-based temporal magnifier.

    Science.gov (United States)

    Okawachi, Yoshitomo; Salem, Reza; Johnson, Adrea R; Saha, Kasturi; Levy, Jacob S; Lipson, Michal; Gaeta, Alexander L

    2012-12-01

    We demonstrate asynchronous, single-shot characterization of an ultrafast, high-repetition-rate pulse source using a time-lens-based temporal magnifier. We measure a 225 GHz repetition-rate pulse train from a microresonator-based frequency comb. In addition, we show that such a system can be used as a frequency compressor for real-time, high-speed RF spectral characterization.

  11. Detector response in time-of-flight mass spectrometry at high pulse repetition frequencies

    Science.gov (United States)

    Gulcicek, Erol E.; Boyle, James G.

    1993-01-01

    Dead time effects in chevron configured dual microchannel plates (MCPs) are investigated. Response times are determined experimentally for one chevron-configured dual MCP-type detector and two discrete dynode-type electron multipliers with 16 and 23 resistively divided stages. All of these detectors are found to be suitable for time-of-flight mass spectrometry (TOF MS), yielding 3-6-ns (FWHM) response times triggered on a single ion pulse. It is concluded that, unless there are viable solutions to overcome dead time disadvantages for continuous dynode detectors, suitable discrete dynode detectors for TOF MS appear to have a significant advantage for high repetition rate operation.

  12. C-band disk-loaded-type accelerating structure for a high acceleration gradient and high-repetition-rate operation

    Directory of Open Access Journals (Sweden)

    T. Sakurai

    2017-04-01

    Full Text Available A high-acceleration-gradient linear accelerator (LINAC for an x-ray free electron laser (XFEL offers the advantages of a short accelerator length and low construction costs. In addition, the high pulse repetition rate of the LINAC, which can drive multiple x-ray beam lines, provides additional user opportunities for experiments involving XFEL. A C-band disk-loaded-type accelerating structure was developed to achieve a high acceleration gradient of >50  MV/m and an rf-pulse repetition rate of 120 pps, which is twice as high as that of the XFEL facility, SACLA (60 pps. The structure has a quasiconstant gradient and a traveling wave type with an accelerating mode of TM01−2π/3. To reduce the surface electric fields, we employed a cross section with an ellipsoidal curvature around an iris aperture. The accelerating structure was manufactured for SACLA. High-power rf conditioning was conducted to investigate its performance. Owing to the conditioning, the acceleration gradient reached a value of more than 50.1  MV/m. The structure was operated without any serious issues at a repetition rate of 120 pps. The accelerating structures were installed in the dedicated accelerator for EUV-FEL at SACLA beam line-1. Finally, we obtained accelerated electron beams with the structures operated at an acceleration gradient of 41.4  MV/m.

  13. C -band disk-loaded-type accelerating structure for a high acceleration gradient and high-repetition-rate operation

    Science.gov (United States)

    Sakurai, T.; Ego, H.; Inagaki, T.; Asaka, T.; Suzuki, D.; Miura, S.; Otake, Y.

    2017-04-01

    A high-acceleration-gradient linear accelerator (LINAC) for an x-ray free electron laser (XFEL) offers the advantages of a short accelerator length and low construction costs. In addition, the high pulse repetition rate of the LINAC, which can drive multiple x-ray beam lines, provides additional user opportunities for experiments involving XFEL. A C -band disk-loaded-type accelerating structure was developed to achieve a high acceleration gradient of >50 MV /m and an rf-pulse repetition rate of 120 pps, which is twice as high as that of the XFEL facility, SACLA (60 pps). The structure has a quasiconstant gradient and a traveling wave type with an accelerating mode of TM 01 -2 π /3 . To reduce the surface electric fields, we employed a cross section with an ellipsoidal curvature around an iris aperture. The accelerating structure was manufactured for SACLA. High-power rf conditioning was conducted to investigate its performance. Owing to the conditioning, the acceleration gradient reached a value of more than 50.1 MV /m . The structure was operated without any serious issues at a repetition rate of 120 pps. The accelerating structures were installed in the dedicated accelerator for EUV-FEL at SACLA beam line-1. Finally, we obtained accelerated electron beams with the structures operated at an acceleration gradient of 41.4 MV /m .

  14. Comparison between phage-open-reading frame typing and automated repetitive-sequence-based PCR for typing MRSA isolates.

    Science.gov (United States)

    Osawa, Kayo; Shigemura, Katsumi; Jikimoto, Takumi; Shirakawa, Toshiro; Fujisawa, Masato; Arakawa, Soichi

    2014-08-01

    The methods for typing and epidemiological study for especially antibiotic-resistant bacteria has been issued but there are the debates regarding which method is best for this purpose. The purpose of this study is to investigate and apply a comparatively new technology, phage-open-reading frame typing (POT) and repetitive-sequence-based PCR (rep-PCR) using DiversiLab system and compare for the discrimination of major methicillin-resistant Staphylococcus aureus (MRSA) lineages in epidemiological surveillance. We analyzed 47 representative MRSA stains isolated in Kobe University Hospital between January and December 2009. We performed MRSA typing using the POT kit and rep-PCR using the DiversiLab system. POT method classified all the MRSA strains into 35 clusters, whereas rep-PCR method typed all the MRSA strains in 10 kinds of clusters with a definition of 95% similarity. The discriminatory power and congruence between the methods were compared using the Simpson's index of diversity, adjusted Rand's and Wallace's coefficients. Our statistical analyses showed that the POT (POT 1-2-3 and POT 2-3) revealed a higher discriminatory power in the Simpson's index of diversity (SID; 0.969, range 0.939-1.000 and 0.967, range 0.935-0.998, respectively) for MRSA isolates than the rep-PCR (0.821 (0.767-0.876)). The adjusted Rand's and Wallace's coefficients did not show higher concordance among the methods. In conclusion, we demonstrated that the POT can perform accurate and reliable epidemiological surveillance studies for analyzing the genetic relatedness of MRSA strains.

  15. Monitoring transmission routes of Listeria spp. in smoked salmon production with repetitive element sequence-based PCR techniques.

    Science.gov (United States)

    Zunabovic, M; Domig, K J; Pichler, I; Kneifel, W

    2012-03-01

    Various techniques have been used for tracing the transmission routes of Listeria species and for the assessment of hygiene standards in food processing plants. The potential of repetitive element sequence-based PCR (Rep-PCR) methods (GTG₅ and REPI + II) for the typing of Listeria isolates (n = 116), including Listeria monocytogenes (n = 46), was evaluated in a particular situation arising from the relocation of a company producing cold-smoked salmon. Pulsed-field gel electrophoresis (PFGE) using three restriction enzymes (ApaI, AscI, and SmaI) was used for comparison. Identical transmission scenarios among two companies could be identified by cluster analysis of L. monocytogenes isolates that were indistinguishable by both Rep-PCR and PFGE. The calculated diversity index (DI) indicates that Rep-PCR subtyping of Listeria species with primer sets GTG₅ and REPI + II has a lower discrimination power than does PFGE. When concatenated Rep-PCR cluster analysis was used, the DI increased from 0.934 (REPI + II) and 0.923 (GTG₅) to 0.956. The discrimination power of this method was similar to that of PFGE typing based on restriction enzyme Apa I (DI = 0.955). Listeria welshimeri may be useful as an indicator for monitoring smoked salmon processing environments. Rep-PCR meets the expectations of a reasonable, fast, and low-cost molecular subtyping method for the routine monitoring of Listeria species. The discriminatory power as characterized by the DI sufficiently quantifies the probability of unrelated isolates being characterized as different subtypes. Therefore, Rep-PCR typing based on two primer systems (GTG₅ and REPI + II) may be a useful tool for monitoring industrial hygiene.

  16. Neuromuscular manifestations of viscoelastic tissue degradation following high and low risk repetitive lumbar flexion.

    Science.gov (United States)

    Solomonow, M

    2012-04-01

    Cumulative lumbar disorder is common in individuals engaged in long term performance of repetitive and static occupational/sports activities with the spine. The triggering source and of the disorder, the tissues involved in the failure and the biomechanical, neuromuscular, and biological processes active in the initiation and development of the disorder are not known. The hypothesis is forwarded that static and repetitive (cyclic) lumbar flexion-extension and the associated repeated stretch of the various viscoelastic tissues (ligaments, fascia, facet capsule, discs, etc.) causes micro-damage in their collagen fibers followed by an acute inflammation, triggering pain and reflexive muscle spasms/hyper-excitability. Continued exposure to activities, over time, converts the acute inflammation into a chronic one, viscoelastic tissues remodeling/degeneration, modified motor control strategy and permanent disability. Changes in lumbar stability are expected during the development of the disorder. A series of experimental data from in-vivo feline is reviewed and integrated with supporting evidence from the literature to gain a valuable insight into the multi-factorial development of the disorder. Prolonged cyclic lumbar flexion-extension at high loads, high velocities, many repetitions and short in between rest periods induced transient creep/laxity in the spine, muscle spasms and reduced stability followed, several hours later, by an acute inflammation/tissue degradation, muscular hyper-excitability and increased stability. The major findings assert that viscoelastic tissues sub-failure damage is the source and inflammation is the process which governs the mechanical and neuromuscular characteristic symptoms of the disorder. A comprehensive model of the disorder is presented. The experimental data validates the hypothesis as well as provide insights into the development of potential treatment and prevention of the disorder. Copyright © 2011 Elsevier Ltd. All rights

  17. High-repetition rate UV lasers with inductive-capacitive discharge stabilization

    Science.gov (United States)

    Andramanov, A. V.; Kabaev, S. A.; Lazhintsev, B. V.; Nor-Arevyan, V. A.; Pisetskaya, A. V.; Selemir, V. D.

    2007-04-01

    The high repetition rate UV lasers (XeF [1], KrF [2] and N II) with a new electrode unit are investigated. A multisectional discharge gap 25 cm length and 1.2 cm height is formed by 25 pairs of anode-cathode plates. The discharge width is ~ 1 mm. The average specific pump power is ~ 9 MW cm -3. The main aim of the work is the achievement of a maximum pulse repetition rate (f m) with high output energy stability. At a rather low gas flow velociity <= 19 m s -1 the frequencies f as high as 4 kHz in the excimer lasers and 4.5 kHz in a nitrogen laser are realized. The relative rms deviations of the output energy (σ) for XeF and KrF lasers is in the range 1-2% for f <= 3 kHz and 3-4% for f = 4 kHz. For the nitrogen laser σ <= 1.3% is at f <= 4.5 κΓ\\tscy.The average output power 10 (12) W for the XeF (KrF) laser and 1.1 W for the nitrogen laser are reached.

  18. Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping.

    Science.gov (United States)

    Cai, Zexi; Liu, Huijun; He, Qunyan; Pu, Mingwei; Chen, Jian; Lai, Jinsheng; Li, Xuexian; Jin, Weiwei

    2014-11-25

    Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9-11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome

  19. The use of commercial thyristors in repetitive high voltage switching devices for plasma sources

    Science.gov (United States)

    Bac, J.; Reess, T.; Pecastaing, L.; Paillol, J.; Domens, P.

    2007-02-01

    This paper presents a commercial high voltage thyristor used as a switch allowing a tank capacitor to discharge in a load. In classical high power pulse technology applications the output voltage pulse has to be characterized mainly by its crest value, its rise-time, the period the thyristor is held in the on-state and the fall-time. These parameters are studied as a function of the power circuit and of the trigger circuit. The thyristor presents two behaviours: the main current is either higher or lower than the latching current. The “low current” behaviour is extensively investigated as it allows repetitive operation of the device. Two pulse power applications triggering electrical discharges are presented. Each one necessitates a specific pulsed power supply using series thyristor stacks or Marx structures. The first pulsed source delivers negative pulses with a crest voltage VoM=-35 kV, a turn on capability of Tr=90 ns and a repetition rate F=900 Hz. The second is built using Marx structure and is characterized by VoM=60 kV, Tr=250 ns, F=900 Hz.

  20. High-speed laser speckle photography. Part 1: repetitively Q-switched ruby laser light source

    Science.gov (United States)

    Huntley, Jonathan M.

    1994-05-01

    A system to record laser speckle photographs at framing rates in the range of 105 to 106 frames/s has been developed, based on a repetitively Q- switched ruby laser and rotating mirror high-speed camera. The laser and electro-optic modulator are described. The circuit diagram for an inexpensive high-voltage amplifier, capable of switching 2.5 kV at up to 1 MHz with fall and rise times of 100 and 200 ns, respectively, is given. The resulting optical pulse trains have pulse energy fluctuations at half the driving frequency. We show how these may be suppressed by reducing the time the Q- switch is left open. Both the subharmonic component and its suppression are explained from limiting cases of the laser rate equations. Representative pulse trains over a range of repetition rates are given; pulse energies greater than 20 mJ with pulse energy fluctuations of less than plus or minus one-half of a stop are obtained at rates of up to 500 kHz.

  1. A high repetition rate laser-heavy water based neutron source

    Science.gov (United States)

    Hah, Jungmoo; He, Zhaohan; Nees, John; Krushelnick, Karl; Thomas, Alexander; CenterUltrafast Optical Science Team

    2015-11-01

    Neutrons have numerous applications in diverse areas, such as medicine, security, and material science. For example, sources of MeV neutrons may be used for active interrogation for nuclear security applications. Recently, alternative ways to generate neutron flux have been studied. Among them, ultrashort laser pulse interactions with dense plasma have attracted significant attention as compact, pulse sources of neutrons. To generate neutrons using a laser through fusion reactions, thin solid density targets have been used in a pitcher-catcher arrangement, using deuterated plastic for example. However, the use of solid targets is limited for high-repetition rate operation due to the need to refresh the target for every laser shot. Here, we use a free flowing heavy water target with a high repetition rate (500 Hz) laser without a catcher. From the interaction between a 10 micron scale diameter heavy water stream with the Lambda-cubed laser system at the Univ. of Michigan (12mJ, 800nm, 35fs), deuterons collide with each other resulting in D-D fusion reactions generating 2.45 MeV neutrons. Under best conditions a time average of ~ 105 n/s of neutrons are generated.

  2. High Repetition Rate Pulsed 2-Micron Laser Transmitter for Coherent CO2 DIAL Measurement

    Science.gov (United States)

    Singh, Uprendra N.; Bai, Yingxin; Yu, Jirong; Petros, Mulugeta; Petzar, Paul J.; Trieu, Bo C.; Lee, Hyung

    2009-01-01

    A high repetition rate, highly efficient, Q-switched 2-micron laser system as the transmitter of a coherent differential absorption lidar for CO2 measurement has been developed at NASA Langley Research Center. Such a laser transmitter is a master-slave laser system. The master laser operates in a single frequency, either on-line or off-line of a selected CO2 absorption line. The slave laser is a Q-switched ring-cavity Ho:YLF laser which is pumped by a Tm:fiber laser. The repetition rate can be adjusted from a few hundred Hz to 10 kHz. The injection seeding success rate is from 99.4% to 99.95%. For 1 kHz operation, the output pulse energy is 5.5mJ with the pulse length of approximately 50 ns. The optical-to-optical efficiency is 39% when the pump power is 14.5W. The measured standard deviation of the laser frequency jitter is about 3 MHz.

  3. Optimization and phase matching of fiber-laser-driven high-order harmonic generation at high repetition rate.

    Science.gov (United States)

    Cabasse, Amélie; Machinet, Guillaume; Dubrouil, Antoine; Cormier, Eric; Constant, Eric

    2012-11-15

    High-repetition-rate sources are very attractive for high-order harmonic generation (HHG). However, due to their pulse characteristics (low energy, long duration), those systems require a tight focusing geometry to achieve the necessary intensity to generate harmonics. In this Letter, we investigate theoretically and experimentally the optimization of HHG in this geometry, to maximize the extreme UV (XUV) photon flux and improve the conversion efficiency. We analyze the influence of atomic gas media (Ar, Kr, or Xe), gas pressure, and interaction geometries (a gas jet and a finite and a semi-infinite gas cell). Numerical simulations allow us to define optimal conditions for HHG in this tight focusing regime and to observe the signature of on-axis phase matching. These conditions are implemented experimentally using a high-repetition-rate Yb-doped fiber laser system. We achieve optimization of emission with a recorded XUV photon flux of 4.5×10(12) photons/s generated in Xe at 100 kHz repetition rate.

  4. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

    Science.gov (United States)

    Zimin, Aleksey V; Puiu, Daniela; Luo, Ming-Cheng; Zhu, Tingting; Koren, Sergey; Marçais, Guillaume; Yorke, James A; Dvořák, Jan; Salzberg, Steven L

    2017-05-01

    Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn create significant problems for downstream analysis; for example, a single indel may shift the reading frame and incorrectly truncate a protein sequence. Here, we describe an algorithm that solves the high error rate problem by combining long, high-error reads with shorter but much more accurate Illumina sequencing reads, whose error rates average assembly algorithm combines these two types of reads to construct mega-reads, which are both long and accurate, and then assembles the mega-reads using the CABOG assembler, which was designed for long reads. We apply this technique to a large data set of Illumina and PacBio sequences from the species Aegilops tauschii, a large and extremely repetitive plant genome that has resisted previous attempts at assembly. We show that the resulting assembled contigs are far larger than in any previous assembly, with an N50 contig size of 486,807 nucleotides. We compare the contigs to independently produced optical maps to evaluate their large-scale accuracy, and to a set of high-quality bacterial artificial chromosome (BAC)-based assemblies to evaluate base-level accuracy. © 2017 Zimin et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns.

    Science.gov (United States)

    Guo, Wenhu; Zhu, Andan; Fan, Weishu; Mower, Jeffrey P

    2017-01-01

    Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  6. A high-brightness repetitively pulsed UV radiation source using a linearly stabilized surface discharge

    Science.gov (United States)

    Bugrimov, S. N.; Kamrukov, A. S.; Kashnikov, G. N.; Kozlov, N. P.; Ovchinnikov, P. A.

    1986-01-01

    A method is proposed for initiating spark plasma discharges on a dielectric surface in the form of strictly rectilinear plasma channels. The method can be implemented using relatively modest (less than 25 kV) working and ignition voltages and does not require any 'hard' electrotechnical loops. Experiments were carried out in order to study the formation dynamics, energy, and spectral brightness characteristics of linearly stabilized surface discharges having linearly stabilized spark channel and the results are discussed. High-speed photographs of the discharges are presented and the spectrum of radiation from the discharges is illustrated in graphic form. It is shown that linearly stabilized discharges can be used to obtain high-power repetitively pulsed sources of CW ultraviolet radiation in the UV region having a brightness temperature of at least 40 K.

  7. Development of a Watt-level gamma-ray source based on high-repetition-rate inverse Compton scattering

    Energy Technology Data Exchange (ETDEWEB)

    Mihalcea, D.; Murokh, A.; Piot, P.; Ruan, J.

    2017-07-01

    A high-brilliance (~1022 photon s-1 mm-2 mrad-2 /0.1%) gamma-ray source experiment is currently being planned at Fermilab (Eγ≃1.1 MeV). The source implements a high-repetition-rate inverse Compton scattering by colliding electron bunches formed in a ~300-MeV superconducting linac with a high-intensity laser pulse. This paper describes the design rationale along with some of technical challenges associated to producing high-repetition-rate collision. The expected performances of the gamma-ray source are also presented.

  8. CA88, a nuclear repetitive DNA sequence identified in Schistosoma mansoni, aids in the genotyping of nine Schistosoma species of medical and veterinary importance

    Directory of Open Access Journals (Sweden)

    Diana Bahia

    2010-07-01

    Full Text Available CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma mansoni. The assembled S. mansoni sequence, which contains the CA88 repeat, has 8,887 nucleotides and at least three repeat units of approximately 360 bp. In addition, CA88 also possesses an internal CA microsatellite, identified as SmBr18. Both PCR and BLAST analysis have been used to analyse and confirm the CA88 sequence in other S. mansoni sequences in the public database. PCR-acquired nuclear repetitive DNA sequence profiles from nine Schistosoma species were used to classify this organism into four genotypes. Included among the nine species analysed were five sequences of both African and Asian lineages that are known to infect humans. Within these genotypes, three of them refer to recognised species groups. A panel of four microsatellite loci, including SmBr18 and three previously published loci, has been used to characterise the nine Schistosoma species. Each species has been identified and classified based on its CA88 DNA fingerprint profile. Furthermore, microsatellite sequences and intra-specific variation have also been observed within the nine Schistosoma species sequences. Taken together, these results support the use of these markers in studying the population dynamics of Schistosoma isolates from endemic areas and also provide new methods for investigating the relationships between different populations of parasites. In addition, these data also indicate that Schistosoma magrebowiei is not a sister taxon to Schistosoma mattheei, prompting a new designation to a basal clade.

  9. Analyzing the effect of high repetition laser shock peening on dynamic corrosion rate of magnesium

    Science.gov (United States)

    Caralapatti, Vinodh Krishna; Narayanswamy, Sivakumar

    2017-08-01

    Magnesium as implant material is being investigated extensively due to its superior suitability. With corrosion rate being the major obstacle, this paper aims to determine the effects of high repetition laser shock peening (HRLSP) on the dynamic corrosion rate of magnesium. While there is lot of research on corrosion of magnesium, in this work, a specially designed test bench was used for characterization of dynamic corrosion to mimic the physiological conditions experienced by the implant inside human body. From the results, it can be inferred that corrosion rate of peened samples reduced by at least 6 times compared to unpeened sample and sample peened with 66% overlap 1 scans exhibited the least corrosion. The wettability of the samples was also determined as a measure to analyze the effects of HRLSP on biocompatibility. In addition, peening is seen to induce surface corrosion, which minimizes the risks of implant failure.

  10. Research of magnetic self-balance used in a repetitive high voltage rectangular waveform pulse adder

    Science.gov (United States)

    Qianyu, ZHOU; Liqing, TONG; Kefu, LIU

    2018-01-01

    Compared with a sinusoidal operation, pulsed operation has more homogeneity and more efficiency in dielectric barrier discharge. In this paper, an improved pulse adder is designed and assembled to create repetitive high voltage rectangular pulses when resistive loads or capacitive loads exist. Beyond the normal pulse adder based on solid-state switches, additional metal–oxide–semiconductor field effect transistors are used in each stage for a faster falling edge. Further, the voltage difference between stages is eliminated by balancing windings. In this paper, we represent our theoretical derivation, software simulations and hardware experiments on magnetic self-balance. The experiments show that the voltage difference between stages is eliminated by balancing windings, which matches the result of simulations with almost identical circuits and parameters.

  11. Neonatal Pasteurella multocida subsp. septica Meningitis Traced to Household Cats: Molecular Linkage Analysis Using Repetitive-Sequence-Based PCR.

    Science.gov (United States)

    Boyanton, Bobby L; Freij, Bishara J; Robinson-Dunn, Barbara; Makin, Jacob; Runge, Jessica K; Luna, Ruth Ann

    2016-01-01

    Pasteurella multocida is a rare cause of neonatal bacterial meningitis. We describe such a case and verify two household cats as the source of infection using repetitive-element PCR (rep-PCR) molecular fingering. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Dentin bond strength after ablation using a CO2 laser operating at high pulse repetition rates

    Science.gov (United States)

    Hedayatollahnajafi, Saba; Staninec, Michal; Watanabe, Larry; Lee, Chulsung; Fried, Daniel

    2009-02-01

    Pulsed CO2 lasers show great promise for the rapid and efficient ablation of dental hard tissues. Our objective was to demonstrate that CO2 lasers operated at high repetition rates can be used for the rapid removal of dentin without excessive thermal damage and without compromising adhesion to restorative materials. Human dentin samples (3x3mm2) were rapidly ablated with a pulsed CO2 laser operating at a wavelength of 9.3-µm, pulse repetition rate of 300-Hz and an irradiation intensity of 18-J/cm2. The bond strength to composite was determined by the modified single plane shear test. There were 8 test groups each containing 10 blocks: negative control (non-irradiated non-etched), positive control (non-irradiated acid-etched), and six laser treated groups (three etched and three non-etched sets). The first and second etched and non-etched sets were ablated at a speed of 25 mm/sec and 50 mm/sec with water, respectively. The third set was also ablated at 50 mm/sec without application of water during laser irradiation. Minimal thermal damage was observed on the dentin surfaces for which water cooling was applied. Bond strengths exceeded 20 MPa for laser treated surfaces that were acid-etched after ablation (25-mm/sec: 29.9-MPa, 50-mm/sec: 21.3-MPa). The water-cooled etched laser groups all produced significantly stronger bonds than the negative control (pbond strength than the positive control (pbond strength than the acid-etched control samples is clinically significant where durability of these bonded restoration supersedes high bond strength.

  13. Compact, high-repetition-rate source for broadband sum-frequency generation spectroscopy

    Science.gov (United States)

    Heiner, Zsuzsanna; Petrov, Valentin; Mero, Mark

    2017-06-01

    We present a high-efficiency optical parametric source for broadband vibrational sum-frequency generation (BB-VSFG) for the chemically important mid-infrared spectral range at 2800-3600 cm-1 to study hydrogen bonding interactions affecting the structural organization of biomolecules at water interfaces. The source consists of a supercontinuum-seeded, dual-beam optical parametric amplifier with two broadband infrared output beams and a chirped sum-frequency mixing stage providing narrowband visible pulses with adjustable bandwidth. Utilizing a pulse energy of only 60 μJ from a turn-key, 1.03-μm pump laser operating at a repetition rate of 100 kHz, the source delivers 6-cycle infrared pulses at 1.5 and 3.2 μm with pulse energies of 4.6 and 1.8 μJ, respectively, and narrowband pulses at 0.515 μm with a pulse energy of 5.0 μJ. The 3.2-μm pulses are passively carrier envelope phase stabilized with fluctuations at the 180-mrad level over a 10-s time period. The 1.5-μm beamline can be exploited to deliver pump pulses for time-resolved studies after suitable frequency up-conversion. The high efficiency, stability, and two orders of magnitude higher repetition rate of the source compared to typically employed systems offer great potential for providing a boost in sensitivity in BB-VSFG experiments at a reduced cost.

  14. High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes.

    Science.gov (United States)

    Krasikova, Alla; Fukagawa, Tatsuo; Zlotina, Anna

    2012-12-01

    Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes.

  15. Stabilization of a premixed methane-air flame with a high repetition nanosecond laser-induced plasma

    Science.gov (United States)

    Yu, Yang; Li, Xiaohui; An, Xiaokang; Yu, Xin; Fan, Rongwei; Chen, Deying; Sun, Rui

    2017-07-01

    Laser-induced plasma ignition has been applied in various combustion systems, however, work on flame stabilization with repetitive laser-induced plasma (LIP) is rather limited. In this paper, stabilization of a premixed methane-air flame with a high repetition nanosecond LIP is reported. The plasma energy coupling and the temporal evolution of the flame kernels generated by the LIPs are investigated with different laser repetition rates, i.e., 1 Hz, 100 Hz and 250 Hz, respectively. The plasma energy coupling is not affected in the air flow and in the premixed methane-air flow with the applied laser repetition rates. Continuous combustion flame stabilization has been achieved with LIPs of 100 Hz and 250 Hz, in terms of catch-up and merging of the consecutive flame kernels. The flame kernel formed by the last LIP does not affect the evolution of the newly formed flame kernel by the next LIP. The catch-up distance, defined as the distance from the LIP initiation site to the flame kernel catch-up position, is estimated for different laser repetition rates based on the temporal evolution of the flame kernels. A higher laser repetition rate will lead to a shorter catch-up distance which is beneficial for flame stabilization. The up limit for the laser repetition rate to realize effective flame stabilization is determined from the critical inter-pulse delay defined from the onset of the LIP to the return of the initially contraflow propagating lower front to the LIP initiation site. The up limit is 377 Hz under the flow conditions of this work (equivalence ratio of 1, flow speed of 2 m/s, and Reynolds number of 1316).

  16. How repetitive are genomes?

    Directory of Open Access Journals (Sweden)

    Wiehe Thomas

    2006-12-01

    Full Text Available Abstract Background Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, Ir, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life. Results The expected value of Ir is zero for random sequences of any G/C content and greater than zero for sequences with excess repeats. We find that the Ir of archaea is significantly smaller than that of eubacteria, which in turn is smaller than that of eukaryotes. Mouse chromosomes have a significantly higher Ir than human chromosomes and within each genome the Y chromosome is most repetitive. A sliding window analysis reveals that the human HOXA cluster and two surrounding genes are characterized by local minima in Ir. A program for calculating the Ir is freely available at http://adenine.biz.fh-weihenstephan.de/ir/. Conclusion The general measure of DNA repetitiveness proposed in this paper can be efficiently computed on a genomic scale. This reveals a broad spectrum of repetitiveness among diverse genomes which agrees qualitatively with previous studies of repeat content. A sliding window analysis helps to analyze the intragenomic distribution of repeats.

  17. Repetition rates of specific interval patterns in single spike train reflect excitation level of specific receptor types, shown by high-speed favored-pattern detection method.

    Science.gov (United States)

    Ku, Yun-Hui; Wang, Ming; Li, Yao-Hua; Sun, Ze-Jin; Guo, Tao; Wu, Jin-Sheng

    2006-10-03

    Interval patterns in single spike train, e.g. "favored patterns (FPs, the FP is a sequence of successive intervals of action potentials that occur more often than what is reasonably expected at random.)", may represent neural codes containing information. The present study developed a "high-speed FP-detection method" which could qualitatively and quantitatively analyze FPs. By using this method, single spike trains of nucleus paraventricularis (NPV) and rostral ventrolateral medulla (RVL) having different firing patterns, being involved in regulation of arterial pressure, and controlled by different transmitters, were chosen for analysis. (1) Corticotropin releasing factor, substance P and agonists of alpha-, beta- and M-receptor microinjected into these brain areas, respectively, induced dominant change of specific FP. Repetition rates of specific FPs reflect excitation level of specific receptor types. It shows that chemical codes (different transmitters with their receptor types or subtypes) are transformed into electrical codes (different FPs). (2) When alpha-, beta- and M-receptors of RVL neurons were activated simultaneously by intrinsic excitatory transmitters released due to activation of input pathway, only repetition rate of the specific FP that represented the predominant activity of the receptor type (alpha-adrenergic receptor) markedly increased. The activities of other receptor types (beta- and M-receptors) were masked. (3) Intrinsic inhibitory transmitters (GABA, beta-endorphin) in the RVL all decreased specific FP repetition rate of dominant receptor type. These results may provide a new way to further explore how information in the CNS is conveyed and processed.

  18. Fuzzy Adaptive Repetitive Control for Periodic Disturbance with Its Application to High Performance Permanent Magnet Synchronous Motor Speed Servo Systems

    Directory of Open Access Journals (Sweden)

    Junxiao Wang

    2016-09-01

    Full Text Available For reducing the steady state speed ripple, especially in high performance speed servo system applications, the steady state precision is more and more important for real servo systems. This paper investigates the steady state speed ripple periodic disturbance problem for a permanent magnet synchronous motor (PMSM servo system; a fuzzy adaptive repetitive controller is designed in the speed loop based on repetitive control and fuzzy information theory for reducing periodic disturbance. Firstly, the various sources of the PMSM speed ripple problem are described and analyzed. Then, the mathematical model of PMSM is given. Subsequently, a fuzzy adaptive repetitive controller based on repetitive control and fuzzy logic control is designed for the PMSM speed servo system. In addition, the system stability analysis is also deduced. Finally, the simulation and experiment implementation are respectively based on the MATLAB/Simulink and TMS320F2808 of Texas instrument company, DSP (digital signal processor hardware platform. Comparing to the proportional integral (PI controller, simulation and experimental results show that the proposed fuzzy adaptive repetitive controller has better periodic disturbance rejection ability and higher steady state precision.

  19. High-power, highly stable KrF laser with a 4-kHz pulse repetition rate

    Energy Technology Data Exchange (ETDEWEB)

    Borisov, V M; El' tsov, A V; Khristoforov, O B [State Research Center of Russian Federation ' Troitsk Institute for Innovation and Fusion Research' , Troitsk, Moscow Region (Russian Federation)

    2015-08-31

    An electric-discharge KrF laser (248 nm) with an average output power of 300 W is developed and studied. A number of new design features are related to the use of a laser chamber based on an Al{sub 2}O{sub 3} ceramic tube. A high power and pulse repetition rate are achieved by using a volume discharge with lateral preionisation by the UV radiation of a creeping discharge in the form of a homogeneous plasma sheet on the surface of a plane sapphire plate. Various generators for pumping the laser are studied. The maximum laser efficiency is 3.1%, the maximum laser energy is 160 mJ pulse{sup -1}, and the pulse duration at half maximum is 7.5 ns. In the case of long-term operation at a pulse repetition rate of 4 kHz and an output power of 300 W, high stability of laser output energy (σ ≤ 0.7%) is achieved using an all-solid-state pump system. (lasers)

  20. High-power, highly stable KrF laser with a 4-kHz pulse repetition rate

    Science.gov (United States)

    Borisov, V. M.; El'tsov, A. V.; Khristoforov, O. B.

    2015-08-01

    An electric-discharge KrF laser (248 nm) with an average output power of 300 W is developed and studied. A number of new design features are related to the use of a laser chamber based on an Al2O3 ceramic tube. A high power and pulse repetition rate are achieved by using a volume discharge with lateral preionisation by the UV radiation of a creeping discharge in the form of a homogeneous plasma sheet on the surface of a plane sapphire plate. Various generators for pumping the laser are studied. The maximum laser efficiency is 3.1%, the maximum laser energy is 160 mJ pulse-1, and the pulse duration at half maximum is 7.5 ns. In the case of long-term operation at a pulse repetition rate of 4 kHz and an output power of 300 W, high stability of laser output energy (σ <= 0.7%) is achieved using an all-solid-state pump system.

  1. High-peak-power, high-repetition-rate LD end-pumped Nd:YVO4 burst mode laser

    Science.gov (United States)

    Pan, Hu; Yan, Renpeng; Fa, Xin; Yu, Xin; Ma, Yufei; Fan, Rongwei; Li, Xudong; Chen, Deying; Zhou, Zhongxiang

    2016-06-01

    A compact high-peak-power, high-repetition-rate burst mode laser is achieved by an acousto-optical Q-switched Nd:YVO4 1064 nm laser directly pumped at 878.6 nm. Pulse trains with 10-100 pulses are obtained using acousto-optical Q-switch at repetition rates of 10-100 kHz under a pulsed pumping with a 1 ms duration. At the maximum pump energy of 108.5 mJ, the pulse energy of 10 kHz burst mode laser reaches 44 mJ corresponding to a single pulse energy of 4.4 mJ and an optical-to-optical efficiency of 40.5 %.The maximum peak power of ~468.1 kW at 10 kHz is obtained with a pulse width of 9.4 ns. The beam quality factor is measured to be M 2 ~1.5 and the pulse jitter is estimated to be less than 1 % in both amplitude and time region.

  2. Phase-stable single-pass cryogenic amplifier for high repetition rate few-cycle laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Ozawa, Akira; Schneider, Waldemar; Haensch, Theodor W; Udem, Thomas; Hommelhoff, Peter [Max-Planck-Institut fuer Quantenoptik, Hans-Kopfermann-Strasse 1, D 85748 Garching (Germany)], E-mail: akira.ozawa@mpq.mpg.de, E-mail: peter.hommelhoff@mpq.mpg.de

    2009-08-15

    We demonstrate cryogenic Ti:sapphire single-pass amplification of sub-7 fs laser pulses with 80 MHz repetition rate. We amplify the output of a broadband Ti:sapphire oscillator by more than a factor of two, re-compress the pulses down to sub-7 fs, and show that the rms carrier-envelope phase jitter stays below 70 as after amplification. The amplified output exceeds 2 MW of peak power and 1 W of average power. In addition, we demonstrate amplification of {approx}200 fs, 75 MHz oscillator pulses up to 1.6 W with a gain of four. This work opens a new way to explore phase sensitive and highly nonlinear phenomena at the full oscillator repetition rate. As a first example, we demonstrate white light generation in a bulk crystal at the full oscillator repetition rate.

  3. Applications of High Throughput Nucleotide Sequencing

    DEFF Research Database (Denmark)

    Waage, Johannes Eichler

    The recent advent of high throughput sequencing of nucleic acids (RNA and DNA) has vastly expanded research into the functional and structural biology of the genome of all living organisms (and even a few dead ones). With this enormous and exponential growth in biological data generation come...... equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......, focusing on oft encountered problems in data processing, such as quality assurance, mapping, normalization, visualization, and interpretation. Presented in the second part are scientific endeavors representing solutions to problems of two sub-genres of next generation sequencing. For the first flavor, RNA-sequencing...

  4. Size and shape of the repetitive domain of high molecular weight wheat gluten proteins. II. Hydrodynamic studies

    NARCIS (Netherlands)

    van Swieten, E; Friesen, RR; de Kruif, CG; Robillard, GT; Kruif, Cees G. de

    This study describes the hydrodynamic properties of the repetitive domain of high molecular weight (HMW) wheat proteins, which complement the small-angle scattering (SANS) experiments performed in the first paper of this series. The sedimentation coefficients, so, and diffusion coefficients, D, were

  5. High Power, Repetitive, Stacked Blumlein Pulse Generators Commuted by a Single Switching Element

    Science.gov (United States)

    Bhawalkar, Jayant Dilip

    In this work, the stacked Blumlein pulsers developed at the University of Texas at Dallas were characterized and shown to be versatile sources of pulse power for a variety of applications. These devices consisted of several triaxial Blumleins stacked in series at one end. The lines were charged in parallel and synchronously commuted repetitively with a single switching element at the other end. In this way, relatively low charging voltages were multiplied to give a high discharge voltage across an arbitrary load without the need for complex Marx bank circuitry. Several pulser parameters such as the number of stacked Blumlein lines, line configuration, type of switching element, and the length of the lines, were varied and the waveform characteristics were observed and analyzed. It was shown that these devices are capable of generating fast rising waveforms with a wide range of peak voltage and current values. The generation of high power waveforms with pulse durations in the range of 80-600 ns was demonstrated without degradation of the voltage gains. The results of this work indicated that unlike generators based on stacked transmission lines, the effects of parasitic modes were not appreciable for the stacked Blumlein pulsers. Opportunities for tactically packaging these pulsers were also investigated and a significant reduction in their size and weight was demonstrated. For this, dielectric lifetime and Blumlein spacing studies were performed on small scale prototypes. In addition to production of intense X-ray pulses, the possible applications for these novel pulsers include driving magnetrons for high power microwave generation, pumping laser media, or powering e-beam diodes. They could also serve as compact, tabletop sources of high power pulses for various research experiments.

  6. A high repetition rate experimental setup for quantum non-linear optics with cold Rydberg atoms

    Science.gov (United States)

    Busche, Hannes; Ball, Simon W.; Huillery, Paul

    2016-12-01

    Using electromagnetically induced transparency and photon storage, the strong dipolar interactions between Rydberg atoms and the resulting dipole blockade can be mapped onto light fields to realise optical non-linearities and interactions at the single photon level. We report on the realisation of an experimental apparatus designed to study interactions between single photons stored as Rydberg excitations in optically trapped microscopic ensembles of ultracold 87Rb atoms. A pair of in-vacuum high numerical aperture lenses focus excitation and trapping beams down to 1 μm, well below the Rydberg blockade. Thanks to efficient magneto-optical trap (MOT) loading from an atomic beam generated by a 2D MOT and the ability to recycle the microscopic ensembles more than 20000 times without significant atom loss, we achieve effective repetition rates exceeding 110 kHz to obtain good photon counting statistics on reasonable time scales. To demonstrate the functionality of the setup, we present evidence of strong photon interactions including saturation of photon storage and the retrieval of non-classical light. Using in-vacuum antennae operating at up to 40 GHz, we perform microwave spectroscopy on photons stored as Rydberg excitations and observe an interaction induced change in lineshape depending on the number of stored photons.

  7. 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.

  8. 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

  9. Chromosomal Mapping of Repetitive DNA Sequences in Five Species of Astyanax (Characiformes, Characidae) Reveals Independent Location of U1 and U2 snRNA Sites and Association of U1 snRNA and 5S rDNA.

    Science.gov (United States)

    Silva, Duilio M Z A; Utsunomia, Ricardo; Pansonato-Alves, José C; Oliveira, Cláudio; Foresti, Fausto

    2015-01-01

    Astyanax is a genus of Characidae fishes currently composed of 155 valid species. Previous cytogenetic studies revealed high chromosomal diversification among them, and several studies have been performed using traditional cytogenetic techniques to investigate karyotypes and chromosomal locations of 18S and 5S rDNA genes. However, only a few studies are currently available about other repetitive sequences. Here, the chromosomal location of small nuclear RNA genes, identified as U1 and U2 snRNA clusters, was established and compared to the distribution of 5S rDNA and histone clusters in 5 Astyanax species (A. paranae, A. fasciatus, A. bockmanni, A. altiparanae, and A. jordani) using FISH. The cytogenetic mapping of U1 and U2 snRNA demonstrated a conserved pattern in the number of sites per genome independent of the location in Astyanax species. The location of the U1 snRNA gene was frequently associated with 5S rDNA sequences, indicating a possible interaction between the distinct repetitive DNA families. Finally, comparisons involving the location of U1 and U2 snRNA clusters in the chromosomes of Astyanax species revealed a very diverse pattern, suggesting that many rearrangements have occurred during the diversification process of this group. © 2015 S. Karger AG, Basel.

  10. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research.

    Science.gov (United States)

    Coates, Brad S; Sumerford, Douglas V; Hellmich, Richard L; Lewis, Leslie C

    2009-01-01

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

  11. A vacuum-sealed, gigawatt-class, repetitively pulsed high-power microwave source

    Science.gov (United States)

    Xun, Tao; Fan, Yu-wei; Yang, Han-wu; Zhang, Zi-cheng; Chen, Dong-qun; Zhang, Jian-de

    2017-06-01

    A compact L-band sealed-tube magnetically insulated transmission line oscillator (MILO) has been developed that does not require bulky external vacuum pump for repetitive operations. This device with a ceramic insulated vacuum interface, a carbon fiber array cathode, and non-evaporable getters has a base vacuum pressure in the low 10-6 Pa range. A dynamic 3-D Monte-Carlo model for the molecular flow movement and collision was setup for the MILO chamber. The pulse desorption, gas evolution, and pressure distribution were exactly simulated. In the 5 Hz repetition rate experiments, using a 600 kV diode voltage and 48 kA beam current, the average radiated microwave power for 25 shots is about 3.4 GW in 45 ns pulse duration. The maximum equilibrium pressure is below 4.0 × 10-2 Pa, and no pulse shortening limitations are observed during the repetitive test in the sealed-tube condition.

  12. 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

    2017-09-21

    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.

  13. Effect of pulse repetition frequency of high-intensity focused ultrasound on in vitro thrombolysis.

    Science.gov (United States)

    Yang, Wenjing; Zhou, Yufeng

    2017-03-01

    Vascular occlusion by the thrombi is the main reason for ischemic stroke and deep vein thrombosis. High-intensity focused ultrasound (HIFU) and histotripsy or microtripsy pulses can effectively dissolve the blood clot with no use of thrombolytic agent and ultrasound contrast agent (microbubbles). In this study, HIFU bursts at the same duty cycle (2%) but varied pulse repetition frequency (PRF) from 1Hz to 1000Hz were delivered to in vitro porcine blood clot for 30s. Thrombolysis efficiency initially increases slightly with the PRF, 86.4±10.3%, 89.9±11.9, and 92.9±12.8% at the PRF of 1Hz, 10Hz, and 100Hz, respectively, without significant difference (p>0.05), but then drops dramatically to 37.9±6.9% at the PRF of 1000Hz (pdissolution is 547.1±129.5nm, which suggests the disruption of thrombi into the subcellular level. Thrombi motion during HIFU exposure shows violent motion and significant curling at the low PRF, rotation about its axis with occasional curling at the moderate PRF, and localized vibration at the high PRF due to the generation of acoustic radiation force and streaming. Quantitative analysis of recorded motion shows the axial displacement decreases with the PRF of delivered HIFU bursts, from 3.9±1.5mm at 1Hz to 0.7±0.4mm at 1000Hz. Bubble cavitation during HIFU exposure to the blood clot was also monitored. The increase of PRF led to the increase of inertial cavitation but the decrease of stable cavitation. In summary, the PRF of delivered HIFU bursts at the same output energy has a significant effect on the thrombi motion, bubble cavitation activities, and subsequently thrombolysis efficiencies. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Raman-shifted wavelength-selectable pulsed fiber laser with high repetition rate and high pulse energy in the visible.

    Science.gov (United States)

    Xu, L; Alam, S; Kang, Q; Shepherd, D P; Richardson, D J

    2017-01-09

    A high-pulse-energy, diffraction-limited, wavelength-selectable, visible source, based on Raman frequency shifting of a frequency-doubled Yb-doped fiber laser, has been studied. The relative length-scaling laws of Raman gain and self-phase modulation push the design towards short fiber lengths with large core size. It is experimentally demonstrated that the Raman clean-up effect in a graded-index multi-mode fiber is not sufficient to obtain diffraction-limited beam quality in the short fiber length. Thus, a large-core photonic crystal fiber is used to maintain diffraction-limited performance and output pulse energies of ~1 μJ, at a 1-MHz repetition rate and 1.3-ns pulse-width are successfully achieved. This step-tunable visible source should find applications in photoacoustic microscopy.

  15. High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome.

    Science.gov (United States)

    Shah, Abhijeet B; Schielzeth, Holger; Albersmeier, Andreas; Kalinowski, Joern; Hoffman, Joseph I

    2016-08-01

    Despite recent advances in high-throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club-legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired-end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild-caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high-throughput sequencing and graph-based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes.

  16. High-q microring resonator with narrow free spectral range for pulse repetition rate multiplication

    DEFF Research Database (Denmark)

    Pu, Minhao; Ji, Hua; Frandsen, Lars Hagedorn

    2009-01-01

    We demonstrate a silicon-on-insulator microring resonator with a free-spectral-range of 0.32 nm, an extinction ratio of 27 dB, and a quality factor of ~140900 at 1550 nm that is used for pulse repetition-rate multiplication from 10 to 40 GHz.......We demonstrate a silicon-on-insulator microring resonator with a free-spectral-range of 0.32 nm, an extinction ratio of 27 dB, and a quality factor of ~140900 at 1550 nm that is used for pulse repetition-rate multiplication from 10 to 40 GHz....

  17. [Optimization and primary application of one molecular typing method of Salmonella, enterobacteia repetitive intergenic consensus sequences-based PCR in Salmonella].

    Science.gov (United States)

    Wang, Chuan; Liu, Hengchuan; Jiang, Xian; Yu, Qian

    2008-09-01

    To optimize the reaction conditions of enterobacteia repetitive intergenic consensus sequences-based PCR (ERIC-PCR), a molecular typing method of Salmonella, study the genomic DNA ERIC-PCR fingerprint maps of Salmonella standard strains and epidemic isolates, and supply data for a system of Salmonella epidemiology investigation and homology tracing. Genomic DNA of S. typhimurium was abstracted and used as the template for PCR. Enterobacteia repetitive intergenic consensus sequences were used as primers to amplify the target sequences in S. typhimurium genomic DNA: Amplification products were separated by agarose gel electrophoresis, and electrophoresis maps were analyzed by gel image analysis system. To optimize template concentration, Mg2+ concentration, primers concentration and annealing temperature of PCR, the factor to be optimized was designed in different concentration grads and other factors were fixed. Analyzed 16 Salmonella strains and one E. coli strain by PCR conditions optimized. The electrophoresis bands of amplified products were entire and most clear when template concentration was 100 ng/25 microl, Mg2+ concentration was 2.0 mmol/L, primers concentrations were 0.4 micromol/L respectively in the total volume of 25 microl of the reaction system, and annealing temperature was 52 degrees C. The ERIC-PCR fingerprint maps of different Salmonella strains with different sources were different. From 250 to 5000 bp, there were 3 to 13 bands, and in those there was a specific 250 bp band. Important reaction conditions of ERIC-PCR had been optimized in this study. ERIC-PCR technique could discriminate Salmonella strains isolated from different regions. It could be used in Salmonella epidemiology investigation and homology tracing, so as to make up for the flaws of the traditional classification methods for salmonella.

  18. High frequency repetitive transcranial magnetic stimulation treatment for major depression: Dissociated effects on psychopathology and neurocognition.

    Science.gov (United States)

    Tovar-Perdomo, Santiago; McGirr, Alexander; Van den Eynde, Frederique; Rodrigues Dos Santos, Nicole; Berlim, Marcelo T

    2017-08-01

    This open-label pilot study explored the effects of a course of accelerated high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) on two neurocognitive domains (decision-making and impulse control) in patients with major depressive disorder (MDD). Participants with MDD and a treatment resistant major depressive episode (n=24) underwent twice-daily HF-rTMS targeted at the left dorsolateral prefrontal cortex (lDLPFC) over two weeks. Psychopathology was assessed by clinician-administered and self-reported measures of depression and anxiety; decision-making was assessed by the Iowa Gambling Task, the Balloon Analog Risk Task and the Game of Dice Task; impulse control was assessed by the Stroop Color-Word Task, the Continuous Performance Task and the Stop-Signal Task. Depression and anxiety scores significantly improved from pre-post HF-rTMS treatment. However, none of the decision-making or impulse control variables of interest changed significantly from pre-post HF-rTMS. Moreover, there was no correlation between changes in psychopathological symptoms and in neurocognition. This is a moderately sized open label trial, and the confounds of ongoing psychotropics and illness chronicity can not be excluded in this treatment resistant sample. There is dissociation between acute symptomatic benefit after a course of accelerated HF-rTMS applied to the lDLPFC in treatment resistant MDD and performance on tests of decision making and impulse control. Though rTMS appears cognitively safe, additional research is warranted to understand this potential dissociation and its putative clinical implications. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Design study of a low-emittance high-repetition rate thermionic rf gun

    Science.gov (United States)

    Opanasenko, A.; Mytrochenko, V.; Zhaunerchyk, V.; Goryashko, V. A.

    2017-05-01

    We propose a novel gridless continuous-wave radiofrequency (rf) thermionic gun capable of generating nC ns electron bunches with a rms normalized slice emittance close to the thermal level of 0.3 mm mrad. In order to gate the electron emission, an externally heated thermionic cathode is installed into a stripline-loop conductor. Two high-voltage pulses propagating towards each other in the stripline-loop overlap in the cathode region and create a quasielectrostatic field gating the electron emission. The repetition rate of pulses is variable and can reach up to one MHz with modern solid-state pulsers. The stripline attached to a rf gun cavity wall has with the wall a common aperture that allows the electrons to be injected into the rf cavity for further acceleration. Thanks to this innovative gridless design, simulations suggest that the bunch emittance is approximately at the thermal level after the bunch injection into the cavity provided that the geometry of the cathode and aperture are properly designed. Specifically, a concave cathode is adopted to imprint an Ƨ-shaped distribution onto the beam transverse phase-space to compensate for an S-shaped beam distribution created by the spherical aberration of the aperture-cavity region. In order to compensate for the energy spread caused by rf fields of the rf gun cavity, a 3rd harmonic cavity is used. A detailed study of the electrodynamics of the stripline and rf gun cavity as well as the beam optics and bunch dynamics are presented.

  20. Real-time energy measurement of high repetition rate ultrashort laser pulses using pulse integration and FPGA processing

    Science.gov (United States)

    Tang, Qi-jie; Yang, Dong-xu; Wang, Jian; Feng, Yi; Zhang, Hong-fei; Chen, Teng-yun

    2016-11-01

    Real-time energy measurement using pulse integration method for high repetition rate ultrashort laser pulses based on FPGA (Field-Programmable Gate Array) and high-speed pipeline ADC (Analog-to-Digital Convertor) is introduced in this paper. There are two parts contained in this method: pulse integration and real-time data processing. The pulse integration circuit will convert the pulse to the step type signals which are linear to the laser pulse energy. Through the real-time data processing part, the amplitude of the step signals will be obtained by ADC sampling and conducting calculation in real time in FPGA. The test result shows that the method with good linearity (4.770%) and without pulse measurement missing is suitable for ultrashort laser pulses with high repetition rate up to 100 MHz.

  1. High-repetition-rate pulse-burst laser for Thomson scattering on the MST reversed-field pinch

    Science.gov (United States)

    Young, W. C.; Morton, L. A.; Parke, E.; Den Hartog, D. J.

    2013-11-01

    A new, high-repetition-rate pulse-burst laser system for the MST Thomson scattering diagnostic has operated with 2 J pulses at repetition rates up to 75 kHz within a burst. The 1064 nm laser currently employs a q-switched, diode pumped Nd:YVO4 master oscillator, four Nd:YAG amplifier stages, and a Nd:glass amplifier, with plans for an additional Nd:glass amplifier. The laser can maintain 1.5-2 J pulses in two operating modes: either at a uniform repetition rate of 5-10 kHz (sustained for 5-8 ms), or reach rates of up to 75 kHz in pulse-burst operation (for 10 bursts of 15 pulses each), limited by flashlamp explosion energy and wall loading. The full system, including an additional Nd:glass amplifier, is designed to produce bursts of 2 J pulses at a repetition rate of at least 250 kHz. Custom programmable square-pulse power supplies drive the amplifier flashlamps, providing fine control of pulse timing, duration, and repetition, and allow for pulse-burst operation. The new laser system integrates with the same collection optics and detectors as used by the previous MST Thomson laser: 21 spatial points across the MST minor radius, filter polychromators with 6 to 8 channels (10 eV-5 keV range), avalanche photodiode detectors, and 1 GSample/s/channel digitization. Use of the previous pulse-burst laser continues concurrently with new laser development. Additional notes on optimization of flashlamp simmering will also be covered, showing that an increase in simmer currents can improve pulse-to-pulse energy consistency on both the new and older lasers.

  2. Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution.

    Science.gov (United States)

    Laprevotte, I

    1992-11-01

    An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. In any case, a common evolutionary origin for the two viruses is not ruled out.

  3. High power fiber laser system for a high repetition rate laserwire

    Directory of Open Access Journals (Sweden)

    L. J. Nevay

    2014-07-01

    Full Text Available We present the development of a high power fiber laser system to investigate its suitability for use in a transverse electron beam profile monitor, i.e., a laserwire. A system capable of producing individual pulses up to 165.8±0.4  μJ at 1036 nm with a full width at half maximum of 1.92±0.12  ps at 6.49 MHz is demonstrated using a master oscillator power amplifier design with a final amplification stage in a rod-type photonic crystal fiber. The pulses are produced in trains of 1 ms in a novel burst mode amplification scheme to match the bunch pattern of the charged particles in an accelerator. This method allows pulse energies up to an order of magnitude greater than the steady-state value of 17.0±0.6  μJ to be achieved at the beginning of the burst with a demonstrated peak power of 25.8±1.7  MW after compression. The system is also shown to demonstrate excellent spatial quality with an M^{2}=1.26±0.01 in both dimensions, which would allow nearly diffraction limited focusing to be achieved.

  4. Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

    National Research Council Canada - National Science Library

    Stiller, Mathias; Knapp, Michael; Stenzel, Udo; Hofreiter, Michael; Meyer, Matthias

    2009-01-01

    Although the emergence of high-throughput sequencing technologies has enabled whole-genome sequencing from extinct organisms, little progress has been made in accelerating targeted sequencing from highly degraded DNA...

  5. Gyromagnetic nonlinear transmission line generator of high voltage pulses modulated at 4 GHz frequency with 1000 Hz pulse repetition rate

    Science.gov (United States)

    Ulmasculov, M. R.; Sharypov, K. A.; Shunailov, S. A.; Shpak, V. G.; Yalandin, M. I.; Pedos, M. S.; Rukin, S. N.

    2017-05-01

    Results of testing of a generator based on a solid-state drive and the parallel gyromagnetic nonlinear transmission lines with external bias are presented. Stable rf-modulated high-voltage nanosecond pulses were shaped in each of the four channels in 1 s packets with 1000 Hz repetition frequencies. Pulse amplitude reaches -175 kV, at a modulation depth of rf-oscillations to 50 % and the effective frequency ∼4 GHz.

  6. Applications of High Throughput Nucleotide Sequencing

    DEFF Research Database (Denmark)

    Waage, Johannes Eichler

    The recent advent of high throughput sequencing of nucleic acids (RNA and DNA) has vastly expanded research into the functional and structural biology of the genome of all living organisms (and even a few dead ones). With this enormous and exponential growth in biological data generation come...... equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......). For the second flavor, DNA-seq, a study presenting genome wide profiling of transcription factor CEBP/A in liver cells undergoing regeneration after partial hepatectomy (article IV) is included....

  7. A simple sub-nanosecond ultraviolet light pulse generator with high repetition rate and peak power.

    Science.gov (United States)

    Binh, P H; Trong, V D; Renucci, P; Marie, X

    2013-08-01

    We present a simple ultraviolet sub-nanosecond pulse generator using commercial ultraviolet light-emitting diodes with peak emission wavelengths of 290 nm, 318 nm, 338 nm, and 405 nm. The generator is based on step recovery diode, short-circuited transmission line, and current-shaping circuit. The narrowest pulses achieved have 630 ps full width at half maximum at repetition rate of 80 MHz. Optical pulse power in the range of several hundreds of microwatts depends on the applied bias voltage. The bias voltage dependences of the output optical pulse width and peak power are analysed and discussed. Compared to commercial UV sub-nanosecond generators, the proposed generator can produce much higher pulse repetition rate and peak power.

  8. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.; Santhana Mariappan, S.V.; Chen, X.; Catasti, P.; Silks, L.A. III; Moyzis, R.K.; Bradbury, E.M.; Garcia, A.E.

    1997-07-01

    This project is aimed at formulating the sequence-structure-function correlations of various microsatellites in the human (and other eukaryotic) genomes. Here the authors have been able to develop and apply structure biology tools to understand the following: the molecular mechanism of length polymorphism microsatellites; the molecular mechanism by which the microsatellites in the noncoding regions alter the regulation of the associated gene; and finally, the molecular mechanism by which the expansion of these microsatellites impairs gene expression and causes the disease. Their multidisciplinary structural biology approach is quantitative and can be applied to all coding and noncoding DNA sequences associated with any gene. Both NIH and DOE are interested in developing quantitative tools for understanding the function of various human genes for prevention against diseases caused by genetic and environmental effects.

  9. 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.

  10. 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.

  11. Repetitive DNA in the Catfish Genome: rDNA, Microsatellites, and Tc1-Mariner Transposon Sequences in Imparfinis Species (Siluriformes, Heptapteridae).

    Science.gov (United States)

    Gouveia, Juceli Gonzalez; Wolf, Ivan Rodrigo; Vilas-Boas, Laurival Antonio; Heslop-Harrison, John Seymour; Schwarzacher, Trude; Dias, Ana Lúcia

    2017-09-01

    Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I. schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. IS1111 insertion sequences of Coxiella burnetii: characterization and use for repetitive element PCR-based differentiation of Coxiella burnetii isolates

    Directory of Open Access Journals (Sweden)

    Massung Robert F

    2007-10-01

    Full Text Available Abstract Background Coxiella burnetii contains the IS1111 transposase which is present 20 times in the Nine Mile phase I (9Mi/I genome. A single PCR primer that binds to each IS element, and primers specific to a region ~500-bp upstream of each of the 20 IS1111 elements were designed. The amplified products were characterized and used to develop a repetitive element PCR genotyping method. Results Isolates Nine Mile phase II, Nine Mile RSA 514, Nine Mile Baca, Scottish, Ohio, Australian QD, Henzerling phase I, Henzerling phase II, M44, KAV, PAV, Q238, Q195 and WAV were tested by PCR and compared to 9Mi/I. Sequencing was used to determine the exact differences in isolates which lacked specific IS elements or produced PCR products of differing size. From this data, an algorithm was created utilizing four primer pairs that allows for differentiation of unknown isolates into five genomic groups. Additional isolates (Priscilla Q177, Idaho Q, Qiyi, Poker Cat, Q229 and Q172 and nine veterinary samples were characterized using the algorithm which resulted in their placement into three distinct genomic groups. Conclusion Through this study significant differences, including missing elements and sequence alterations within and near IS element coding regions, were found between the isolates tested. Further, a method for differentiation of C. burnetii isolates into one of five genomic groups was created. This algorithm may ultimately help to determine the relatedness between known and unknown isolates of C. burnetii.

  13. 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.

  14. TeloPCR-seq: a high-throughput sequencing approach for telomeres

    Science.gov (United States)

    Bennett, Henrietta W.; Liu, Na; Hu, Yan; King, Megan C.

    2017-01-01

    We have developed a high-throughput sequencing approach that enables us to determine terminal telomere sequences from tens of thousands of individual Schizosaccharomyces pombe telomeres. This method provides unprecedented coverage of telomeric sequence complexity in fission yeast. S. pombe telomeres are composed of modular degenerate repeats that can be explained by variation in usage of the TER1 RNA template during reverse transcription. Taking advantage of this deep sequencing approach, we find that “like” repeat modules are highly correlated within individual telomeres. Moreover, repeat module preference varies with telomere length, suggesting that existing repeats promote the incorporation of like repeats and/or that specific conformations of the telomerase holoenzyme efficiently and/or processively add repeats of like nature. After the loss of telomerase activity, this sequencing and analysis pipeline defines a population of telomeres with altered sequence content. This approach will be adaptable to study telomeric repeats in other organisms and also to interrogate repetitive sequences throughout the genome that are inaccessible to other sequencing methods. PMID:27714790

  15. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

    Science.gov (United States)

    Lou, Dianne I.; Hussmann, Jeffrey A.; McBee, Ross M.; Acevedo, Ashley; Andino, Raul; Press, William H.; Sawyer, Sara L.

    2013-01-01

    A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ∼0.1–1 × 10−2 per base sequenced. These technologies typically produce billions of base calls per experiment, translating to millions of errors. We have developed a unique library preparation strategy, “circle sequencing,” which allows for robust downstream computational correction of these errors. In this strategy, DNA templates are circularized, copied multiple times in tandem with a rolling circle polymerase, and then sequenced on any high-throughput sequencing machine. Each read produced is computationally processed to obtain a consensus sequence of all linked copies of the original molecule. Physically linking the copies ensures that each copy is independently derived from the original molecule and allows for efficient formation of consensus sequences. The circle-sequencing protocol precedes standard library preparations and is therefore suitable for a broad range of sequencing applications. We tested our method using the Illumina MiSeq platform and obtained errors in our processed sequencing reads at a rate as low as 7.6 × 10−6 per base sequenced, dramatically improving the error rate of Illumina sequencing and putting error on par with low-throughput, but highly accurate, Sanger sequencing. Circle sequencing also had substantially higher efficiency and lower cost than existing barcode-based schemes for correcting sequencing errors. PMID:24243955

  16. Chromosome Mapping of Repetitive Sequences in Rachycentron canadum (Perciformes: Rachycentridae): Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

    Science.gov (United States)

    Jacobina, Uedson Pereira; Cioffi, Marcelo de Bello; Souza, Luiz Gustavo Rodrigues; Calado, Leonardo Luiz; Tavares, Manoel; Manzella, João; Bertollo, Luiz Antonio Carlos; Molina, Wagner Franco

    2011-01-01

    The cobia, Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes) showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3 (CMA3)/DAPI staining, C-banding, early replication banding (RGB), and in situ fluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGG)n. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question. PMID:21541243

  17. Effects of low-load, higher-repetition versus high-load, lower-repetition resistance training not performed to failure on muscle strength, mass, and echo intensity in healthy young men: a time-course study.

    Science.gov (United States)

    Ikezoe, T; Kobayashi, T; Nakamura, M; Ichihashi, N

    2017-10-07

    The aim of the present study was to compare the effects of low-load, higher-repetition training (LLHR) with those of high-load, lower-repetition training (HLLR) on muscle strength, mass, and echo intensity in healthy young men. Fifteen healthy men (age, 23.1 ± 2.6 years) were randomly assigned to one of the two groups: LLHR or HLLR group. Resistance training on knee extensor muscles was performed 3 days per week for 8 weeks. One-repetition maximum (1RM) strength, maximum isometric strength, muscle thickness and muscle echo intensity on ultrasonography of the rectus femoris muscle were assessed every 2 weeks. Analysis of variance showed no significant group × time interaction, and only a significant main effect of time was observed for all variables. The 8-week resistance training increased 1RM, maximum isometric muscle strength, and muscle thickness by 36.2%-40.9%, 24.0%-25.5%, and 11.3%-20.4%, respectively, whereas it decreased echo intensity by 8.05%-16.3%. Significant improvements in muscle strength, thickness, and echo intensity were observed at weeks 2, 4, and 8, respectively. The lack of difference in time-course changes between LLHR and HLLR programs suggests that low-load training can exert similar effects on muscle mass and characteristics as high-load training by increasing the number of repetitions, even when not performed to failure.

  18. Diversity of Enterococcus faecalis Genotypes from Multiple Oral Sites Associated with Endodontic Failure Using Repetitive Sequence-based Polymerase Chain Reaction and Arbitrarily Primed Polymerase Chain Reaction.

    Science.gov (United States)

    Delboni, Maraísa G; Gomes, Brenda P F A; Francisco, Priscila A; Teixeira, Fabrício B; Drake, David

    2017-03-01

    The aim of this study was to evaluate the diversity and similarity of Enterococcus faecalis genotype isolates from multiple oral sites using repetitive sequence-based polymerase chain reaction and arbitrarily primed polymerase chain reaction (AP-PCR). Forty-two endodontically treated teeth with apical periodontitis were selected. A total of 126 microbial samples were collected from 3 different sites (saliva, pulp chamber, and root canals, all n = 42) during the nonsurgical retreatment procedures. After growth on m-Enterococcus agar, the colonies were isolated, characterized as gram-positive catalase negative cocci, and identified using an API 20 Strep kit (bioMérieux, Marcy-l'Etoile, France). Seventy-four colonies from 10 patients were confirmed as E. faecalis by polymerase chain reaction (16S ribosomal RNA). Repetitive sequence-based polymerase chain reactions using ERIC and AP-PCR using RW3A primers were performed in all 74 colonies. Fingerprints were analyzed and separated into genotypic groups based on the Dice coefficient percentage of similarity (82% or greater) as determined by ERIC reproducibility assays involving E. faecalis controls. Seven different E. faecalis genotypes (GTs) (GT1 = 27%, GT2 = 17.6%, GT3 = 1.3%, GT4 = 18.9%, GT5 = 9.5%, GT6 = 14.9%, and GT7 = 10.8%) were observed in different subjects and oral sites associated with endodontic failure. Remarkably, in 4 of 5 patients, the same GTs present in the infected root canals were also isolated from either the pulp chamber or the saliva samples. In particular, GT6 was detected in all 3 oral sites of patient 37. E. faecalis GTs isolated from saliva, the pulp chamber, and the root canal were similar using the Rep-PCR and AP-PCR methods. These findings suggest that coronal microleakage is a conceivable cause of endodontic failure. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  19. Development of high energy, sub-15 fs OPCPA system operating at 1 kHz repetition rate for ELI-Beamlines facility

    Science.gov (United States)

    Bakule, Pavel; Antipenkov, Roman; Green, Jonathan T.; Novák, Jakub; Batysta, František; Rus, Bedřich; Boge, Robert; Hubka, Zbyněk.; Naylon, Jack A.; Horáček, Martin; Horáček, Jakub; Strkula, Petr; Snopek, David; Indra, Lukaš; Tykalewicz, Boguslaw

    2017-05-01

    We report on the status of the high repetition rate, high energy, L1 laser beamline at the ELI-Beamlines facility. The beamline is based on picosecond optical parametric chirped pulse amplification (OPCPA) of pulses from a mode-locked Ti:Sapphire oscillator and has a target energy/repetition rate of 100 mJ/1 kHz with architecture design considerations to achieve our goals of long term stability are discussed.

  20. A Compact, Transportable, Microchip-Based System for High Repetition Rate Production of Bose-Einstein Condensates

    CERN Document Server

    Farkas, Daniel M; Salim, Evan A; Segal, Stephen R; Squires, Matthew B; Anderson, Dana Z

    2009-01-01

    We present a compact, transportable system that produces Bose-Einstein condensates (BECs) near the surface of an integrated atom microchip. The system occupies a volume of 0.4 m^3 and operates at a repetition rate as high as 0.3 Hz. Evaporative cooling in a chip trap with trap frequencies of several kHz leads to nearly pure condensates containing 1.9x10^4 87Rb atoms. Partial condensates are observed at a temperature of 1.58(8) \\mu K, close to the theoretical transition temperature of 1.1 \\mu K.

  1. Saturated 13.2 nm high-repetition-rate laser in nickellike cadmium

    Science.gov (United States)

    Rocca, J. J.; Wang, Y.; Larotonda, M. A.; Luther, B. M.; Berrill, M.; Alessi, D.

    2005-10-01

    We report gain-saturated operation of a 13.2 nm tabletop laser in Ni-like Cd at a 5 Hz repetition rate. A gain-length product G×L=17.6 was obtained by heating a precreated plasma with 8 ps duration Ti:sapphire laser pulses with an energy of only 1 J impinging at a grazing angle of 23°. With an average power of ˜1 µW, this laser is an attractive coherent source for at-wavelength metrology of extreme UV lithography optics and other applications. [Note: Due to a production error in the print version abstract, the value "1 µW" is incorrectly stated as "1 mW." This value is stated correctly in the online PDF.

  2. 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.

  3. Adaptive-Repetitive Visual-Servo Control of Low-Flying Aerial Robots via Uncalibrated High-Flying Cameras

    Science.gov (United States)

    Guo, Dejun; Bourne, Joseph R.; Wang, Hesheng; Yim, Woosoon; Leang, Kam K.

    2017-08-01

    This paper presents the design and implementation of an adaptive-repetitive visual-servo control system for a moving high-flying vehicle (HFV) with an uncalibrated camera to monitor, track, and precisely control the movements of a low-flying vehicle (LFV) or mobile ground robot. Applications of this control strategy include the use of high-flying unmanned aerial vehicles (UAVs) with computer vision for monitoring, controlling, and coordinating the movements of lower altitude agents in areas, for example, where GPS signals may be unreliable or nonexistent. When deployed, a remote operator of the HFV defines the desired trajectory for the LFV in the HFV's camera frame. Due to the circular motion of the HFV, the resulting motion trajectory of the LFV in the image frame can be periodic in time, thus an adaptive-repetitive control system is exploited for regulation and/or trajectory tracking. The adaptive control law is able to handle uncertainties in the camera's intrinsic and extrinsic parameters. The design and stability analysis of the closed-loop control system is presented, where Lyapunov stability is shown. Simulation and experimental results are presented to demonstrate the effectiveness of the method for controlling the movement of a low-flying quadcopter, demonstrating the capabilities of the visual-servo control system for localization (i.e.,, motion capturing) and trajectory tracking control. In fact, results show that the LFV can be commanded to hover in place as well as track a user-defined flower-shaped closed trajectory, while the HFV and camera system circulates above with constant angular velocity. On average, the proposed adaptive-repetitive visual-servo control system reduces the average RMS tracking error by over 77% in the image plane and over 71% in the world frame compared to using just the adaptive visual-servo control law.

  4. 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.

  5. 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

  6. Targeted capture sequencing in whitebark pine reveals range-wide demographic and adaptive patterns despite challenges of a large, repetitive genome

    Directory of Open Access Journals (Sweden)

    John eSyring

    2016-04-01

    Full Text Available Whitebark pine (Pinus albicaulis inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the tree to be listed as ‘globally endangered’ by the International Union for Conservation of Nature (IUCN and ‘endangered’ by the Canadian government. Conservation collections (in situ and ex situ are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 30+ GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp, and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits, targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect

  7. High-repetition-rate, deep-infrared, picosecond optical parametric oscillator based on CdSiP2.

    Science.gov (United States)

    Chaitanya Kumar, S; Zawilski, K T; Schunemann, P G; Ebrahim-Zadeh, M

    2017-09-15

    We report a high-repetition-rate picosecond optical parametric oscillator (OPO) based on CdSiP2 (CSP) that is synchronously pumped by an Yb-fiber laser at 1064 nm and provides high average power in the deep-infrared (deep-IR) at 79.5 MHz. The OPO is tunable across 6205-6710 nm in the idler, providing as much as 105 mW of average power at 6205 nm and >55  mW over nearly the entire tuning range. The deep-IR idler output exhibits passive power stability better than 2.3% rms over 12 h in good beam quality. The near-IR signal pulses from the OPO have a Gaussian pulse duration of ∼19  ps, measured at 1284 nm. We have investigated the temperature tuning characteristics of the OPO and compared the data with the theoretical calculations using the most recent Sellmeier equations and thermo-optic coefficients for the crystal. To the best of our knowledge, this is the first picosecond OPO based on CSP operating at MHz repetition rates.

  8. Investigation on repetition rate and pulse duration influences on ablation efficiency of metals using a high average power Yb-doped ultrafast laser

    Directory of Open Access Journals (Sweden)

    Lopez J.

    2013-11-01

    Full Text Available Ultrafast lasers provide an outstanding processing quality but their main drawback is the low removal rate per pulse compared to longer pulses. This limitation could be overcome by increasing both average power and repetition rate. In this paper, we report on the influence of high repetition rate and pulse duration on both ablation efficiency and processing quality on metals. All trials have been performed with a single tunable ultrafast laser (350 fs to 10ps.

  9. NEO-LISP: Deflecting near-Earth objects using high average power, repetitively pulsed lasers

    Science.gov (United States)

    Phipps, C. R.; Michaelis, M. M.

    Several kinds of Near-Earth objects exist for which one would like to cause modest orbit perturbations, but which are inaccessible to normal means of interception because of their number, distance or the lack of early warning. For these objects, LISP (Laser Impulse Space Propulsion) is an appropriate technique for rapidly applying the required mechanical impulse from a ground-based station. In order of increasing laser energy required, examples are: (1) repositioning specially prepared geosynchronous satellites for an enhanced lifetime; (2) causing selected items of space junk to re-enter and burn up in the atmosphere on a computed trajectory; and (3) safely deflecting Earth-directed comet nuclei and earth-crossing asteroids (ECA's) a few tens of meters in size (the most hazardous size). They will discuss each of these problems in turn and show that each application is best matched by its own matrix of LISP laser pulse width, pulse repetition rate, wavelength and average power. The latter ranges from 100W to 3GW for the cases considered. They will also discuss means of achieving the active beam phase error correction during passage through the atmosphere and very large exit pupil in the optical system which are required in each of these cases.

  10. NEO-LISP: Deflecting near-earth objects using high average power, repetitively pulsed lasers

    Energy Technology Data Exchange (ETDEWEB)

    Phipps, C.R. [Los Alamos National Lab., NM (United States). Chemical Science and Technology Div.; Michaelis, M.M. [Univ. of Natal, Durban (South Africa). Physics Dept.

    1994-10-01

    Several kinds of Near-Earth objects exist for which one would like to cause modest orbit perturbations, but which are inaccessible to normal means of interception because of their number, distance or the lack of early warning. For these objects, LISP (Laser Impulse Space Propulsion) is an appropriate technique for rapidly applying the required mechanical impulse from a ground-based station. In order of increasing laser energy required, examples are: (1) repositioning specially prepared geosynchronous satellites for an enhanced lifetime, (2) causing selected items of space junk to re-enter and burn up in the atmosphere on a computed trajectory, and (3) safely deflecting Earth-directed comet nuclei and earth-crossing asteroids (ECA`s) a few tens of meters in size (the most hazardous size). They will discuss each of these problems in turn and show that each application is best matched by its own matrix of LISP laser pulse width, pulse repetition rate, wavelength and average power. The latter ranges from 100W to 3GW for the cases considered. They will also discuss means of achieving the active beam phase error correction during passage through the atmosphere and very large exit pupil in the optical system which are required in each of these cases.

  11. Initial operation of a pulse-burst laser system for high-repetition-rate Thomson scattering

    Energy Technology Data Exchange (ETDEWEB)

    Harris, W. S.; Hurst, N. C. [Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Den Hartog, D. J. [Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Center for Magnetic Self-Organization in Laboratory and Astrophysical Plasmas, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

    2010-10-15

    A pulse-burst laser has been installed for Thomson scattering measurements on the Madison Symmetric Torus reversed-field pinch. The laser design is a master-oscillator power-amplifier. The master oscillator is a commercial Nd:YVO{sub 4} laser (1064 nm) which is capable of Q-switching at frequencies between 5 and 250 kHz. Four Nd:YAG (yttrium aluminum garnet) amplifier stages are in place to amplify the Nd:YVO{sub 4} emission. Single pulses through the Nd:YAG amplifier stages gives energies up to 1.5 J and the gain for each stage has been measured. Repetitive pulsing at 10 kHz has also been performed for 2 ms bursts, giving average pulse energies of 0.53 J with {Delta}E/E of 4.6%, where {Delta}E is the standard deviation between pulses. The next step will be to add one of two Nd:glass (silicate) amplifier stages to produce final pulse energies of 1-2 J for bursts up to 250 kHz.

  12. 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.

  13. A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

    DEFF Research Database (Denmark)

    Enroth, Stefan; Andersson, Claes; Andersson, Robin

    2012-01-01

    High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a backg......High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive regions or non-specific antibody interactions. The noise will appear in the form...... of a background distribution of reads that must be taken into account in the downstream analysis, for example when detecting enriched regions (peak-calling). Several reported peak-callers can take experimental measurements of background tag distribution into account when analysing a data set. Unfortunately...

  14. Highly efficient, versatile, self-Q-switched, high-repetition-rate microchip laser generating Ince–Gaussian modes for optical trapping

    Energy Technology Data Exchange (ETDEWEB)

    Jun Dong; Yu He; Xiao Zhou; Shengchuang Bai [Department of Electronics Engineering, School of Information Science and Engineering, Xiamen, 361005 (China)

    2016-03-31

    Lasers operating in the Ince-Gaussian (IG) mode have potential applications for optical manipulation of microparticles and formation of optical vortices, as well as for optical trapping and optical tweezers. Versatile, self-Q-switched, high-peak-power, high-repetition-rate Cr, Nd:YAG microchip lasers operating in the IG mode are implemented under tilted, tightly focused laser-diode pumping. An average output power of over 2 W is obtained at an absorbed pump power of 6.4 W. The highest optical-to-optical efficiency of 33.2% is achieved at an absorbed pump power of 3.9 W. Laser pulses with a pulse energy of 7.5 μJ, pulse width of 3.5 ns and peak power of over 2 kW are obtained. A repetition rate up to 335 kHz is reached at an absorbed pump power of 5.8 W. Highly efficient, versatile, IG-mode lasers with a high repetition rate and a high peak power ensure a better flexibility in particle manipulation and optical trapping. (control of laser radiation parameters)

  15. 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.

  16. Mitochondrial genomes and divergence times of crocodile newts: inter-islands distribution of Echinotriton andersoni and the origin of a unique repetitive sequence found in Tylototriton mt genomes.

    Science.gov (United States)

    Kurabayashi, Atsushi; Nishitani, Takuma; Katsuren, Seiki; Oumi, Shohei; Sumida, Masayuki

    2012-01-01

    Crocodile newts, which constitute the genera Echinotriton and Tylototriton, are known as living fossils, and these genera comprise many endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered taxa, we determined the complete nucleotide sequences of the mt genomes of the Japanese crocodile newt Echinotriton andersoni and Himalayan crocodile newt Tylototriton verrucosus. Although the control region (CR) is known as the most variable mtDNA region in many animal taxa, the CRs of crocodile newts are highly conservative. Rather, the genes of NADH dehydrogenase subunits and ATPase subunit 6 were found to have high sequence divergences and to be usable for population genetics studies. To estimate the inter-population divergence ages of E. andersoni endemic to the Ryukyu Islands, we performed molecular dating analysis using whole and partial mt genomic data. The estimated divergence ages of the inter-island individuals are older than the paleogeographic segmentation ages of the islands, suggesting that the lineage splits of E. andersoni populations were not caused by vicariant events. Our phylogenetic analysis with partial mt sequence data also suggests the existence of at least two more undescribed species in the genus Tylototriton. We also found unusual repeat sequences containing the 3' region of cytochrome apoenzyme b gene, whole tRNA-Thr gene, and a noncoding region (the T-P noncoding region characteristic in caudate mtDNAs) from T. verrucosus mtDNA. Similar repeat sequences were found in two other Tylototriton species. The Tylototriton taxa with the repeats become a monophyletic group, indicating a single origin of the repeat sequences. The intra-and inter-specific comparisons of the repeat sequences suggest the occurrences of homologous recombination-based concerted evolution among the repeat sequences.

  17. 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 ...

  18. Applications of High Throughput Sequencing for Immunology and Clinical Diagnostics

    OpenAIRE

    Kim, Hyunsung John

    2014-01-01

    High throughput sequencing methods have fundamentally shifted the manner in which biological experiments are performed. In this dissertation, conventional and novel high throughput sequencing and bioinformatics methods are applied to immunology and diagnostics. In order to study rare subsets of cells, an RNA sequencing method was first optimized for use with minimal levels of RNA and cellular input. The optimized RNA sequencing method was then applied to study the transcriptional differences ...

  19. Optimum design on thermal lensing effect of high-repetition-frequency laser based on LGS Q-switched

    Science.gov (United States)

    Li, Gang; Li, Li; Sun, Xinhua; Jin, Yezhou; Mao, Shaojuan; Wang, Yuanbo

    2014-12-01

    The thermal lensing effect of crystal is the biggest problem for the output of laser pulse with high power and high beam quality. Through the design of laser cavity, this effect can be removed a certain extent. In this paper, a high-repetition-frequency laser based on electro-optic Q-switch made of LGS is designed. Using flat-flat cavity, the purposes of simple structure and steady output are achieved. Firstly, using a LGS as Q-switched crystal, a Brewster plate as a polarizer, a xenon flash-lamp pumped 1064 nm high-repetition-frequency pulsed Nd:YAG laser with flat-flat cavity is demonstrated. Then, the stability of the laser cavity is analysed. Considering the thermal lensing effect of Nd:YAG crystal, the focal length of thermal lens is calculated. Utilizing MathCAD, the ABCD matrix of laser cavity is calculated, and the G value is obtained, that is G=0.792<1, so the laser cavity is steady. Furthermore, the distribution of light beam in the laser cavity is also simulated by using LAS-CAD, the results indicate that the laser works at stead state. Thirdly, the thermal lensing effect of Nd:YAG crystal is analysed by using LAS-CAD. The temperature and refractive index distributions of Nd:YAG crystal are simulated, the results show that the crystal can be equivalented as a lens with certain focal length. Furthermore, utilizing finite element analysis (FEA) method, the three-dimensional view of temperature field is obtained.

  20. Time-resolved studies at PETRA III with a highly repetitive synchronized laser system

    Energy Technology Data Exchange (ETDEWEB)

    Schlie, Mortiz

    2013-09-15

    Atomic and molecular processes can nowadays be directly followed in the time domain. This is a core technique for a better understanding of the involved fundamental physics, thus auguring new applications in the future as well. Usually the so-called pump-probe technique making use of two synchronized ultrashort light pulses is utilized to obtain this time-resolved data. In this work, the development and characterization of a synchronization system enabling such pump-probe studies at the storage ring PETRA III in combination with an external, then synchronized fs-laser system is described. The synchronization is based on an extended PLL approach with three interconnected feedback loops allowing to monitor short-time losses of the lock and thus prevent them. This way, the jitter between the laser PHAROS and the PETRA III reference signal is reduced to {sigma} <5 ps. Thus the system allows to conduct experiments at a repetition rate of 130 kHz with a temporal resolution limited only by the X-ray pulse length. A major emphasis in the fundamental introductory chapters is an intuitive explanation of the basic principles of phase locked loops and the different aspects of phase noise to allow a deeper understanding of the synchronization. Furthermore, first pump-probe experiments conducted at different beamlines at PETRA III are presented, demonstrating the usability of the laser system in a scientific environment as well. In first characterizing experiments the pulse duration of PETRA III X-ray pulses has been measured to be 90 ps FWHM. In particular, there have been time resolved X-ray absorption spectroscopy experiments on Gaq3 and Znq2 conducted at beamline P11. First results show dynamics of the electronic excitation on the timescale of a few hundred pico seconds up to a few nano seconds and provide a basic understanding for further research on those molecules. For Gaq3 this data is analyzed in detail and compared with visible fluorescence measurements suggesting at

  1. Generation of tunable, high repetition rate frequency combs with equalized spectra using carrier injection based silicon modulators

    Science.gov (United States)

    Nagarjun, K. P.; Selvaraja, Shankar Kumar; Supradeepa, V. R.

    2016-03-01

    High repetition-rate frequency combs with tunable repetition rate and carrier frequency are extensively used in areas like Optical communications, Microwave Photonics and Metrology. A common technique for their generation is strong phase modulation of a CW-laser. This is commonly implemented using Lithium-Niobate based modulators. With phase modulation alone, the combs have poor spectral flatness and significant number of missing lines. To overcome this, a complex cascade of multiple intensity and phase modulators are used. A comb generator on Silicon based on these principles is desirable to enable on-chip integration with other functionalities while reducing power consumption and footprint. In this work, we analyse frequency comb generation in carrier injection based Silicon modulators. We observe an interesting effect in these comb generators. Enhanced absorption accompanying carrier injection, an undesirable effect in data modulators, shapes the amplitude here to enable high quality combs from a single modulator. Thus, along with reduced power consumption to generate a specific number of lines, the complexity has also been significantly reduced. We use a drift-diffusion solver and mode solver (Silvaco TCAD) along with Soref-Bennett relations to calculate the variations in refractive indices and absorption of an optimized Silicon PIN - waveguide modulator driven by an unbiased high frequency (10 Ghz) voltage signal. Our simulations demonstrate that with a device length of 1 cm, a driving voltage of 2V and minor shaping with a passive ring-resonator filter, we obtain 37 lines with a flatness better than 5-dB across the band and power consumption an order of magnitude smaller than Lithium-Niobate modulators.

  2. Effective treatment of narcolepsy-like symptoms with high-frequency repetitive transcranial magnetic stimulation: A case report.

    Science.gov (United States)

    Lai, Jian-Bo; Han, Mao-Mao; Xu, Yi; Hu, Shao-Hua

    2017-11-01

    Narcolepsy is a rare sleep disorder with disrupted sleep-architecture. Clinical management of narcolepsy lies dominantly on symptom-driven pharmacotherapy. The treatment role of repetitive transcranial magnetic stimulation (rTMS) for narcolepsy remains unexplored. In this paper, we present a case of a 14-year-old young girl with excessive daytime sleepiness (EDS), cataplexy and hypnagogic hallucinations. After excluding other possible medical conditions, this patient was primarily diagnosed with narcolepsy. The patient received 25 sessions of high-frequency rTMS over the left dorsolateral prefrontal cortex (DLPFC). The symptoms of EDS and cataplexy significantly improved after rTMS treatment. Meanwhile, her score in the Epworth sleep scale (ESS) also remarkably decreased. This case indicates that rTMS may be selected as a safe and effective alternative strategy for treating narcolepsy-like symptoms. Well-designed researches are warranted in future investigations on this topic.

  3. Application of a high-repetition-rate laser diagnostic system for single-cycle-resolved imaging in internal combustion engines.

    Science.gov (United States)

    Hult, Johan; Richter, Mattias; Nygren, Jenny; Aldén, Marcus; Hultqvist, Anders; Christensen, Magnus; Johansson, Bengt

    2002-08-20

    High-repetition-rate laser-induced fluorescence measurements of fuel and OH concentrations in internal combustion engines are demonstrated. Series of as many as eight fluorescence images, with a temporal resolution ranging from 10 micros to 1 ms, are acquired within one engine cycle. A multiple-laser system in combination with a multiple-CCD camera is used for cycle-resolved imaging in spark-ignition, direct-injection stratified-charge, and homogeneous-charge compression-ignition engines. The recorded data reveal unique information on cycle-to-cycle variations in fuel transport and combustion. Moreover, the imaging system in combination with a scanning mirror is used to perform instantaneous three-dimensional fuel-concentration measurements.

  4. Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris

    Directory of Open Access Journals (Sweden)

    Dongying Gao

    2016-07-01

    Full Text Available Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T. Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.

  5. High frequency repetitive sensory stimulation as intervention to improve sensory loss in patients with complex regional pain syndrome (CRPS I

    Directory of Open Access Journals (Sweden)

    Marianne eDavid

    2015-11-01

    Full Text Available Achieving perceptual gains in healthy individuals, or facilitating rehabilitation in patients is generally considered to require intense training to engage neuronal plasticity mechanisms. Recent work, however, suggested that beneficial outcome similar to training can be effectively acquired by a complementary approach in which the learning occurs in response to mere exposure to repetitive sensory stimulation (rSS. For example, high-frequency repetitive sensory stimulation (HF-rSS enhances tactile performance and induces cortical reorganization in healthy subjects and patients after stroke. Patients with complex regional pain syndrome (CRPS show impaired tactile performance associated with shrinkage of cortical maps. We here investigated the feasibility and efficacy of HF-rSS, and low-frequency rSS (LF-rSS to enhance tactile performance and reduce pain intensity in 20 patients with CRPS type I. Intermittent high or low frequency electrical stimuli were applied for 45min/day to all fingertips of the affected hand for 5 days. Main outcome measures were spatial 2-point-discrimination thresholds and mechanical detection thresholds measured on the tip of the index finger bilaterally. Secondary endpoint was current pain intensity. All measures were assessed before and on day 5 after the last stimulation session. HF-rSS applied in 16 patients improved tactile discrimination on the affected hand significantly without changes contralaterally. Current pain intensity remained unchanged on average, but decreased in 4 patients by 30%. This limited pain relief might be due to the short stimulation period of 5 days only. In contrast, after LF-rSS, tactile discrimination was impaired in all 4 patients, while detection thresholds and pain were not affected. Our data suggest that HF-rSS could be used as a novel approach in CRPS treatment to improve sensory loss. Longer treatment periods might be required to induce consistent pain relief.

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

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

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

  7. Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis

    Science.gov (United States)

    Bradic, Martina; Warring, Sally D.; Tooley, Grace E.; Scheid, Paul; Secor, William E.; Land, Kirkwood M.; Huang, Po-Jung; Chen, Ting-Wen; Lee, Chi-Ching; Tang, Petrus; Sullivan, Steven A.

    2017-01-01

    Abstract Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance. Reduced representation genome sequencing of ∼100 T. vaginalis clinical isolates identified 3,923 SNP markers and presence of a bipartite population structure. Linkage disequilibrium was found to decay rapidly, suggesting genome-wide recombination and the feasibility of genetic association studies in the parasite. We identified 72 SNPs associated with metronidazole resistance, and a comparison of SNPs within several lab-derived resistant lines revealed an overlap with the clinically resistant isolates. We identified SNPs in genes for which no function has yet been assigned, as well as in functionally-characterized genes relevant to drug resistance (e.g., pyruvate:ferredoxin oxidoreductase). Transcription profiles of resistant strains showed common changes in genes involved in drug activation (e.g., flavin reductase), accumulation (e.g., multidrug resistance pump), and detoxification (e.g., nitroreductase). Finally, we identified convergent genetic changes in lab-derived resistant lines of Tritrichomonas foetus, a distantly related species that causes venereal disease in cattle. Shared genetic changes within and between T. vaginalis and Tr. foetus parasites suggest conservation of the pathways through which adaptation has occurred. These findings extend our knowledge of drug resistance in the parasite, providing a panel of markers that can be used as a diagnostic tool. PMID:28633446

  8. Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis.

    Science.gov (United States)

    Bradic, Martina; Warring, Sally D; Tooley, Grace E; Scheid, Paul; Secor, William E; Land, Kirkwood M; Huang, Po-Jung; Chen, Ting-Wen; Lee, Chi-Ching; Tang, Petrus; Sullivan, Steven A; Carlton, Jane M

    2017-06-01

    Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance. Reduced representation genome sequencing of ∼100 T. vaginalis clinical isolates identified 3,923 SNP markers and presence of a bipartite population structure. Linkage disequilibrium was found to decay rapidly, suggesting genome-wide recombination and the feasibility of genetic association studies in the parasite. We identified 72 SNPs associated with metronidazole resistance, and a comparison of SNPs within several lab-derived resistant lines revealed an overlap with the clinically resistant isolates. We identified SNPs in genes for which no function has yet been assigned, as well as in functionally-characterized genes relevant to drug resistance (e.g., pyruvate:ferredoxin oxidoreductase). Transcription profiles of resistant strains showed common changes in genes involved in drug activation (e.g., flavin reductase), accumulation (e.g., multidrug resistance pump), and detoxification (e.g., nitroreductase). Finally, we identified convergent genetic changes in lab-derived resistant lines of Tritrichomonas foetus, a distantly related species that causes venereal disease in cattle. Shared genetic changes within and between T. vaginalis and Tr. foetus parasites suggest conservation of the pathways through which adaptation has occurred. These findings extend our knowledge of drug resistance in the parasite, providing a panel of markers that can be used as a diagnostic tool. © The Author 2017. Published by Oxford University Press on behalf of the Society for

  9. Thin Disk Ti:Sapphire amplifiers for Joule-class ultrashort pulses with high repetition rate (Conference Presentation)

    Science.gov (United States)

    Nagymihály, Roland S.; Cao, Huabao; Kalashnikov, Mikhail P.; Khodakovskiy, Nikita; Ehrentraut, Lutz; Osvay, Károly; Chvykov, Vladimir V.

    2017-05-01

    High peak power CPA laser systems can deliver now few petawatt pulses [1]. Reaching the high energies with broad spectral bandwidth necessary for these pulses was possible by the use of large aperture Ti:Sa crystals as final amplifier media. Wide applications for these systems will be possible if the repetition rate could be increased. Therefore, thermal deposition in Ti:Sa amplifiers is a key issue, which has to be solved in case of high average power pumping. The thin disk (TD) laser technology, which is intensively developed nowadays by using new laser materials, is able to overcome thermal distortions and damages of laser crystals [2]. TD technique also has the potential to be used in systems with both high peak and average power. For this, the commonly used laser materials with low absorption and emission cross sections, also low heat conductivity, like Yb:YAG, need to be replaced by a gain medium that supports broad enough emission spectrum and high thermal conductivity to obtain few tens of fs pulses with high repetition rates. Parasitic effects during the amplification process however seriously limit the energy that can be extracted from the gain medium and also they distort the gain profile. Nevertheless, the application of the Extraction During Pumping (EDP) technique can mitigate the depopulation losses in the gain medium with high aspect ratio [3]. We proposed to use Ti:Sa in combination with TD and EDP techniques to reach high energies at high repetition rates, and we presented numerical simulations for different amplifier geometries and parameters of the amplification [4,5]. We present the results of the proof-of-principle experiment, where a EDP-TD Ti:Sa amplifier was tested for the first time. In our experiment, the final cryogenically cooled Ti:Sa amplifier in a 100 TW/10 Hz/28 fs laser system was replaced with the EDP-TD room temperature cooled arrangement. Amplified seed pulse energy of 2.6 J was reached only for 3 passes through TD with 0.5 J of

  10. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...... and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  11. Fluid dynamics analysis of a gas attenuator for X-ray FELs under high-repetition-rate operation.

    Science.gov (United States)

    Yang, Bo; Wu, Juhao; Raubenheimer, Tor O; Feng, Yiping

    2017-05-01

    Newtonian fluid dynamics simulations were performed using the Navier-Stokes-Fourier formulations to elucidate the short time-scale (µs and longer) evolution of the density and temperature distributions in an argon-gas-filled attenuator for an X-ray free-electron laser under high-repetition-rate operation. Both hydrodynamic motions of the gas molecules and thermal conductions were included in a finite-volume calculation. It was found that the hydrodynamic wave motions play the primary role in creating a density depression (also known as a filament) by advectively transporting gas particles away from the X-ray laser-gas interaction region, where large pressure and temperature gradients have been built upon the initial energy deposition via X-ray photoelectric absorption and subsequent thermalization. Concurrent outward heat conduction tends to reduce the pressure in the filament core region, generating a counter gas flow to backfill the filament, but on an initially slower time scale. If the inter-pulse separation is sufficiently short so the filament cannot recover, the depth of the filament progressively increases as the trailing pulses remove additional gas particles. Since the rate of hydrodynamic removal decreases while the rate of heat conduction back flow increases as time elapses, the two competing mechanisms ultimately reach a dynamic balance, establishing a repeating pattern for each pulse cycle. By performing simulations at higher repetition rates but lower per pulse energies while maintaining a constant time-averaged power, the amplitude of the hydrodynamic motion per pulse becomes smaller, and the evolution of the temperature and density distributions approach asymptotically towards, as expected, those calculated for a continuous-wave input of the equivalent power.

  12. Compact experimental apparatus for producing high-repetition-rate 87Rb Bose-Einstein condensation on an atom chip

    Science.gov (United States)

    Yu, Hoon; Kim, Seung Jin; Moon, Ye Lin; Kim, Jung Bog; Lee, Jin Seung

    2013-08-01

    We construct a compact experimental apparatus for producing high-repetition-rate ultra cold 87Rb atom based on an external atom chip. Initially, we produce an atomic flux from a 2D+ MOT (magneto-optical trap) in a nearly isolated 2D+ MOT chamber and improve the flux by adjusting the cooling beam detuning of the 2D+ MOT. The flux is trapped in the 3D MOT for 1.2 s and is further cooled by performing compressing the MOT for 20 ms and using polarization gradient cooling for 6.2 ms. After optical pumping into the 5 S F = 2 ( m F = 2) ground state, we transport atoms toward the chip surface by performing external Z coil trapping. At 1 mm below the chip surface, the external Z coil trap is completely switched to an atom chip trap by using a Z wire and a dimple wire on the chip with external bias fields. The transport and the switching take totally 520 ms. The number of atoms trapped on the atom chip is measured to be about 2 × 107. After the atoms has been compressed for 100 ms to increase trap frequencies, we perform RF evaporative cooling in the RF frequency range from 32 MHz to 6.82 MHz for 2.4 seconds. The final number of atoms in the atomic cloud after RF cooling is 1.2 × 105 atoms, and we are able to observe some Bose-Einstein condensation. The repetition rate for producing the condensation is 0.234 Hz. In this paper, we describe our experimental apparatus and processes.

  13. The Effects of Elbow Bracing on Medial Elbow Joint Space Gapping Associated With Repetitive Throwing in High School Baseball Players.

    Science.gov (United States)

    Hattori, Hiroshi; Akasaka, Kiyokazu; Otsudo, Takahiro; Takei, Keiichi; Yamamoto, Mitsuru

    2017-04-01

    Throwing athletes risk medial elbow injury from extreme valgus stress generated across the medial elbow during throwing. Braces have been developed to protect the elbow joint; however, no previous study has investigated the effects of elbow bracing on medial elbow joint space gapping associated with repetitive throwing. The purpose of this study was to investigate the effects of elbow bracing on medial elbow joint space gapping during repetitive throwing. Our hypothesis was that an elbow brace may reduce mechanical stress on the elbow by reducing medial elbow joint space gapping. Controlled laboratory study. Twenty-five high school baseball players participated in this study. Each subject pitched 100 times under 2 conditions: control (without elbow brace) and elbow brace. The ulnohumeral joint space was measured ultrasonically before pitching and after every block of 20 pitches. Measurement of the ulnohumeral joint space was carried out using ultrasound with the forearm hanging by the side. Two-way repeated-measures analysis of variance and post hoc tests were used to compare ulnohumeral joint space with repeated pitching and between the elbow brace and control conditions. In the control condition, ulnohumeral joint space after 60 pitches was significantly greater than that before pitching ( P space was not significantly different after repeated pitching. When comparing these 2 conditions, ulnohumeral joint space in the control condition was significantly greater than that in the elbow brace condition after 60 pitches ( P space gapping with repeated throwing when determined ultrasonically by measuring the ulnohumeral joint space under gravity load. An elbow brace worn during baseball pitching practice may help reduce mechanical stress on the elbow by reducing medial elbow joint space gapping.

  14. Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.

    Directory of Open Access Journals (Sweden)

    Bob Zimmermann

    Full Text Available BACKGROUND: SELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection. METHODOLOGY/PRINCIPAL FINDINGS: To evaluate SELEX and assess the extent of these effects, we designed and performed a Neutral SELEX experiment omitting the selection step, such that the sequences are under the sole selective pressure of SELEX's amplification steps. Using high-throughput sequencing, we obtained thousands of full-length sequences from the initial genomic library and the pools after each of the 10 rounds of Neutral SELEX. We compared these to sequences obtained from a Genomic SELEX experiment deriving from the same initial library, but screening for RNAs binding with high affinity to the E. coli regulator protein Hfq. With each round of Neutral SELEX, sequences became less stable and changed in nucleotide content, but no sequences were enriched. In contrast, we detected substantial enrichment in the Hfq-selected set with enriched sequences having structural stability similar to the neutral sequences but with significantly different nucleotide selection. CONCLUSIONS/SIGNIFICANCE: Our data indicate that positive selection in SELEX acts independently of the neutral selective requirements imposed on the sequences. We conclude that Genomic SELEX, when combined with high-throughput sequencing of positively and neutrally selected pools, as well as the gnomic library, is a powerful method to identify genomic aptamers.

  15. Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.

    Science.gov (United States)

    Zimmermann, Bob; Gesell, Tanja; Chen, Doris; Lorenz, Christina; Schroeder, Renée

    2010-02-11

    SELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection. To evaluate SELEX and assess the extent of these effects, we designed and performed a Neutral SELEX experiment omitting the selection step, such that the sequences are under the sole selective pressure of SELEX's amplification steps. Using high-throughput sequencing, we obtained thousands of full-length sequences from the initial genomic library and the pools after each of the 10 rounds of Neutral SELEX. We compared these to sequences obtained from a Genomic SELEX experiment deriving from the same initial library, but screening for RNAs binding with high affinity to the E. coli regulator protein Hfq. With each round of Neutral SELEX, sequences became less stable and changed in nucleotide content, but no sequences were enriched. In contrast, we detected substantial enrichment in the Hfq-selected set with enriched sequences having structural stability similar to the neutral sequences but with significantly different nucleotide selection. Our data indicate that positive selection in SELEX acts independently of the neutral selective requirements imposed on the sequences. We conclude that Genomic SELEX, when combined with high-throughput sequencing of positively and neutrally selected pools, as well as the gnomic library, is a powerful method to identify genomic aptamers.

  16. High-average-power 2 μm few-cycle optical parametric chirped pulse amplifier at 100 kHz repetition rate.

    Science.gov (United States)

    Shamir, Yariv; Rothhardt, Jan; Hädrich, Steffen; Demmler, Stefan; Tschernajew, Maxim; Limpert, Jens; Tünnermann, Andreas

    2015-12-01

    Sources of long wavelengths few-cycle high repetition rate pulses are becoming increasingly important for a plethora of applications, e.g., in high-field physics. Here, we report on the realization of a tunable optical parametric chirped pulse amplifier at 100 kHz repetition rate. At a central wavelength of 2 μm, the system delivered 33 fs pulses and a 6 W average power corresponding to 60 μJ pulse energy with gigawatt-level peak powers. Idler absorption and its crystal heating is experimentally investigated for a BBO. Strategies for further power scaling to several tens of watts of average power are discussed.

  17. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  18. High Energy Single Frequency Fiber Laser at Low Repetition Rate Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR phase I project proposes a tunable single frequency high energy fiber laser system for coherent Lidar systems for remote sensing. Current state-of-art...

  19. Semi-automated repetitive-sequence-based polymerase chain reaction compared to pulsed-field gel electrophoresis for Listeria monocytogenes subtyping.

    Science.gov (United States)

    Roussel, Sophie; Félix, Benjamin; Colanéri, Cécile; Vignaud, Marie-Léone; Dao, Trinh Tam; Marault, Muriel; Brisabois, Anne

    2010-09-01

    Listeriosis is a severe infection that mainly affects pregnant women, neonates, and immuno-compromised adults. The commercially available semi-automated repetitive-sequence-based polymerase chain reaction assay system, DiversiLab, has been successfully used for subtyping several species of bacteria. In this article we compare the DiversiLab System with macrorestriction analysis by pulsed-field gel electrophoresis (PFGE), which is currently the gold standard for molecular subtyping of Listeria monocytogenes. We used a panel of 116 human and food L. monocytogenes isolates for the comparative evaluation. Among these isolates, there were 4 pairs of duplicates, 13 strains were epidemiologically related, and the remaining food isolates were epidemiologically unrelated. The isolates of different serotypes represented distinct DiversiLab types (DTs) and ApaI/AscI-PFGE types except for one DT-containing isolates of two serotypes, 4b and 1/2b. The four duplicates displayed the same DT and ApaI/AscI PFGE type demonstrating the good reproducibility of the two methods. The epidemiologically related strains were clustered in the same DT and PFGE type. The Simpson's index of diversity was 0.954; 0.988; 0.994; and 0.998 for DiversiLab, AscI-PFGE, ApaI-PFGE, and AscI/ApaI-PFGE, respectively. Thus, PFGE was more discriminating than DiversiLab. However, for 1/2a serotype strains, six AscI-PFGE, three ApaI-PFGE, and one ApaI/AscI PFGE type were divided into different DTs. DiversiLab enabled a good discrimination between serotype 1/2a strains. DiversiLab is less labor intensive than PFGE and provides results in <24 hours compared with 30 hours to 3 days for PFGE from the time a pure culture of the bacteria has been obtained. On the basis of these results, DiversiLab may be useful for tracking the source of contamination in food-processing facilities and their environments. Also, DiversiLab may be more appropriate for long-term epidemiological studies where less discrimination is needed.

  20. Microstructural Characteristic of the Al-Fe-Cu Alloy During High-Speed Repetitive Continuous Extrusion Forming

    Science.gov (United States)

    Hu, Jiamin; Teng, Jie; Ji, Xiankun; Kong, Xiangxin; Jiang, Fulin; Zhang, Hui

    2016-11-01

    High-speed repetitive continuous extrusion forming process (R-Conform process) was performed on the Al-Fe-Cu alloy. The microstructural evolution and mechanical properties were studied by x-ray diffraction, electron backscatter diffraction, transmission electron microscopy and tensile testing. The results show that a significant improvement of tensile ductility concurs with a considerable loss of tensile strength before four passes, after that the process on mechanical properties variation tends to be steady, indicating an accelerated mechanical softening occurs when comparing to low-speed R-Conform process. Microstructure characterization indicates that the accumulated strain promotes the transformation of low angle boundaries to high angle boundaries, thus leading to the acceleration of continuous dynamic recrystallization process, and the precipitates are broken, spheroidized and homogeneously distribute in Al matrix as increasing R-Conform passes. Massive microshear bands are observed after initial passes of R-Conform process, which may promote continuous dynamic recrystallization and further grain refinement during high-speed R-Conform process.

  1. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  2. High-throughput sequence alignment using Graphics Processing Units.

    Science.gov (United States)

    Schatz, Michael C; Trapnell, Cole; Delcher, Arthur L; Varshney, Amitabh

    2007-12-10

    The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  3. Barcoded sequencing workflow for high throughput digitization of hybridoma antibody variable domain sequences.

    Science.gov (United States)

    Chen, Yongmei; Kim, Si Hyun; Shang, Yonglei; Guillory, Joseph; Stinson, Jeremy; Zhang, Qing; Hötzel, Isidro; Hoi, Kam Hon

    2018-01-20

    Since the invention of Hybridoma technology by Milstein and Köhler in 1975, its application has greatly advanced the antibody discovery process. The technology enables both functional screening and long-term archival of the immortalized monoclonal antibody producing B cells. Despite the dependable cryopreservation technology for hybridoma cells, practicality of long-term storage has been outpaced by recent progress in robotics and automations, which enables routine identification of thousands of antigen specific hybridoma clones. Such throughput increase imposes two nascent challenges in the antibody discovery process, namely limited cryopreservation storage space and limited throughput in conventional antibody sequencing. We herein provide a barcoded sequencing workflow that utilizes next generation sequencing to expand the conventional sequencing capacity. Accompanied with the bioinformatics tools we describe, the barcoded sequencing workflow robustly reports unambiguous antibody sequences as confirmed with Sanger sequencing controls. In complement with the commonly accessible recombinant DNA technology, the barcoded sequencing workflow allows for high throughput digitization of the antibody sequences and provides an effective solution to the limitations imposed by physical storage and sequencing capacity. Copyright © 2018 Genentech, Inc. Published by Elsevier B.V. All rights reserved.

  4. Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    Miri eMichaeli

    2012-12-01

    Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

  5. High throughput sequencing of microRNAs in chicken somites.

    Science.gov (United States)

    Rathjen, Tina; Pais, Helio; Sweetman, Dylan; Moulton, Vincent; Munsterberg, Andrea; Dalmay, Tamas

    2009-05-06

    High throughput Solexa sequencing technology was applied to identify microRNAs in somites of developing chicken embryos. We obtained 651,273 reads, from which 340,415 were mapped to the chicken genome representing 1701 distinct sequences. Eighty-five of these were known microRNAs and 42 novel miRNA candidates were identified. Accumulation of 18 of 42 sequences was confirmed by Northern blot analysis. Ten of the 18 sequences are new variants of known miRNAs and eight short RNAs are novel miRNAs. Six of these eight have not been reported by other deep sequencing projects. One of the six new miRNAs is highly enriched in somite tissue suggesting that deep sequencing of other specific tissues has the potential to identify novel tissue specific miRNAs.

  6. Modulation of the Left Prefrontal Cortex with High Frequency Repetitive Transcranial Magnetic Stimulation Facilitates Gait in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Amer M. Burhan

    2015-01-01

    Full Text Available Multiple Sclerosis (MS is a chronic central nervous system (CNS demyelinating disease. Gait abnormalities are common and disabling in patients with MS with limited treatment options available. Emerging evidence suggests a role of prefrontal attention networks in modulating gait. High-frequency repetitive transcranial magnetic stimulation (rTMS is known to enhance cortical excitability in stimulated cortex and its correlates. We investigated the effect of high-frequency left prefrontal rTMS on gait parameters in a 51-year-old Caucasian male with chronic relapsing/remitting MS with residual disabling attention and gait symptoms. Patient received 6 Hz, rTMS at 90% motor threshold using figure of eight coil centered on F3 location (using 10-20 electroencephalography (EEG lead localization system. GAITRite gait analysis system was used to collect objective gait measures before and after one session and in another occasion three consecutive daily sessions of rTMS. Two-tailed within subject repeated measure t-test showed significant enhancement in ambulation time, gait velocity, and cadence after three consecutive daily sessions of rTMS. Modulating left prefrontal cortex excitability using rTMS resulted in significant change in gait parameters after three sessions. To our knowledge, this is the first report that demonstrates the effect of rTMS applied to the prefrontal cortex on gait in MS patients.

  7. New concept for a high-repetition-rate reactor for inertial-confinement fusion

    Energy Technology Data Exchange (ETDEWEB)

    Monsler, M.J.

    1980-11-01

    A new design concept was developed that has three additional features that are very important in reducing program risk: (1) through a proper choice of the working temperature (400 to 540/sup 0/C) and of the liquid metal (lithium or lead-lithium eutectic alloy), we can select a chamber pressure within the range of 10/sup -1/ to 10/sup -4/ Torr, required for the propagation of either a laser-beam or a heavy-ion-beam driver; (2) presently available ferritic steels can be used for the structural material; and (3) the new concept allows flexibility in irradiaton geometry. Although two-sided irradiation at high f/Nos. seems most attractive from the standpoints of minimizing the number of chamber penetrations and of simplifing the layout of the balance of plant, we must provide for the possibility that target-implosion physics will require a more symmetrical illumination geometry.

  8. Preliminary Evidence of the Effects of High-frequency Repetitive Transcranial Magnetic Stimulation (rTMS) on Swallowing Functions in Post-Stroke Individuals with Chronic Dysphagia

    Science.gov (United States)

    Cheng, Ivy K. Y.; Chan, Karen M. K.; Wong, C. S.; Cheung, Raymond T. F.

    2015-01-01

    Background: There is growing evidence of potential benefits of repetitive transcranial magnetic stimulation (rTMS) in the rehabilitation of dysphagia. However, the site and frequency of stimulation for optimal effects are not clear. Aims: The aim of this pilot study is to investigate the short-term effects of high-frequency 5 Hz rTMS applied to…

  9. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Science.gov (United States)

    Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

    2015-01-01

    In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

  10. High-throughput sequencing in mitochondrial DNA research.

    Science.gov (United States)

    Ye, Fei; Samuels, David C; Clark, Travis; Guo, Yan

    2014-07-01

    Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels. Mitochondrial research has also benefitted greatly from high-throughput sequencing; sequencing technology now allows for screening of all 16,569 base pairs of the mitochondrial genome simultaneously for SNPs and low level heteroplasmy and, in some cases, the estimation of mitochondrial DNA copy number. It is important to realize the full potential of high-throughput sequencing for the advancement of mitochondrial research. To this end, we review how high-throughput sequencing has impacted mitochondrial research in the categories of SNPs, low level heteroplasmy, copy number, and structural variants. We also discuss the different types of mitochondrial DNA sequencing and their pros and cons. Based on previous studies conducted by various groups, we provide strategies for processing mitochondrial DNA sequencing data, including assembly, variant calling, and quality control. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  11. Accumulation effects in modulation spectroscopy with high-repetition-rate pulses: Recursive solution of optical Bloch equations

    Science.gov (United States)

    Osipov, Vladimir Al.; Pullerits, Tõnu

    2017-10-01

    Application of the phase-modulated pulsed light for advance spectroscopic measurements is the area of growing interest. The phase modulation of the light causes modulation of the signal. Separation of the spectral components of the modulations allows to distinguish the contributions of various interaction pathways. The lasers with high repetition rate used in such experiments can lead to appearance of the accumulation effects, which become especially pronounced in systems with long-living excited states. Recently it was shown that such accumulation effects can be used to evaluate parameters of the dynamical processes in the material. In this work we demonstrate that the accumulation effects are also important in the quantum characteristics measurements provided by modulation spectroscopy. In particular, we consider a model of quantum two-level system driven by a train of phase-modulated light pulses, organized in analogy with the two-dimensional spectroscopy experiments. We evaluate the harmonics' amplitudes in the fluorescent signal and calculate corrections appearing from the accumulation effects. We show that the corrections can be significant and have to be taken into account at analysis of experimental data.

  12. Study of Key Non-dimensional Parameters for Wave Drag Reduction with High-Frequency Repetitive Laser Pulse Energy Depositions

    Directory of Open Access Journals (Sweden)

    Qing Zexu

    2016-01-01

    Full Text Available The problem of wave drag reduction with high-frequency repetitive laser pulse energy depositions is multivariable. Three key non-dimensional parameters, non-dimensional energy, non-dimensional depositing position and Mach number, were constructed from a number of original variables by using Buckingham pi theorem. Influences of these non-dimensional parameters on energy deposition performance, namely drag reduction and energy deposition efficiency, were investigated numerically by solving three-dimensional Navier-Stokes equations with an upwind scheme. Optimizing method of non-dimensional energy and non-dimensional depositing position is proposed. Drag reduction and energy deposition efficiency have exponential relationships with non-dimensional energy; Drag reduction and energy deposition efficiency have quadratic relationships with non-dimensional depositing position. Drag reduction has exponential relationship with freestream Mach number and energy deposition efficiency has quadratic relationship with Mach number. Non-dimensional laser energy and non-dimensional depositing position should be optimized synthetically for a given freestream.

  13. Vernier effect within a versatile femtosecond optical parametric oscillator for broad-tunable, high-repetition-rate oscillator

    CERN Document Server

    Jin, Yuwei; Harren, Frans J M; Mandon, Julien

    2015-01-01

    Within a synchronously pumped optical parametric oscillator (SPOPO), the inherent synchronism between the pump and the resonating signal is the magic to partly transfer the coherence property of the pump to the signal. In our demonstration, Vernier effect is observed within a femtosecond SPOPO by simply detuning the FSR of the cavity, generating signal pulses at tunable repetition rate from several GHz to 1 THz with a maximum 22.58 nm full width half maximum (FWHM) bandwidth supporting 160 fs pulses covering the C- and L-bands of the telecom wavelength region. This technique offers a simple method of active ?filtering of dense frequency comb lines instead of using Fabry-P?erot (FP) cavities with complex locking system for astro-comb generation. Beside, as a promising source for frequency combs with tunable and large comb-spacing, it offers potential opportunities for applications such as high speed coherent data transmission, line-by-line pulse shaping, optical clocks and precision metrology.

  14. The sequence of learning cycle activities in high school chemistry

    Science.gov (United States)

    Abraham, Michael R.; Renner, John W.

    The sequence of the three phases of two high school learning cycles in chemistry was altered in order to: (I ) give insights into the factors which account for the success of the learning cycle, (2) serve as an indirect test of the association between Piaget's theory and the learning cycle, and (3) to compare the learning cycle with traditional instruction. Each of the six sequences (one n o d and five altered) was studied with content and atritudc measures. The outcomes of the study supported the contention that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge.

  15. Polymorphism in Brucella strains detected by studying distribution of two short repetitive DNA elements.

    OpenAIRE

    Mercier, E; Jumas-Bilak, E; Allardet-Servent, A; O'Callaghan, D; Ramuz, M

    1996-01-01

    Thirty-four Brucella reference or field strains representing all the species and biovars were studied by repetitive element sequence-based PCR, a PCR using primers complementary to two enterobacterial short repetitive sequences: repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequences. All the stains showed a positive amplification, suggesting that the Brucella genome contains such sequences. Repetitive extragenic palindromic PCR was less discriminating ...

  16. Highly heterogeneous Ty3/Gypsy -like retrotransposon sequences ...

    African Journals Online (AJOL)

    like), sequences to be highly heterogeneous. Some Megyps clustered with other plants' Ty3/Gypsy-like retrotransposons, while some clustered with Gypsy of Drosophila melanogaster and Ty3-2 of Saccharomyces cerevisiae in the comparative ...

  17. Validation of high throughput sequencing and microbial forensics applications

    OpenAIRE

    Budowle, Bruce; Connell, Nancy D.; Bielecka-Oder, Anna; Rita R Colwell; Corbett, Cindi R.; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A.; Murch, Randall S; Sajantila, Antti; Schemes, Sarah E; Ternus, Krista L; Turner, Stephen D

    2014-01-01

    Abstract High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results a...

  18. The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: large repetitive sequences between trnE and trnF in aphids.

    Science.gov (United States)

    Zhang, Bo; Ma, Chuan; Edwards, Owain; Fuller, Susan; Kang, Le

    2014-01-01

    To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A+T content (84.76%) and strong C skew (-0.26) was arranged in the same gene order as that of the ancestral insect. Unlike typical insect mitogenomes, D. noxia possessed a large tandem repeat region (644 bp) located between trnE and trnF. Sequencing partial mitogenome of the cotton aphid (Aphis gossypii) further confirmed the presence of the large repeat region in aphids, but with different repeat length and copy number. Another motif (58 bp) tandemly repeated 2.3 times in the control region of D. noxia. All repeat units in D. noxia could be folded into stem-loop secondary structures, which could further promote an increase in copy numbers. Characterization of the D. noxia mitogenome revealed distinct mitogenome architectures, thus advancing our understanding of insect mitogenomic diversities and evolution. © 2013 Elsevier B.V. All rights reserved.

  19. Theoretical and experimental analysis of instability of continuous wave mode locking: Towards high fundamental repetition rate in Tm3+-doped fiber lasers.

    Science.gov (United States)

    Cheng, H; Lin, W; Qiao, T; Xu, S; Yang, Z

    2016-12-26

    With increasing demand on a laser source in the gigahertz pulse repetition rate regime, clarification on the mechanism of instability in high repetition rate fiber lasers - a promising alternative to solid state lasers - is of great importance and can potentially offer guideline for continuous wave (CW) mode locking. Here we present a theoretical approach together with relevant experimental corroboration to analyze the instabilities. By means of appropriate approximations, regimes from Q-switched mode locking, CW mode locking and pulsation are theoretically identified. Meanwhile, a critical curve that characterizes pump level for triggering Q-switched mode locking and pulsation for different repetition rates is given by virtue of both analytical and numerical procedures. In experiment, a passively mode-locked fiber laser with 1.6 GHz fundamental repetition rate is realized. The three regimes and corresponding pump power intervals are revealed, which are in consistence with theoretical prediction. Pulsation, as a relatively exotic phenomenon in GHz fiber laser, is well reproduced by the present model, which further verifies the accuracy of the approach as well as enriches the nonlinear dynamics.

  20. High similarity of U2 snDNA sequence between A and B chromosomes in the grasshopper Abracris flavolineata.

    Science.gov (United States)

    Menezes-de-Carvalho, Nahanna Zimmermann; Palacios-Gimenez, Octavio Manuel; Milani, Diogo; Cabral-de-Mello, Diogo Cavalcanti

    2015-10-01

    B chromosomes are frequently enriched for a wide variety of repetitive DNAs. Among grasshoppers in the species Abracris flavolineata (Ommatolampidinae) the B chromosomes are submetacentric, C-negative and harbor repetitive DNAs such as, U2 snDNA, C 0 t-1 DNA, two Mariner-like elements and some microsatellites. Here, we provide evidence showing the intragenome similarity between the B chromosome and the A complement in A. flavolineata, combining analysis of microdissection and chromosome painting and B chromosome-specific amplification through polymerase chain reaction (PCR) of U2 snDNA. Chromosome painting revealed signals spread through the C-negative regions, including the A and B chromosomes. Moreover, significant clustered signals forming bands were observed in some A chromosomes, and for the B chromosome, significant signals were located on both arms, which could be caused by accumulation of repetitive DNA sequences. The C-positive regions did not reveal any signals. Sequence comparison of U2 snDNA between that obtained from a genome without the B chromosome and that from µB-DNA revealed high similarity with the occurrence of four shared haplotypes, one of them (i.e., Hap1) being highly prevalent and putatively ancestral. The highest divergence from Hap1 was observed for Hap3, which was caused by only six mutational steps. These data support an intraspecific origin of the B chromosome in A. flavolineata that is highly similar with the A complement, and the low U2 snDNA sequence diversity observed in the B chromosome could be related to its recent origin, besides intrachromosomal concerted evolution for U2 snDNA repeats in the B chromosome.

  1. Changes in Restricted Repetitive Behaviors with Age: A Study of High-Functioning Adults with Autism Spectrum Disorders

    Science.gov (United States)

    Chowdhury, Monali; Benson, Betsey A.; Hillier, Ashleigh

    2010-01-01

    The existing literature suggests that while impairments in Autism Spectrum Disorders (ASDs) continue into adulthood, some behavioral symptoms tend to abate with age. However, there is a dearth of research examining changes in ASD symptoms from childhood to adulthood, especially for Restricted Repetitive Behaviors (RRBs). We examined age-related…

  2. Repetition and the Concept of Repetition

    Directory of Open Access Journals (Sweden)

    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.

  3. High-throughput DNA sequencing: a genomic data manufacturing process.

    Science.gov (United States)

    Huang, G M

    1999-01-01

    The progress trends in automated DNA sequencing operation are reviewed. Technological development in sequencing instruments, enzymatic chemistry and robotic stations has resulted in ever-increasing capacity of sequence data production. This progress leads to a higher demand on laboratory information management and data quality assessment. High-throughput laboratories face the challenge of organizational management, as well as technology management. Engineering principles of process control should be adopted in this biological data manufacturing procedure. While various systems attempt to provide solutions to automate different parts of, or even the entire process, new technical advances will continue to change the paradigm and provide new challenges.

  4. PULSAR: A High-Repetition-Rate, High-Power, CE Phase-Locked Laser for the J.R. Macdonald Laboratory at Kansas State University

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Itzhak, Itzik [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Carnes, Kevin D. [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Cocke, C. Lew [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Fehrenbach, Charles W. [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Kumarappan, Vinod [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Rudenko, Artem [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.; Trallero, Carlos [Kansas State Univ., Manhattan, KS (United States). Physics Dept. J.R. Macdonald Lab.

    2014-05-09

    This instrumentation grant funded the development and installation of a state-of-the-art laser system to be used for the DOE funded research at the J.R. Macdonald Laboratory at Kansas State University. Specifically, we purchased a laser based on the KMLABs Red-Dragon design, which has a high repetition rate of 10-20 kHz crucial for multi-parameter coincidence measurements conducted in our lab. This laser system is carrier-envelope phase (CEP) locked and provides pulses as short as 21 fs directly from the amplifier (see details below). In addition, we have developed a pulse compression setup that provides sub 5 fs pulses and a CEP tagging capability that allows for long measurements of CEP dependent processes.

  5. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  6. High repetition rate multiple optical parametric oscillator by an aperiodically poled lithium niobate around 1.57 and 3.84 μm

    Science.gov (United States)

    Yu, Yongji; Chen, Xinyu; Cheng, Libo; Dong, Yuan; Wu, Chunting; Li, Shutao; Fu, Yuegang; Jin, Guangyong

    2017-12-01

    This paper presents a high repetition rate and high power 1.57 μm and 3.84 μm multiple optical parametric oscillator based on a single MgO:APLN crystal and pumped by a pulsed 1.064 μm MOPA laser for the first time. In the experiment, with a repetition rate of 200 kHz, a maximum average output powers of 6.5 W at 1.57 μm and 4.3 W at 3.84 μm were obtained under 49 W of 1064 nm pump power, corresponding to optical-optical conversion efficiencies of 13.3% and 8.8%, respectively. The pulse widths were 12.8 and 11.2 ns for 1.57 μm and 3.84 μm, respectively, at the maximum output power.

  7. Varianish: Jamming with Pattern Repetition

    Directory of Open Access Journals (Sweden)

    Jort Band

    2014-10-01

    Full Text Available In music, patterns and pattern repetition are often regarded as a machine-like task, indeed often delegated to drum Machines and sequencers. Nevertheless, human players add subtle differences and variations to repeated patterns that are musically interesting and often unique. Especially when looking at minimal music, pattern repetitions create hypnotic effects and the human mind blends out the actual pattern to focus on variation and tiny differences over time. Varianish is a musical instrument that aims at turning this phenomenon into a new musical experience for musician and audience: Musical pattern repetitions are found in live music and Varianish generates additional (musical output accordingly that adds substantially to the overall musical expression. Apart from the theory behind the pattern finding and matching and the conceptual design, a demonstrator implementation of Varianish is presented and evaluated.

  8. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r...

  9. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  10. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

    Directory of Open Access Journals (Sweden)

    Samson Gaelle

    2008-12-01

    Full Text Available Abstract Background Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input. Results We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors. Conclusion High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.

  11. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.

    Science.gov (United States)

    Aury, Jean-Marc; Cruaud, Corinne; Barbe, Valérie; Rogier, Odile; Mangenot, Sophie; Samson, Gaelle; Poulain, Julie; Anthouard, Véronique; Scarpelli, Claude; Artiguenave, François; Wincker, Patrick

    2008-12-16

    Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input. We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors. High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.

  12. An improved high throughput sequencing method for studying oomycete communities

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Nicolaisen, Mogens

    2015-01-01

    Culture-independent studies using next generation sequencing have revolutionizedmicrobial ecology, however, oomycete ecology in soils is severely lagging behind. The aimof this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete...... agricultural fields in Denmark, and 11 samples from carrot tissue with symptoms of Pythium infection. Sequence data from the Pythium and Phytophthora mock communities showed that our strategy successfully detected all included species. Taxonomic assignments of OTUs from 26 soil sample showed that 95...... the usefulness of the method not only in soil DNA but also in a plant DNA background. In conclusion, we demonstrate a successful approach for pyrosequencing of oomycete communities using ITS1 as the barcode sequence with well-known primers for oomycete DNA amplification....

  13. Exome Sequence Analysis of 14 Families With High Myopia.

    Science.gov (United States)

    Kloss, Bethany A; Tompson, Stuart W; Whisenhunt, Kristina N; Quow, Krystina L; Huang, Samuel J; Pavelec, Derek M; Rosenberg, Thomas; Young, Terri L

    2017-04-01

    To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sanger sequencing was used to confirm variants in original DNA, and to test for disease cosegregation in additional family members. Candidate genes and chromosomal loci previously associated with myopic refractive error and its endophenotypes were comprehensively screened. In 14 high myopia families, we identified 73 rare and 31 novel gene variants as candidates for pathogenicity. In seven of these families, two of the novel and eight of the rare variants were within known myopia loci. A total of 104 heterozygous nonsynonymous rare variants in 104 genes were identified in 10 out of 14 probands. Each variant cosegregated with affection status. No rare variants were identified in genes known to cause myopia or in genes closest to published genome-wide association study association signals for refractive error or its endophenotypes. Whole exome sequencing was performed to determine gene variants implicated in the pathogenesis of AD high myopia. This study provides new genes for consideration in the pathogenesis of high myopia, and may aid in the development of genetic profiling of those at greatest risk for attendant ocular morbidities of this disorder.

  14. Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping

    Directory of Open Access Journals (Sweden)

    Nelly Cubizolles

    2016-03-01

    Full Text Available Transposable elements (TEs account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs in the hexaploid wheat ( L. genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele-specific polymerase chain reaction genotyping technology. Finally, through genetic diversity and genome-wide association studies, we also demonstrate that ISBP-derived SNPs can be used in marker-assisted breeding programs.

  15. Exome sequencing identifies ZNF644 mutations in high myopia.

    Directory of Open Access Journals (Sweden)

    Yi Shi

    2011-06-01

    Full Text Available Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644 was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE. Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

  16. Alteration of default mode network in high school football athletes due to repetitive subconcussive mild traumatic brain injury: a resting-state functional magnetic resonance imaging study.

    Science.gov (United States)

    Abbas, Kausar; Shenk, Trey E; Poole, Victoria N; Breedlove, Evan L; Leverenz, Larry J; Nauman, Eric A; Talavage, Thomas M; Robinson, Meghan E

    2015-03-01

    Long-term neurological damage as a result of head trauma while playing sports is a major concern for football athletes today. Repetitive concussions have been linked to many neurological disorders. Recently, it has been reported that repetitive subconcussive events can be a significant source of accrued damage. Since football athletes can experience hundreds of subconcussive hits during a single season, it is of utmost importance to understand their effect on brain health in the short and long term. In this study, resting-state functional magnetic resonance imaging (rs-fMRI) was used to study changes in the default mode network (DMN) after repetitive subconcussive mild traumatic brain injury. Twenty-two high school American football athletes, clinically asymptomatic, were scanned using the rs-fMRI for a single season. Baseline scans were acquired before the start of the season, and follow-up scans were obtained during and after the season to track the potential changes in the DMN as a result of experienced trauma. Ten noncollision-sport athletes were scanned over two sessions as controls. Overall, football athletes had significantly different functional connectivity measures than controls for most of the year. The presence of this deviation of football athletes from their healthy peers even before the start of the season suggests a neurological change that has accumulated over the years of playing the sport. Football athletes also demonstrate short-term changes relative to their own baseline at the start of the season. Football athletes exhibited hyperconnectivity in the DMN compared to controls for most of the sessions, which indicates that, despite the absence of symptoms typically associated with concussion, the repetitive trauma accrued produced long-term brain changes compared to their healthy peers.

  17. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.

    Directory of Open Access Journals (Sweden)

    Alex R Hastie

    Full Text Available Next-generation sequencing (NGS technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum. Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.

  18. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.

    Science.gov (United States)

    Hastie, Alex R; Dong, Lingli; Smith, Alexis; Finklestein, Jeff; Lam, Ernest T; Huo, Naxin; Cao, Han; Kwok, Pui-Yan; Deal, Karin R; Dvorak, Jan; Luo, Ming-Cheng; Gu, Yong; Xiao, Ming

    2013-01-01

    Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.

  19. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Directory of Open Access Journals (Sweden)

    Charlotte Rehm

    Full Text Available In prokaryotes simple sequence repeats (SSRs with unit sizes of 1-5 nucleotides (nt are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4 structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc, Xanthomonas axonopodis pv. citri str. 306 (Xac, and Nostoc sp. strain PCC7120 (Ana. In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

  20. Savant: genome browser for high-throughput sequencing data.

    Science.gov (United States)

    Fiume, Marc; Williams, Vanessa; Brook, Andrew; Brudno, Michael

    2010-08-15

    The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictions and understand the functional effects, especially in the context of other datasets. We introduce Savant, the Sequence Annotation, Visualization and ANalysis Tool, a desktop visualization and analysis browser for genomic data. Savant was developed for visualizing and analyzing HTS data, with special care taken to enable dynamic visualization in the presence of gigabases of genomic reads and references the size of the human genome. Savant supports the visualization of genome-based sequence, point, interval and continuous datasets, and multiple visualization modes that enable easy identification of genomic variants (including single nucleotide polymorphisms, structural and copy number variants), and functional genomic information (e.g. peaks in ChIP-seq data) in the context of genomic annotations. Savant is freely available at http://compbio.cs.toronto.edu/savant.

  1. Ultra-high-resolution inelastic X-ray scattering at high-repetition-rate self-seeded X-ray free-electron lasers

    Energy Technology Data Exchange (ETDEWEB)

    Chubar, Oleg [Brookhaven National Laboratory, Upton, NY 11973 (United States); Geloni, Gianluca [European X-ray Free-Electron Laser, Albert-Einstein-Ring 19, 22761 Hamburg (Germany); Kocharyan, Vitali [Deutsches Elektronen-Synchrotron, 22761 Hamburg (Germany); Madsen, Anders [European X-ray Free-Electron Laser, Albert-Einstein-Ring 19, 22761 Hamburg (Germany); Saldin, Evgeni; Serkez, Svitozar [Deutsches Elektronen-Synchrotron, 22761 Hamburg (Germany); Shvyd’ko, Yuri, E-mail: shvydko@aps.anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States); Sutter, John [Diamond Light Source Ltd, Didcot OX11 0DE (United Kingdom)

    2016-02-12

    This article explores novel opportunities for ultra-high-resolution inelastic X-ray scattering (IXS) at high-repetition-rate self-seeded XFELs. These next-generation light sources are promising a more than three orders of magnitude increase in average spectral flux compared with what is possible with storage-ring-based radiation sources. In combination with the advanced IXS spectrometer described here, this may become a real game-changer for ultra-high-resolution X-ray spectroscopies, and hence for the studies of dynamics in condensed matter systems. Inelastic X-ray scattering (IXS) is an important tool for studies of equilibrium dynamics in condensed matter. A new spectrometer recently proposed for ultra-high-resolution IXS (UHRIX) has achieved 0.6 meV and 0.25 nm{sup −1} spectral and momentum-transfer resolutions, respectively. However, further improvements down to 0.1 meV and 0.02 nm{sup −1} are required to close the gap in energy–momentum space between high- and low-frequency probes. It is shown that this goal can be achieved by further optimizing the X-ray optics and by increasing the spectral flux of the incident X-ray pulses. UHRIX performs best at energies from 5 to 10 keV, where a combination of self-seeding and undulator tapering at the SASE-2 beamline of the European XFEL promises up to a 100-fold increase in average spectral flux compared with nominal SASE pulses at saturation, or three orders of magnitude more than what is possible with storage-ring-based radiation sources. Wave-optics calculations show that about 7 × 10{sup 12} photons s{sup −1} in a 90 µeV bandwidth can be achieved on the sample. This will provide unique new possibilities for dynamics studies by IXS.

  2. Next-generation sequencing: big data meets high performance computing.

    Science.gov (United States)

    Schmidt, Bertil; Hildebrandt, Andreas

    2017-04-01

    The progress of next-generation sequencing has a major impact on medical and genomic research. This high-throughput technology can now produce billions of short DNA or RNA fragments in excess of a few terabytes of data in a single run. This leads to massive datasets used by a wide range of applications including personalized cancer treatment and precision medicine. In addition to the hugely increased throughput, the cost of using high-throughput technologies has been dramatically decreasing. A low sequencing cost of around US$1000 per genome has now rendered large population-scale projects feasible. However, to make effective use of the produced data, the design of big data algorithms and their efficient implementation on modern high performance computing systems is required. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

    Science.gov (United States)

    Caboche, Ségolène; Audebert, Christophe; Lemoine, Yves; Hot, David

    2014-04-05

    The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark

  4. Mitochondrial genomes and divergence times of crocodile newts : Inter-islands distribution of Echinotriton andersoni and the origin of a unique repetitive sequence found in Tylototriton mt genomes

    OpenAIRE

    Kurabayashi, Atsushi; Nishitani, Takuma; Katsuren, Seiki; Oumi, Shohei; Sumida, Masayuki

    2012-01-01

    Crocodile newts, which constitute the genera Echinotriton and Tylototriton, are known as living fossils, and these genera comprise many endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered taxa, we determined the complete nucleotide sequences of the mt genomes of the Japanese crocodile newt Echinotriton andersoni and Himalayan crocodile newt Tylototriton verrucosus. Although the control region (CR) is known as the most variabl...

  5. Formation of the active medium in high-power repetitively pulsed gas lasers pumped by an electron-beam-controlled discharge

    Science.gov (United States)

    Bulaev, V. D.; Lysenko, S. L.

    2015-07-01

    A high-power repetitively pulsed e-beam-controlled discharge CO2 laser is simulated numerically; the simulation results are compared with experimental data. Optimal sizes and design of electrodes and configuration of the external magnetic field are found, which allow one to introduce no less than 90% electric pump energy into a specified volume of the active medium, including the active volume of a laser with an aperture of 110 × 110 cm. The results obtained can also be used to design other types of highpower gas lasers.

  6. High resolution characterization of modifications in fused silica after exposure to low fluence 355 nm laser at different repetition frequencies.

    Science.gov (United States)

    Li, C H; Ju, X; Jiang, X D; Huang, J; Zhou, X D; Zheng, Z; Wu, W D; Zheng, W G; Li, Z X; Wang, B Y; Yu, X H

    2011-03-28

    We report on the characterization of modifications in fused silica after exposure to low fluence (2 J/cm2) 355 nm laser at repetition frequencies of 1 Hz, 5 Hz and 10 Hz. Synchrotron based XRF spectroscopy is employed to study concentration variation of metal inclusions in the surface layer. Positron annihilation lifetime spectroscopy is used to probe atomic size defects variation in bulk silica. FT-IR is used to characterize changes of bond length and angle of Si-O-Si covalent bond of irradiated silica. Compared to the basic frequency, the big loss of cerium and iron concentration, the size enlargement of vacancy cluster and the decrease of Si-O-Si covalent bond length after 10 Hz laser irradiation are illustrated by our data. These tiny modifications provide important data to investigate laser damage mechanism.

  7. Phase-amplitude characterization of a high-repetition-rate quantum dash passively mode-locked laser.

    Science.gov (United States)

    Gosset, C; Merghem, K; Moreau, G; Martinez, A; Aubin, G; Oudar, J-L; Ramdane, A; Lelarge, F

    2006-06-15

    We apply a novel phase-amplitude characterization method to a one-section quantum dash-based passively mode-locked laser at a 42.2 GHz repetition rate. The method relies on the measurement of the spectral phase of the longitudinal modes by the successive analysis of the correlation signal of a group of three adjacent modes. It provides both the temporal shape of the intensity and the phase of the emitted signal. A pulse of 1.5 ps of width is measured, and a pedestal is exhibited. Extinction ratio limitation is explained by investigating the origin of this pedestal. The accuracy of the method is estimated by comparing the measured autocorrelation signal and the calculated one from the phase analysis.

  8. A HIGH COVERAGE GENOME SEQUENCE FROM AN ARCHAIC DENISOVAN INDIVIDUAL

    Science.gov (United States)

    Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; Li, Heng; Racimo, Fernando; Mallick, Swapan; Schraiber, Joshua G.; Jay, Flora; Prüfer, Kay; de Filippo, Cesare; Sudmant, Peter H.; Alkan, Can; Fu, Qiaomei; Do, Ron; Rohland, Nadin; Tandon, Arti; Siebauer, Michael; Green, Richard E.; Bryc, Katarzyna; Briggs, Adrian W.; Stenzel, Udo; Dabney, Jesse; Shendure, Jay; Kitzman, Jacob; Hammer, Michael F.; Shunkov, Michael V.; Derevianko, Anatoli P.; Patterson, Nick; Andrés, Aida M.; Eichler, Evan E.; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante

    2013-01-01

    We present a DNA library preparation method that has allowed us to reconstruct a high coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans. PMID:22936568

  9. Validation of high throughput sequencing and microbial forensics applications.

    Science.gov (United States)

    Budowle, Bruce; Connell, Nancy D; Bielecka-Oder, Anna; Colwell, Rita R; Corbett, Cindi R; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A; Murch, Randall S; Sajantila, Antti; Schmedes, Sarah E; Ternus, Krista L; Turner, Stephen D; Minot, Samuel

    2014-01-01

    High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

  10. Sequencing of endurance and high-velocity strength training.

    Science.gov (United States)

    Bell, G J; Petersen, S R; Quinney, H A; Wenger, H A

    1988-12-01

    To compare two sequences of endurance (E) and high-velocity resistance (HVR) training, sixteen male oarsmen were separated into Group ES which trained endurance prior to strength and Group SE which trained strength prior to endurance. The endurance program consisted of up to 60 min a session, five days a week for five weeks. HVR exercise was conducted on 12 stations of variable resistance hydraulic equipment, four sessions per week for five weeks. Endurance training significantly improved VO2max and submaximal heart rate and blood lactate responses in both groups regardless of the sequence followed. HVR training improved VO2max in group SE only and had no effect on submaximal response to exercise. Peak torque increases for knee extension and flexion with HVR training were greater in group SE than group ES. These results show that organizing strength and endurance training into sequential programs can influence the physiological adaptation to training.

  11. Applications of High-Throughput Nucleotide Sequencing (PhD)

    DEFF Research Database (Denmark)

    Waage, Johannes

    The recent advent of high throughput sequencing of nucleic acids (RNA and DNA) has vastly expanded research into the functional and structural biology of the genome of all living organisms (and even a few dead ones). With this enormous and exponential growth in biological data generation come...... equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......). For the second flavor, DNA-seq, a study presenting genome wide profiling of transcription factor CEBP/A in liver cells undergoing regeneration after partial hepatectomy (article IV) is included....

  12. Probing ultra-fast processes with high dynamic range at 4th-generation light sources: Arrival time and intensity binning at unprecedented repetition rates

    Directory of Open Access Journals (Sweden)

    S. Kovalev

    2017-03-01

    Full Text Available Understanding dynamics on ultrafast timescales enables unique and new insights into important processes in the materials and life sciences. In this respect, the fundamental pump-probe approach based on ultra-short photon pulses aims at the creation of stroboscopic movies. Performing such experiments at one of the many recently established accelerator-based 4th-generation light sources such as free-electron lasers or superradiant THz sources allows an enormous widening of the accessible parameter space for the excitation and/or probing light pulses. Compared to table-top devices, critical issues of this type of experiment are fluctuations of the timing between the accelerator and external laser systems and intensity instabilities of the accelerator-based photon sources. Existing solutions have so far been only demonstrated at low repetition rates and/or achieved a limited dynamic range in comparison to table-top experiments, while the 4th generation of accelerator-based light sources is based on superconducting radio-frequency technology, which enables operation at MHz or even GHz repetition rates. In this article, we present the successful demonstration of ultra-fast accelerator-laser pump-probe experiments performed at an unprecedentedly high repetition rate in the few-hundred-kHz regime and with a currently achievable optimal time resolution of 13 fs (rms. Our scheme, based on the pulse-resolved detection of multiple beam parameters relevant for the experiment, allows us to achieve an excellent sensitivity in real-world ultra-fast experiments, as demonstrated for the example of THz-field-driven coherent spin precession.

  13. The 1 Repetition Maximum Mechanics of a High-Handle Hexagonal Bar Deadlift Compared With a Conventional Deadlift as Measured by a Linear Position Transducer.

    Science.gov (United States)

    Lockie, Robert G; Moreno, Matthew R; Lazar, Adrina; Risso, Fabrice G; Liu, Tricia M; Stage, Alyssa A; Birmingham-Babauta, Samantha A; Torne, Ibett A; Stokes, John J; Giuliano, Dominic V; Davis, DeShaun L; Orjalo, Ashley J; Callaghan, Samuel J

    2018-01-01

    Lockie, RG, Moreno, MR, Lazar, A, Risso, FG, Liu, TM, Stage, AA, Birmingham-Babauta, SA, Torne, IA, Stokes, JJ, Giuliano, DV, Davis, DL, Orjalo, AJ, and Callaghan, SJ. The 1 repetition maximum mechanics of a high-handle hexagonal bar deadlift compared with a conventional deadlift as measured by a linear position transducer. J Strength Cond Res 32(1): 150-161, 2018-The high-handle hexagonal bar deadlift (HHBD), a variation of the conventional deadlift (CD), is said to reduce the lift range of motion, which may change the mechanics of the lift. However, no research has investigated this. This study compared the mechanics between a 1 repetition maximum (1RM) CD and HHBD. Thirty-one strength-trained subjects (21 men, 10 women) completed a 1RM CD and HHBD. A linear position transducer measured lift distance, duration, and work; and peak and mean power, velocity, and force. The presence of a sticking region (SR) was determined for each lift. A repeated-measures analysis of variance (ANOVA) calculated differences between 1RM CD and HHBD mechanics. A one-way ANOVA compared the mechanics of each lift between subjects who exhibited an SR or not, and the SR between the CD and HHBD. Significance was set at p mechanics between subjects with or without an SR, and no differences in SR region distance or duration between the CD and HHBD. Greater force can be generated in the HHBD, which could have implications for strength-training adaptations over time.

  14. The Negative Repetition Effect

    Science.gov (United States)

    Mulligan, Neil W.; Peterson, Daniel J.

    2013-01-01

    A fundamental property of human memory is that repetition enhances memory. Peterson and Mulligan (2012) recently documented a surprising "negative repetition effect," in which participants who studied a list of cue-target pairs twice recalled fewer targets than a group who studied the pairs only once. Words within a pair rhymed, and…

  15. Repetition in Schizophrenic Speech.

    Science.gov (United States)

    Manschreck, Theo C.; And Others

    1985-01-01

    Describes an investigation into the relationship of schizophrenic thought disorder to measures of repetition that include phrase units, proximity of repetitions, and word frequencies to determine whether such measures distinguish schizophrenics from non-schizophrenics and to what extent they are associated with certain attributes of schizophrenia,…

  16. Experimental study of the inverse diffusion flame using high repetition rate OH/acetone PLIF and PIV

    KAUST Repository

    Elbaz, Ayman M.

    2015-10-29

    Most previous work on inverse diffusion flames (IDFs) has focused on laminar IDF emissions and the soot formation characteristics. Here, we investigate the characteristics and structure of methane IDFs using high speed planar laser-induced fluorescence (PLIF) images of OH, particle image velocimetry (PIV), and acetone PLIF imaging for non-reacting cases. First, the flame appearance was investigated with fixed methane loading (mass flux) but with varying airflow rates, yielding a central air jet Reynolds number (Re) of 1,000 to 6,000 (when blow-off occurs). Next, it was investigated a fixed central air jet Re of 4500, but with varied methane mass flux such that the global equivalence ratio spanned 0.5 to 4. It was observed that at Re smaller than 2000, the inner air jet promotes the establishment of an inverse diffusion flame surrounded by a normal diffusion flame. However, when the Re was increased to 2500, two distinct zones became apparent in the flame, a lower entrainment zone and an upper mixing and combustion zone. 10 kHz OH-PLIF images, and 2D PIV allow the identification of the fate and spatial flame structure. Many flame features were identified and further analyzed using simple but effective image processing methods, where three types of structure in all the flames investigated here: flame holes or breaks; closures; and growing kernels. Insights about the rate of evolution of these features, the dynamics of local extinction, and the sequence of events that lead to re-ignition are reported here. In the lower entrainment zone, the occurrence of the flame break events is counterbalanced by closure events, and the edge propagation appears to control the rate at which the flame holes and closures propagate. The rate of propagation of holes was found to be statistically faster than the rate of closure. As the flames approach blow-off, flame kernels become the main mechanism for flame re-ignition further downstream. The simultaneous OH-PLIF/Stereo PIV

  17. High-throughput sequencing: a roadmap toward community ecology.

    Science.gov (United States)

    Poisot, Timothée; Péquin, Bérangère; Gravel, Dominique

    2013-04-01

    High-throughput sequencing is becoming increasingly important in microbial ecology, yet it is surprisingly under-used to generate or test biogeographic hypotheses. In this contribution, we highlight how adding these methods to the ecologist toolbox will allow the detection of new patterns, and will help our understanding of the structure and dynamics of diversity. Starting with a review of ecological questions that can be addressed, we move on to the technical and analytical issues that will benefit from an increased collaboration between different disciplines.

  18. Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome

    Directory of Open Access Journals (Sweden)

    Zhuang Xuan

    2012-07-01

    Full Text Available Abstract Background Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP gene family in the recently sequenced Atlantic cod genome serves as an example. Results The Atlantic cod (Gadus morhua genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the

  19. Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome

    Science.gov (United States)

    2012-01-01

    Background Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. Results The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene

  20. Chromosomal distribution patterns of the (AC)10microsatellite and other repetitive sequences, and their use in chromosome rearrangement analysis of species of the genus Avena.

    Science.gov (United States)

    Fominaya, Araceli; Loarce, Yolanda; Montes, Alexander; Ferrer, Esther

    2017-03-01

    Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC) 10 microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC) 10 microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions. New large chromosome rearrangements were detected in two polyploid species: an intergenomic translocation involving chromosomes 17AL and 21DS in Avena sativa 'Araceli' and another involving chromosomes 4CL and 21DS in the analyzed cultivars of Avena byzantina. The latter 4CL-21DS intergenomic translocation differentiates clearly between A. sativa and A. byzantina. Searches for common hybridization patterns on the chromosomes of different species revealed chromosome 10A of Avena magna and 21D of hexaploid oats to be very similar in terms of the distribution of 45S and Am1 sequences. This suggests a common origin for these chromosomes and supports a CCDD rather than an AACC genomic designation for this species.

  1. Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process.

    Science.gov (United States)

    Shapland, Elaine B; Holmes, Victor; Reeves, Christopher D; Sorokin, Elena; Durot, Maxime; Platt, Darren; Allen, Christopher; Dean, Jed; Serber, Zach; Newman, Jack; Chandran, Sunil

    2015-07-17

    In recent years, next-generation sequencing (NGS) technology has greatly reduced the cost of sequencing whole genomes, whereas the cost of sequence verification of plasmids via Sanger sequencing has remained high. Consequently, industrial-scale strain engineers either limit the number of designs or take short cuts in quality control. Here, we show that over 4000 plasmids can be completely sequenced in one Illumina MiSeq run for less than $3 each (15× coverage), which is a 20-fold reduction over using Sanger sequencing (2× coverage). We reduced the volume of the Nextera tagmentation reaction by 100-fold and developed an automated workflow to prepare thousands of samples for sequencing. We also developed software to track the samples and associated sequence data and to rapidly identify correctly assembled constructs having the fewest defects. As DNA synthesis and assembly become a centralized commodity, this NGS quality control (QC) process will be essential to groups operating high-throughput pipelines for DNA construction.

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

    Directory of Open Access Journals (Sweden)

    Gilbert Greub

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

  3. Representation of motor habit in a sequence of repetitive reach and grasp movements performed by macaque monkeys: evidence for a contribution of the dorsolateral prefrontal cortex.

    Science.gov (United States)

    Kaeser, Mélanie; Wannier, Thierry; Brunet, Jean-François; Wyss, Alexander; Bloch, Jocelyne; Rouiller, Eric M

    2013-05-01

    In the context of an autologous cell transplantation study, a unilateral biopsy of cortical tissue was surgically performed from the right dorsolateral prefrontal cortex (dlPFC) in two intact adult macaque monkeys (dlPFC lesioned group), together with the implantation of a chronic chamber providing access to the left motor cortex. Three other monkeys were subjected to the same chronic chamber implantation, but without dlPFC biopsy (control group). All monkeys were initially trained to perform sequential manual dexterity tasks, requiring precision grip. The motor performance and the prehension's sequence (temporal order to grasp pellets from different spatial locations) were analysed for each hand. Following the surgery, transient and moderate deficits of manual dexterity per se occurred in both groups, indicating that they were not due to the dlPFC lesion (most likely related to the recording chamber implantation and/or general anaesthesia/medication). In contrast, changes of motor habit were observed for the sequential order of grasping in the two monkeys with dlPFC lesion only. The changes were more prominent in the monkey subjected to the largest lesion, supporting the notion of a specific effect of the dlPFC lesion on the motor habit of the monkeys. These observations are reminiscent of previous studies using conditional tasks with delay that have proposed a specialization of the dlPFC for visuo-spatial working memory, except that this is in a different context of "free-will", non-conditional manual dexterity task, without a component of working memory. Copyright © 2013. Published by Elsevier Ltd.

  4. Molecular genetic analysis of ICEF, an integrative conjugal element that is present as a repetitive sequence in the chromosome of Mycoplasma fermentans PG18.

    Science.gov (United States)

    Calcutt, Michael J; Lewis, Michelle S; Wise, Kim S

    2002-12-01

    Mycoplasma genomes contain compact gene sets that approach the minimal complement necessary for life and reflect multiple evolutionary instances of genomic reduction. Lateral gene transfer may play a critical role in shaping the mobile gene pool in these organisms, yet complex mobile elements have not been reported within this genus. We describe here a large ( approximately 23-kb) genetic element with unique features that is present in four copies in the Mycoplasma fermentans PG18 chromosome, accounting for approximately 8% of the genome. These novel elements, designated ICEF (integrative conjugal elements of M. fermentans), resemble conjugative, self-transmissible integrating elements (constins) in that circular, nonreplicative extrachromosomal forms occur in which the left and right termini of the integrated element are juxtaposed and separated by a coupling sequence derived from direct repeats flanking chromosomal copies of ICEF as a result of target site duplication. ICEF contain multiple similarly oriented open reading frames (ORFs), of which some have homology to products of known conjugation genes but others have no known counterparts. Surprisingly, unlike other constins, ICEF lack homologs of known integrases, transposases, or recombinases, suggesting that a novel enzyme may be employed for integration-excision. Skewed distribution and varied sites of chromosomal integration among M. fermentans isolates suggest a role for ICEF in promoting genomic and phenotypic variation in this species. Identification of homologs of terminal ICEF ORFs in two additional mycoplasma species indicates that ICEF is the prototype member of a family of ICE-related elements that may be widespread among pathogenic mycoplasmas infecting diverse vertebrate hosts.

  5. Fusion genes and their discovery using high throughput sequencing.

    Science.gov (United States)

    Annala, M J; Parker, B C; Zhang, W; Nykter, M

    2013-11-01

    Fusion genes are hybrid genes that combine parts of two or more original genes. They can form as a result of chromosomal rearrangements or abnormal transcription, and have been shown to act as drivers of malignant transformation and progression in many human cancers. The biological significance of fusion genes together with their specificity to cancer cells has made them into excellent targets for molecular therapy. Fusion genes are also used as diagnostic and prognostic markers to confirm cancer diagnosis and monitor response to molecular therapies. High-throughput sequencing has enabled the systematic discovery of fusion genes in a wide variety of cancer types. In this review, we describe the history of fusion genes in cancer and the ways in which fusion genes form and affect cellular function. We also describe computational methodologies for detecting fusion genes from high-throughput sequencing experiments, and the most common sources of error that lead to false discovery of fusion genes. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  6. Large scale library generation for high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Erik Borgström

    Full Text Available BACKGROUND: Large efforts have recently been made to automate the sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols. METHODOLOGY/PRINCIPAL FINDINGS: In this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions. CONCLUSIONS/SIGNIFICANCE: The method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.

  7. High Throughput Sequencing of Extracellular RNA from Human Plasma.

    Directory of Open Access Journals (Sweden)

    Kirsty M Danielson

    Full Text Available The presence and relative stability of extracellular RNAs (exRNAs in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids. At the same time, the use of RNA sequencing for biofluids poses unique challenges, including low amounts of input RNAs, the presence of exRNAs in different compartments with varying degrees of vulnerability to isolation techniques, and the high abundance of specific RNA species (thereby limiting the sensitivity of detection of less abundant species. Moreover, discovery in human diseases often relies on archival biospecimens of varying age and limiting amounts of samples. In this study, we have tested RNA isolation methods to optimize profiling exRNAs by RNA sequencing in individuals without any known diseases. Our findings are consistent with other recent studies that detect microRNAs and ribosomal RNAs as the major exRNA species in plasma. Similar to other recent studies, we found that the landscape of biofluid microRNA transcriptome is dominated by several abundant microRNAs that appear to comprise conserved extracellular miRNAs. There is reasonable correlation of sets of conserved miRNAs across biological replicates, and even across other data sets obtained at different investigative sites. Conversely, the detection of less abundant miRNAs is far more dependent on the exact methodology of RNA isolation and profiling. This study highlights the challenges in detecting and quantifying less abundant plasma miRNAs in health and disease using RNA sequencing platforms.

  8. Flipping the sign of refractive index changes in ultrafast and temporally shaped laser-irradiated borosilicate crown optical glass at high repetition rates

    Science.gov (United States)

    Mermillod-Blondin, A.; Burakov, I. M.; Meshcheryakov, Yu. P.; Bulgakova, N. M.; Audouard, E.; Rosenfeld, A.; Husakou, A.; Hertel, I. V.; Stoian, R.

    2008-03-01

    Ultrafast subpicosecond laser exposure usually induces negative refractive index changes in optical glasses with strong thermal expansion such as borosilicate BK7 due to volume expansion and mechanical rarefaction. We show that temporally shaped laser excitation on picosecond scales and at high repetition rates can invert the regular material response resulting in a significant refractive index increase. Simulations of pulse propagation and evolution of heat and strain waves in BK7 glass exposed to different pulse durations were performed to understand mechanisms of refractive index increase. Narrow spatial distribution of energy for optimized picosecond pulses determines shock-induced plastic deformations accompanied by partial healing of the lateral strain due to preferential heat flow. The matter momentum relaxation produces directional on-axis material compaction.

  9. Digital repetitive control under varying frequency conditions

    CERN Document Server

    Ramos, Germán A; Olm, Josep M

    2013-01-01

    The tracking/rejection of periodic signals constitutes a wide field of research in the control theory and applications area. Repetitive Control has proven to be an efficient way to face this topic. However, in some applications the frequency of the reference/disturbance signal is time-varying or uncertain. This causes an important performance degradation in the standard Repetitive Control scheme. This book presents some solutions to apply Repetitive Control in varying frequency conditions without loosing steady-state performance. It also includes a complete theoretical development and experimental results in two representative systems. The presented solutions are organized in two complementary branches: varying sampling period Repetitive Control and High Order Repetitive Control. The first approach allows dealing with large range frequency variations while the second allows dealing with small range frequency variations. The book also presents applications of the described techniques to a Roto-magnet plant and...

  10. 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.

  11. High-repetition-rate, widely tunable terahertz generation in GaSe pumped by a dual-wavelength KTP-OPO

    Science.gov (United States)

    Yan, Dexian; Xu, Degang; Wang, Yuye; Shi, Wei; Zhong, Kai; Liu, Pengxiang; Yan, Chao; Sheng, Quan; Mei, Jialin; Shi, Jia; Yao, Jianquan

    2016-11-01

    High-repetition-rate, monochromatic and tunable terahertz (THz) source is demonstrated. We use an orthogonally polarized dual-wavelength intracavity OPO to complete the type-II phase-matched collinear difference-frequency generation in GaSe. A high average-power 2 μm laser with 12 W output power and good beam quality based on an intracavity KTP OPO is experimentally designed. The KTP OPO is intracavity pumped by an acousto-optical Q-switched side-pumped Nd:YAG with the repetition rate of 10 kHz. Two identical KTP crystals were 7 × 8 × 15 mm3 in size, cut at θ = 51.2°, φ = 0°, which were tuned in the x-z plane to achieve type-II phase-matching. The KTP OPO consists of two identical KTP crystals to reduce the walk-off effect and improve the beam overlap area of the output signal and idler waves. The pulse-width of the 2-μm KTP OPO laser is about 11 ns with the linewidth about 0.8 nm. The focused OPO beam is injected into the uncoated GaSe with the length of 8 mm, and the generated THz wave is detected with a 4.2-K Si-bolometer after focusing with a polyethylene lens. The tunable and coherent radiation from 0.2 to 3 THz has been achieved based on the type-II phase-matching DFG when the two pump waves are in the range of 2.1064 - 2.1272 μm and 2.1516 - 2.1304 μm while symmetrically tuning the phase-matching angle of the KTPs. The maximum output THz average power can reach μW-level around 1.48 THz.

  12. Effect of pulse repetition rate and number of pulses in the analysis of polypropylene and high density polyethylene by nanosecond infrared laser induced breakdown spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Leme, Flavio O. [Laboratorio de Quimica Analitica ' Henrique Bergamin Filho' , Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Av. Centenario 303, 13416-000 Piracicaba, SP (Brazil); Godoi, Quienly [Laboratorio de Quimica Analitica ' Henrique Bergamin Filho' , Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Av. Centenario 303, 13416-000 Piracicaba, SP (Brazil); Departamento de Quimica, Universidade Federal de Sao Carlos, Rod. Washington Luis, km 235, 13565-905 Sao Carlos, SP (Brazil); Kiyataka, Paulo H.M. [Centro de Tecnologia de Embalagens, Instituto de Tecnologia de Alimentos, Av. Brasil 2880, 13070-178 Campinas, SP (Brazil); Santos, Dario [Departamento de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo, Rua Prof. Artur Riedel 275, 09972-270 Diadema, SP (Brazil); Agnelli, Jose A.M. [Departamento de Engenharia de Materiais, Universidade Federal de Sao Carlos, Rod. Washington Luis, km 235, 13565-905 Sao Carlos, SP (Brazil); and others

    2012-02-01

    Pulse repetition rates and the number of laser pulses are among the most important parameters that do affect the analysis of solid materials by laser induced breakdown spectroscopy, and the knowledge of their effects is of fundamental importance for suggesting analytical strategies when dealing with laser ablation processes of polymers. In this contribution, the influence of these parameters in the ablated mass and in the features of craters was evaluated in polypropylene and high density polyethylene plates containing pigment-based PbCrO{sub 4}. Surface characterization and craters profile were carried out by perfilometry and scanning electron microscopy. Area, volume and profile of craters were obtained using Taylor Map software. A laser induced breakdown spectroscopy system consisted of a Q-Switched Nd:YAG laser (1064 nm, 5 ns) and an Echelle spectrometer equipped with ICCD detector were used. The evaluated operating conditions consisted of 10, 25 and 50 laser pulses at 1, 5 and 10 Hz, 250 mJ/pulse (85 J cm{sup -2}), 2 {mu}s delay time and 6 {mu}s integration time gate. Differences in the topographical features among craters of both polymers were observed. The decrease in the repetition rate resulted in irregular craters and formation of edges, especially in polypropylene sample. The differences in the topographical features and ablated masses were attributed to the influence of the degree of crystallinity, crystalline melting temperature and glass transition temperature in the ablation process of the high density polyethylene and polypropylene. It was also observed that the intensities of chromium and lead emission signals obtained at 10 Hz were two times higher than at 5 Hz by keeping the number of laser pulses constant.

  13. 76 FR 28990 - Ultra High Throughput Sequencing for Clinical Diagnostic Applications-Approaches To Assess...

    Science.gov (United States)

    2011-05-19

    ... Clinical Diagnostic Applications--Approaches To Assess Analytical Validity.'' The purpose of the public... approaches to assess analytical validity of ultra high throughput sequencing for clinical diagnostic... HUMAN SERVICES Food and Drug Administration Ultra High Throughput Sequencing for Clinical Diagnostic...

  14. Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes.

    Directory of Open Access Journals (Sweden)

    Seung Chul Shin

    Full Text Available Next-generation sequencing has become the most widely used sequencing technology in genomics research, but it has inherent drawbacks when dealing with high-GC content genomes. Recently, single-molecule real-time sequencing technology (SMRT was introduced as a third-generation sequencing strategy to compensate for this drawback. Here, we report that the unbiased and longer read length of SMRT sequencing markedly improved genome assembly with high GC content via gap filling and repeat resolution.

  15. Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis.

    Science.gov (United States)

    Goldfeder, Rachel L; Wall, Dennis P; Khoury, Muin J; Ioannidis, John P A; Ashley, Euan A

    2017-10-15

    Most human diseases have underlying genetic causes. To better understand the impact of genes on disease and its implications for medicine and public health, researchers have pursued methods for determining the sequences of individual genes, then all genes, and now complete human genomes. Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequencing continues to decline, more and more individuals are having their genomes sequenced. This may facilitate better population-level disease subtyping and characterization, as well as individual-level diagnosis and personalized treatment and prevention plans. In this review, we describe several massively parallel high-throughput DNA sequencing technologies and their associated strengths, limitations, and error modes, with a focus on applications in epidemiologic research and precision medicine. We detail the methods used to computationally process and interpret sequence data to inform medical or preventative action. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Diamond-like carbon film preparation using a high-repetition nanosecond pulsed glow discharge plasma at gas pressure of 1 kPa generated by a SiC-MOSFET inverter power supply

    Science.gov (United States)

    Kikuchi, Yusuke; Ogura, Masataka; Maegawa, Takuya; Otsubo, Akira; Nishimura, Yoshimi; Nagata, Masayoshi; Yatsuzuka, Mitsuyasu

    2017-10-01

    A high-repetition nanosecond pulsed glow discharge plasma at a gas pressure of 1 kPa was generated using a SiC-MOSFET inverter power supply for diamond-like carbon (DLC) film preparation. At a high repetition frequency above 50 kHz, the period of the nanosecond voltage pulse became shorter than the decay time of the afterglow plasma, and many ions and radicals remained in the gap space. The deposition rate was 0.1 µm/min, which was 5 times higher than that of a conventional plasma CVD process. An increase in hardness to 13 GPa and a decrease in hydrogen content in the DLC film were confirmed by increasing the repetition frequency to 200 kHz.

  17. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Science.gov (United States)

    Nakazato, Takeru; Ohta, Tazro; Bono, Hidemasa

    2013-01-01

    High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA.

  18. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Directory of Open Access Journals (Sweden)

    Takeru Nakazato

    Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

  19. A short pulse (7 micros FWHM) and high repetition rate (dc-5 kHz) cantilever piezovalve for pulsed atomic and molecular beams.

    Science.gov (United States)

    Irimia, Daniel; Dobrikov, Dimitar; Kortekaas, Rob; Voet, Han; van den Ende, Daan A; Groen, Wilhelm A; Janssen, Maurice H M

    2009-11-01

    In this paper we report on the design and operation of a novel piezovalve for the production of short pulsed atomic or molecular beams. The high speed valve operates on the principle of a cantilever piezo. The only moving part, besides the cantilever piezo itself, is a very small O-ring that forms the vacuum seal. The valve can operate continuous (dc) and in pulsed mode with the same drive electronics. Pulsed operation has been tested at repetition frequencies up to 5 kHz. The static deflection of the cantilever, as mounted in the valve body, was measured as a function of driving field strength with a confocal microscope. The deflection and high speed dynamical response of the cantilever can be easily changed and optimized for a particular nozzle diameter or repetition rate by a simple adjustment of the free cantilever length. Pulsed molecular beams with a full width at half maximum pulse width as low as 7 micros have been measured at a position 10 cm downstream of the nozzle exit. This represents a gas pulse with a length of only 10 mm making it well matched to for instance experiments using laser beams. Such a short pulse with 6 bar backing pressure behind a 150 microm nozzle releases about 10(16) particles/pulse and the beam brightness was estimated to be 4x10(22) particles/(s str). The short pulses of the cantilever piezovalve result in a much reduced gas load in the vacuum system. We demonstrate operation of the pulsed valve with skimmer in a single vacuum chamber pumped by a 520 l/s turbomolecular pump maintaining a pressure of 5x10(-6) Torr, which is an excellent vacuum to have the strong and cold skimmed molecular beam interact with laser beams only 10 cm downstream of the nozzle to do velocity map slice imaging with a microchannel-plate imaging detector in a single chamber. The piezovalve produces cold and narrow (Delta v/v=2%-3%) velocity distributions of molecules seeded in helium or neon at modest backing pressures of only 6 bar. The low gas load of the

  20. A short pulse (7 μs FWHM) and high repetition rate (dc-5kHz) cantilever piezovalve for pulsed atomic and molecular beams

    Science.gov (United States)

    Irimia, Daniel; Dobrikov, Dimitar; Kortekaas, Rob; Voet, Han; van den Ende, Daan A.; Groen, Wilhelm A.; Janssen, Maurice H. M.

    2009-11-01

    In this paper we report on the design and operation of a novel piezovalve for the production of short pulsed atomic or molecular beams. The high speed valve operates on the principle of a cantilever piezo. The only moving part, besides the cantilever piezo itself, is a very small O-ring that forms the vacuum seal. The valve can operate continuous (dc) and in pulsed mode with the same drive electronics. Pulsed operation has been tested at repetition frequencies up to 5 kHz. The static deflection of the cantilever, as mounted in the valve body, was measured as a function of driving field strength with a confocal microscope. The deflection and high speed dynamical response of the cantilever can be easily changed and optimized for a particular nozzle diameter or repetition rate by a simple adjustment of the free cantilever length. Pulsed molecular beams with a full width at half maximum pulse width as low as 7 μs have been measured at a position 10 cm downstream of the nozzle exit. This represents a gas pulse with a length of only 10 mm making it well matched to for instance experiments using laser beams. Such a short pulse with 6 bar backing pressure behind a 150 μm nozzle releases about 1016 particles/pulse and the beam brightness was estimated to be 4×1022 particles/(s str). The short pulses of the cantilever piezovalve result in a much reduced gas load in the vacuum system. We demonstrate operation of the pulsed valve with skimmer in a single vacuum chamber pumped by a 520 l/s turbomolecular pump maintaining a pressure of 5×10-6 Torr, which is an excellent vacuum to have the strong and cold skimmed molecular beam interact with laser beams only 10 cm downstream of the nozzle to do velocity map slice imaging with a microchannel-plate imaging detector in a single chamber. The piezovalve produces cold and narrow (Δv /v=2%-3%) velocity distributions of molecules seeded in helium or neon at modest backing pressures of only 6 bar. The low gas load of the cantilever

  1. Probabilistic Methods for Processing High-Throughput Sequencing Signals

    DEFF Research Database (Denmark)

    Sørensen, Lasse Maretty

    for reconstructing transcript sequences from RNA sequencing data. The method is based on a novel sparse prior distribution over transcript abundances and is markedly more accurate than existing approaches. The second chapter describes a new method for calling genotypes from a fixed set of candidate variants...

  2. Algorithms for mapping high-throughput DNA sequences

    DEFF Research Database (Denmark)

    Frellsen, Jes; Menzel, Peter; Krogh, Anders

    2014-01-01

    of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads...

  3. The influence of vocabulary size, phonotactic probability, and wordlikeness on nonword repetitions of children with and without specific language impairment.

    Science.gov (United States)

    Munson, Benjamin; Kurtz, Beth A; Windsor, Jennifer

    2005-10-01

    Research has shown that children repeat high-probability phoneme sequences more accurately than low-probability ones. This effect attenuates with age, and its decrease is predicted by developmental changes in the size of the lexicon (J. Edwards, M. E. Beckman, & B. Munson, 2004; B. Munson, 2001; B. Munson, J. Edwards, & M. Beckman, 2005). This study expands on these findings by examining relationships between vocabulary size and repetition accuracy of nonwords varying in phonotactic probability by 16 children with specific language impairment (SLI), 16 chronological-age-matched (CA) peers with typical speech and language development, and 16 younger children matched with the children with SLI on vocabulary size (VS). As in previous research, children with SLI repeated nonwords less accurately than did CA children. The children with SLI and the VS children showed similar levels of nonword repetition accuracy. Phonotactic probability affected repetition accuracy more for children with SLI and VS children than for CA children. Regression analyses showed that measures of vocabulary size were the best predictor of the difference in repetition accuracy between high- and low-probability sequences. Analyses by items showed that measures of phonotactic probability were stronger predictors of repetition accuracy than judgments of wordlikeness. Taken together, the results support research demonstrating that vocabulary size mediates the influence of phonotactic probability on nonword repetition, perhaps due to its influence on the ongoing refinement of phonological categories.

  4. High-Frequency Repetitive Transcranial Magnetic Stimulation (rTMS Improves Functional Recovery by Enhancing Neurogenesis and Activating BDNF/TrkB Signaling in Ischemic Rats

    Directory of Open Access Journals (Sweden)

    Jing Luo

    2017-02-01

    Full Text Available Repetitive transcranial magnetic stimulation (rTMS has rapidly become an attractive therapeutic approach for stroke. However, the mechanisms underlying this remain elusive. This study aimed to investigate whether high-frequency rTMS improves functional recovery mediated by enhanced neurogenesis and activation of brain-derived neurotrophic factor (BDNF/tropomyosin-related kinase B (TrkB pathway and to compare the effect of conventional 20 Hz rTMS and intermittent theta burst stimulation (iTBS on ischemic rats. Rats after rTMS were sacrificed seven and 14 days after middle cerebral artery occlusion (MCAO, following evaluation of neurological function. Neurogenesis was measured using specific markers: Ki67, Nestin, doublecortin (DCX, NeuN and glial fibrillary acidic protein (GFAP, and the expression levels of BDNF were visualized by Western blotting and RT-PCR analysis. Both high-frequency rTMS methods significantly improved neurological function and reduced infarct volume. Moreover, 20 Hz rTMS and iTBS significantly promoted neurogenesis, shown by an increase of Ki67/DCX, Ki67/Nestin, and Ki67/NeuN-positive cells in the peri-infarct striatum. These beneficial effects were accompanied by elevated protein levels of BDNF and phosphorylated-TrkB. In conclusion, high-frequency rTMS improves functional recovery possibly by enhancing neurogenesis and activating BDNF/TrkB signaling pathway and conventional 20 Hz rTMS is better than iTBS at enhancing neurogenesis in ischemic rats.

  5. Recent research on the high-probability instructional sequence: A brief review.

    Science.gov (United States)

    Lipschultz, Joshua; Wilder, David A

    2017-04-01

    The high-probability (high-p) instructional sequence consists of the delivery of a series of high-probability instructions immediately before delivery of a low-probability or target instruction. It is commonly used to increase compliance in a variety of populations. Recent research has described variations of the high-p instructional sequence and examined the conditions under which the sequence is most effective. This manuscript reviews the most recent research on the sequence and identifies directions for future research. Recommendations for practitioners regarding the use of the high-p instructional sequence are also provided. © 2017 Society for the Experimental Analysis of Behavior.

  6. Repetition suppression in auditory-motor regions to pitch and temporal structure in music.

    Science.gov (United States)

    Brown, Rachel M; Chen, Joyce L; Hollinger, Avrum; Penhune, Virginia B; Palmer, Caroline; Zatorre, Robert J

    2013-02-01

    Music performance requires control of two sequential structures: the ordering of pitches and the temporal intervals between successive pitches. Whether pitch and temporal structures are processed as separate or integrated features remains unclear. A repetition suppression paradigm compared neural and behavioral correlates of mapping pitch sequences and temporal sequences to motor movements in music performance. Fourteen pianists listened to and performed novel melodies on an MR-compatible piano keyboard during fMRI scanning. The pitch or temporal patterns in the melodies either changed or repeated (remained the same) across consecutive trials. We expected decreased neural response to the patterns (pitch or temporal) that repeated across trials relative to patterns that changed. Pitch and temporal accuracy were high, and pitch accuracy improved when either pitch or temporal sequences repeated over trials. Repetition of either pitch or temporal sequences was associated with linear BOLD decrease in frontal-parietal brain regions including dorsal and ventral premotor cortex, pre-SMA, and superior parietal cortex. Pitch sequence repetition (in contrast to temporal sequence repetition) was associated with linear BOLD decrease in the intraparietal sulcus (IPS) while pianists listened to melodies they were about to perform. Decreased BOLD response in IPS also predicted increase in pitch accuracy only when pitch sequences repeated. Thus, behavioral performance and neural response in sensorimotor mapping networks were sensitive to both pitch and temporal structure, suggesting that pitch and temporal structure are largely integrated in auditory-motor transformations. IPS may be involved in transforming pitch sequences into spatial coordinates for accurate piano performance.

  7. Evolution of repetitive proteins: spider silks from Nephila clavipes (Tetragnathidae) and Araneus bicentenarius (Araneidae).

    Science.gov (United States)

    Beckwitt, R; Arcidiacono, S; Stote, R

    1998-03-01

    Spider silks are highly repetitive proteins, characterized by regions of polyalanine and glycine-rich repeating units. We have obtained two variants of the Spidroin 1 (NCF-1) silk gene sequence from Nephila clavipes. One sequence (1726 bp) was from a cloned cDNA, and the other (1951 bp) was from PCR of genomic DNA. When these sequences are compared with each other and the previously published Spidroin 1 sequence, there are differences due to sequence rearrangements, as well as single base substitutions. These variations are similar to those that have been reported from other highly repetitive genes, and probably represent the results of unequal cross-overs. We have also obtained 708 bp of sequence from pCR of genomic DNA from Araneus biocentenarius. This sequence shows considerable similarity to a dragline sequence (ADF-3) from A. diadematus, as well as Spidroin 2 (NCF-2) from N. clavipes. Minor but consistent differences in the repeating unit sequence between A. bicentenarius and A. diadematus suggest that concerted evolution or gene conversion processes are acting to maintain similarity among repeat units within a single gene.

  8. Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.

    Directory of Open Access Journals (Sweden)

    Kathy N Lam

    Full Text Available High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.

  9. Communicating the Benefits of a Full Sequence of High School Science Courses

    Science.gov (United States)

    Nicholas, Catherine Marie

    2014-01-01

    High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit…

  10. Disparate molecular evolution of two types of repetitive DNAs in the genome of the grasshopper Eyprepocnemis plorans.

    Science.gov (United States)

    Teruel, M; Ruíz-Ruano, F J; Marchal, J A; Sánchez, A; Cabrero, J; Camacho, J Pm; Perfectti, F

    2014-05-01

    Wide arrays of repetitive DNA sequences form an important part of eukaryotic genomes. These repeats appear to evolve as coherent families, where repeats within a family are more similar to each other than to other orthologous representatives in related species. The continuous homogenization of repeats, through selective and non-selective processes, is termed concerted evolution. Ascertaining the level of variation between repeats is crucial to determining which evolutionary model best explains the homogenization observed for these sequences. Here, for the grasshopper Eyprepocnemis plorans, we present the analysis of intragenomic diversity for two repetitive DNA sequences (a satellite DNA (satDNA) and the 45S rDNA) resulting from the independent microdissection of several chromosomes. Our results show different homogenization patterns for these two kinds of paralogous DNA sequences, with a high between-chromosome structure for rDNA but no structure at all for the satDNA. This difference is puzzling, considering the adjacent localization of the two repetitive DNAs on paracentromeric regions in most chromosomes. The disparate homogenization patterns detected for these two repetitive DNA sequences suggest that several processes participate in the concerted evolution in E. plorans, and that these mechanisms might not work as genome-wide processes but rather as sequence-specific ones.

  11. Effect of high-frequency repetitive transcranial magnetic stimulation on motor cortical excitability and sensory nerve conduction velocity in subacute-stage incomplete spinal cord injury patients.

    Science.gov (United States)

    Cha, Hyun Gyu; Ji, Sang-Goo; Kim, Myoung-Kwon

    2016-07-01

    [Purpose] The aim of the present study was to determine whether repetitive transcranial magnetic stimulation can improve sensory recovery of the lower extremities in subacute-stage spinal cord injury patients. [Subjects and Methods] This study was conducted on 20 subjects with diagnosed paraplegia due to spinal cord injury. These 20 subjects were allocated to an experimental group of 10 subjects that underwent active repetitive transcranial magnetic stimulation or to a control group of 10 subjects that underwent sham repetitive transcranial magnetic stimulation. The SCI patients in the experimental group underwent active repetitive transcranial magnetic stimulation and conventional rehabilitation therapy, whereas the spinal cord injury patients in the control group underwent sham repetitive transcranial magnetic stimulation and conventional rehabilitation therapy. Participants in both groups received therapy five days per week for six-weeks. Latency, amplitude, and sensory nerve conduction velocity were assessed before and after the six week therapy period. [Results] A significant intergroup difference was observed for posttreatment velocity gains, but no significant intergroup difference was observed for amplitude or latency. [Conclusion] repetitive transcranial magnetic stimulation may be improve sensory recovery of the lower extremities in subacute-stage spinal cord injury patients.

  12. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

    National Research Council Canada - National Science Library

    Glaubitz, Jeffrey C; Casstevens, Terry M; Lu, Fei; Harriman, James; Elshire, Robert J; Sun, Qi; Buckler, Edward S

    2014-01-01

    Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers...

  13. Transparent Si–DLC coatings on metals with high repetition bi-polar pulses of a PBII system

    Energy Technology Data Exchange (ETDEWEB)

    Ikeyama, Masami, E-mail: ikeyama3@aist.go.jp; Sonoda, Tsutomu, E-mail: tsutomu.sonoda@aist.go.jp

    2013-07-15

    Diamond-like carbon (DLC) is widely used because of its good properties. However, the color of DLC is usually dark brown or black. Recently, we have made fairly transparent Si contained DLC (Si–DLC) coatings in visible light region. The fairly transparent Si–DLC was made by using our original bi-polar pulse type plasma based ion implantation (PBII) system, with recently introduced high slew rate pulse power supply. The colors of metal sample surface were uniformly changed as subdued red, yellow, subdued green and subdued blue or violet, with the change of Si–DLC coating’s thickness. The colors come from the interference between reflected lights at the surface of the Si–DLC coatings and the surface of the metal samples. The colors were also changed with the angle of glancing. Estimated refractive indexes show well agreements among almost all Si–DLC coatings, instead of the differences of coating conditions. Generally, the longer coating time or slower coating process makes the higher refractive index in near infrared region. Estimated band gap of a Si–DLC coating was about 1.5 eV. The developed Si–DLC coatings must be useful as not only protective but also decorative coatings.

  14. Practice Makes Perfect: Correlations Between Prior Experience in High-level Athletics and Robotic Surgical Performance Do Not Persist After Task Repetition.

    Science.gov (United States)

    Shee, Kevin; Ghali, Fady M; Hyams, Elias S

    Robotic surgical skill development is central to training in urology as well as in other surgical disciplines. Here, we describe a pilot study assessing the relationships between robotic surgery simulator performance and 3 categories of activities, namely, videogames, musical instruments, and athletics. A questionnaire was administered to preclinical medical students for general demographic information and prior experiences in surgery, videogames, musical instruments, and athletics. For follow-up performance studies, we used the Matchboard Level 1 and 2 modules on the da Vinci Skills Simulator, and recorded overall score, time to complete, economy of motion, workspace range, instrument collisions, instruments out of view, and drops. Task 1 was run once, whereas task 2 was run 3 times. All performance studies on the da Vinci Surgical Skills Simulator took place in the Simulation Center at Dartmouth-Hitchcock Medical Center. All participants were medical students at the Geisel School of Medicine. After excluding students with prior hands-on experience in surgery, a total of 30 students completed the study. We found a significant correlation between athletic skill level and performance for both task 1 (p = 0.0002) and task 2 (p = 0.0009). No significant correlations were found for videogame or musical instrument skill level. Students with experience in certain athletics (e.g., volleyball, tennis, and baseball) tended to perform better than students with experience in other athletics (e.g., track and field). For task 2, which was run 3 times, this association did not persist after the third repetition due to significant improvements in students with low-level athletic skill (levels 0-2). Our study suggests that prior experience in high-level athletics, but not videogames or musical instruments, significantly influences surgical proficiency in robot-naive students. Furthermore, our study suggests that practice through task repetition can overcome initial differences

  15. A shock tube with a high-repetition-rate time-of-flight mass spectrometer for investigations of complex reaction systems.

    Science.gov (United States)

    Dürrstein, Steffen H; Aghsaee, Mohammad; Jerig, Ludger; Fikri, Mustapha; Schulz, Christof

    2011-08-01

    A conventional membrane-type stainless steel shock tube has been coupled to a high-repetition-rate time-of-flight mass spectrometer (HRR-TOF-MS) to be used to study complex reaction systems such as the formation of pollutants in combustion processes or formation of nanoparticles from metal containing organic compounds. Opposed to other TOF-MS shock tubes, our instrument is equipped with a modular sampling unit that allows to sample with or without a skimmer. The skimmer unit can be mounted or removed in less than 10 min. Thus, it is possible to adjust the sampling procedure, namely, the mass flux into the ionization chamber of the HRR-TOF-MS, to the experimental situation imposed by species-specific ionization cross sections and vapor pressures. The whole sampling section was optimized with respect to a minimal distance between the nozzle tip inside the shock tube and the ion source inside the TOF-MS. The design of the apparatus is presented and the influence of the skimmer on the measured spectra is demonstrated by comparing data from both operation modes for conditions typical for chemical kinetics experiments. The well-studied thermal decomposition of acetylene has been used as a test system to validate the new setup against kinetics mechanisms reported in literature.

  16. Welding of glasses in optical and partial-optical contact via focal position adjustment of femtosecond-laser pulses at moderately high repetition rate

    Science.gov (United States)

    Tan, Hua; Duan, Ji'an

    2017-07-01

    We used 1030-nm femtosecond-laser pulses focused above/at/below the interface of two fused-silica glass substrates in optical and partial-optical contact to successfully weld them at a moderately high repetition rate of 600 kHz. Variation in the laser focal position for these two gap-distance regimes (optical and partial-optical contact) yields different bonding strengths (BSs) and machining mechanisms. The maximum bonding strength (58.2 MPa) can be achieved for a gap distance ≤λ /4 for optical-contact welding when laser focused below the interface, and the corresponding height of the welding seam was 23 μm. In addition, our results demonstrated that the "filamentation welding technique" is critical to the femtosecond-laser direct welding of glasses. Furthermore, line welding is significantly easier to realize when the femtosecond laser focuses at the interface in partial-optical-contact welding applications due to the combined effects of filamentation welding and ablation.

  17. High-power repetitively pulsed CO{sub 2} laser with mechanical Q-switching and its application to studies in aerodynamic installations

    Energy Technology Data Exchange (ETDEWEB)

    Malov, Aleksei N; Orishich, Anatolii M; Shulyat' ev, Viktor B [S.A. Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch, Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2011-11-30

    A new method for organising the repetitively pulsed regime of CO{sub 2} laser oscillation at the expense of a self-filtering resonator and two concave cylindrical mirrors with equal curvature in the intracavity modulator is considered. The studies of the energy and temporal characteristics of the laser radiation show that the constructed laser has high efficiency close to that of a cw laser. The mean and pulse power of 4.5 and 200 kW, respectively, are obtained. For a wide range of gas-dynamic characteristics the possibility of the optical breakdown in the supersonic wide-aperture air flow is demonstrated. The coefficient of absorption of laser radiation in optical breakdown plasma in a supersonic air flow is investigated and its value amounting to 60% is obtained. For the first time it is found that the threshold density of air, corresponding to the efficiency jump, is equal to 1.8 - 2 kg m{sup -3} and independent of the Mach number M = 1.7 - 3.7. (lasers)

  18. Shock-tube study of the decomposition of tetramethylsilane using gas chromatography and high-repetition-rate time-of-flight mass spectrometry.

    Science.gov (United States)

    Sela, P; Peukert, S; Herzler, J; Fikri, M; Schulz, C

    2018-01-05

    The decomposition of tetramethylsilane was studied in shock-tube experiments in a temperature range of 1270-1580 K and pressures ranging from 1.5 to 2.3 bar behind reflected shock waves combining gas chromatography/mass spectrometry (GC/MS) and high-repetition-rate time-of-flight mass spectrometry (HRR-TOF-MS). The main observed products were methane (CH4), ethylene (C2H4), ethane (C2H6), and acetylene (C2H2). In addition, the formation of a solid deposit was observed, which was identified to consist of silicon- and carbon-containing nanoparticles. A kinetics sub-mechanism with 13 silicon species and 20 silicon-containing reactions was developed. It was combined with the USC_MechII mechanism for hydrocarbons, which was able to simulate the experimental observations. The main decomposition channel of TMS is the Si-C bond scission forming methyl (CH3) and trimethylsilyl radicals (Si(CH3)3). The rate constant for TMS decomposition is represented by the Arrhenius expression ktotal[TMS → products] = 5.9 × 1012 exp(-267 kJ mol-1/RT) s-1.

  19. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental and comp......In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental...... with known priming sites....

  20. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA

    Directory of Open Access Journals (Sweden)

    McDonald John F

    2008-05-01

    Full Text Available Abstract Background The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs. It is becoming increasingly apparent that many of these repetitive DNA sequence elements encode gene regulatory functions. This fact has important evolutionary implications, since repetitive DNA is the most dynamic part of the genome. We set out to assess the evolutionary rate and pattern of experimentally characterized human transcription factor binding sites (TFBS that are derived from repetitive versus non-repetitive DNA to test whether repeat-derived TFBS are in fact rapidly evolving. We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA. Results We found numerous experimentally characterized TFBS in the human genome, 7–10% of all mapped sites, which are derived from repetitive DNA sequences including simple sequence repeats (SSRs and TEs. TE-derived TFBS sequences are far less conserved between species than TFBS derived from SSRs and non-repetitive DNA. Despite their rapid evolution, several lines of evidence indicate that TE-derived TFBS are functionally constrained. First of all, ancient TE families, such as MIR and L2, are enriched for TFBS relative to younger families like Alu and L1. Secondly, functionally important positions in TE-derived TFBS, specifically those residues thought to physically interact with their cognate protein binding factors (TF, are more evolutionarily conserved than adjacent TFBS positions. Finally, TE-derived TFBS show position-specific patterns of sequence variation that are highly distinct from random patterns and similar to the variation seen for non-repeat derived sequences of the same TFBS. Conclusion The abundance of experimentally characterized human TFBS that are derived from repetitive DNA speaks to the substantial regulatory effects that this class of

  1. Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence.

    Science.gov (United States)

    Nejad, Maryam Imani; Shi, Ruicheng; Zhang, Xinyue; Gu, Li-Qun; Gates, Kent S

    2017-07-18

    Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Highly conserved D-loop-like nuclear mitochondrial sequences ...

    Indian Academy of Sciences (India)

    -1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses ...

  3. Putting Physics First: Three Case Studies of High School Science Department and Course Sequence Reorganization

    Science.gov (United States)

    Larkin, Douglas B.

    2016-01-01

    This article examines the process of shifting to a "Physics First" sequence in science course offerings in three school districts in the United States. This curricular sequence reverses the more common U.S. high school sequence of biology/chemistry/physics, and has gained substantial support in the physics education community over the…

  4. Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing.

    Science.gov (United States)

    Shafer, Aaron B A; Northrup, Joseph M; Wikelski, Martin; Wittemyer, George; Wolf, Jochen B W

    2016-01-01

    Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.

  5. An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition.

    Directory of Open Access Journals (Sweden)

    Jason D Wittenbach

    2015-10-01

    Full Text Available Consecutive repetition of actions is common in behavioral sequences. Although integration of sensory feedback with internal motor programs is important for sequence generation, if and how feedback contributes to repetitive actions is poorly understood. Here we study how auditory feedback contributes to generating repetitive syllable sequences in songbirds. We propose that auditory signals provide positive feedback to ongoing motor commands, but this influence decays as feedback weakens from response adaptation during syllable repetitions. Computational models show that this mechanism explains repeat distributions observed in Bengalese finch song. We experimentally confirmed two predictions of this mechanism in Bengalese finches: removal of auditory feedback by deafening reduces syllable repetitions; and neural responses to auditory playback of repeated syllable sequences gradually adapt in sensory-motor nucleus HVC. Together, our results implicate a positive auditory-feedback loop with adaptation in generating repetitive vocalizations, and suggest sensory adaptation is important for feedback control of motor sequences.

  6. Construction and analysis of high-density linkage map using high-throughput sequencing data.

    Directory of Open Access Journals (Sweden)

    Dongyuan Liu

    Full Text Available Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS, which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/.

  7. Spaced planar laminations formed by repetitive basal erosion and resurgence to high-sedimentation-rate regime: new insight from a bedform-like structures and laterally continuous exposures

    Science.gov (United States)

    Ishihara, Yoshiro; Yuri, Onishi; Tsuda, Keisuke; Yokokawa, Miwa

    2017-04-01

    Spaced planar laminations (SPL), or so-called traction carpet deposits, are frequently observed in deposits of sediment gravity flows. Several sedimentation models for a succession of inversely graded units have been suggested from field observations and flume experiments. The formation of the inversely graded unit could be summarized as follows: (1) abrupt sedimentation on freezing of an inversely graded layer, or (2) interruptions in flow causing a freezing of an inversely graded layer at the most basal part of flow. In either case, traction carpets as a bed load overlying the erosive boundary at the base of flow are required. Although some descriptions have reported SPLs forming antidune bedform-like structures and the association of SPLs with structureless massive deposits have not been clearly explained. In this study, we suggest a novel model of SPL formation by repetition of basal erosion and resurgence to high-sedimentation rates, based on detail examinations of SPLs both showing bedform-like structures and lateral extents of hundreds of meters. SPLs were investigated in the Mio-Pliocene Kiyosumi Formation in central Japan and the Miocene Aoshima Formation in southwest Japan. In a turbidite in the Kiyosumi Formation, SPLs show three mound-like structures, suggesting antidune bedforms with wavelengths of about 6 to 7 m. On the upcurrent flanks, SPLs show lenticular cross laminations or pinching out of units; those units do not show clear inverse grading. Rip-up mud clasts and relatively high-angle imbrications are also observed. On the other hand, SPLs on the downcurrent flanks show relatively clear inverse grading and transition downcurrent into a massive structureless bed. In the Aoshima Formation, SPLs with ca. 1 cm unit thickness continue approximately 50 m along a palaeocurrent direction without changes in thickness. These SPLs gradually transition upward into a massive structureless unit. From the observations described above, in addition to

  8. Sequencing of 50 human exomes reveals adaptation to high altitude

    DEFF Research Database (Denmark)

    Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

    2010-01-01

    represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency......Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus...

  9. Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia

    OpenAIRE

    Iqbal, Zafar; Rydning, Siri L.; Wedding, Iselin M.; Koht, Jeanette; Pihlstr?m, Lasse; Rengmark, Aina H.; Henriksen, Sandra P.; Tallaksen, Chantal M. E.; Toft, Mathias

    2017-01-01

    Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed. Here, we have assessed molecular diagnosis by gene panel sequencing in 105 early and late-onset hereditary ataxia and spastic paraplegia probands, in whom extensive previous investigations had failed to identify the genetic cause of disease. Pathogenic and likely-pathogenic variants were identified in 20 probands (19%)...

  10. Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia.

    Science.gov (United States)

    Iqbal, Zafar; Rydning, Siri L; Wedding, Iselin M; Koht, Jeanette; Pihlstrøm, Lasse; Rengmark, Aina H; Henriksen, Sandra P; Tallaksen, Chantal M E; Toft, Mathias

    2017-01-01

    Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed. Here, we have assessed molecular diagnosis by gene panel sequencing in 105 early and late-onset hereditary ataxia and spastic paraplegia probands, in whom extensive previous investigations had failed to identify the genetic cause of disease. Pathogenic and likely-pathogenic variants were identified in 20 probands (19%) and variants of uncertain significance in ten probands (10%). Together these accounted for 30 probands (29%) and involved 18 different genes. Among several interesting findings, dominantly inherited KIF1A variants, p.(Val8Met) and p.(Ile27Thr) segregated in two independent families, both presenting with a pure spastic paraplegia phenotype. Two homozygous missense variants, p.(Gly4230Ser) and p.(Leu4221Val) were found in SACS in one consanguineous family, presenting with spastic ataxia and isolated cerebellar atrophy. The average disease duration in probands with pathogenic and likely-pathogenic variants was 31 years, ranging from 4 to 51 years. In conclusion, this study confirmed and expanded the clinical phenotypes associated with known disease genes. The results demonstrate that gene panel sequencing and similar sequencing approaches can serve as efficient diagnostic tools for different heterogeneous disorders. Early use of such strategies may help to reduce both costs and time of the diagnostic process.

  11. Preparation of highly multiplexed small RNA sequencing libraries.

    Science.gov (United States)

    Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

    2017-08-01

    MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

  12. A two-site pilot randomized 3 day trial of high dose left prefrontal repetitive transcranial magnetic stimulation (rTMS) for suicidal inpatients.

    Science.gov (United States)

    George, Mark S; Raman, Rema; Benedek, David M; Pelic, Christopher G; Grammer, Geoffrey G; Stokes, Karen T; Schmidt, Matthew; Spiegel, Chad; Dealmeida, Nancy; Beaver, Kathryn L; Borckardt, Jeffrey J; Sun, Xiaoying; Jain, Sonia; Stein, Murray B

    2014-01-01

    Suicide attempts and completed suicides are common, yet there are no proven acute medication or device treatments for treating a suicidal crisis. Repeated daily left prefrontal repetitive transcranial magnetic stimulation (rTMS) for 4-6 weeks is a new FDA-approved treatment for acute depression. Some open-label rTMS studies have found rapid reductions in suicidality. This study tests whether a high dose of rTMS to suicidal inpatients is feasible and safe, and also whether this higher dosing might rapidly improve suicidal thinking. This prospective, 2-site, randomized, active sham-controlled (1:1 randomization) design incorporated 9 sessions of rTMS over 3 days as adjunctive to usual inpatient suicidality treatment. The setting was two inpatient military hospital wards (one VA, the other DOD). Research staff screened approximately 377 inpatients, yielding 41 adults admitted for suicidal crisis. Because of the funding source, all patients also had either post-traumatic stress disorder, mild traumatic brain injury, or both. Repetitive TMS (rTMS) was delivered to the left prefrontal cortex with a figure-eight solid core coil at 120% motor threshold, 10 Hertz (Hz), 5 second (s) train duration, 10 s intertrain interval for 30 minutes (6000 pulses) 3 times daily for 3 days (total 9 sessions; 54,000 stimuli). Sham rTMS used a similar coil that contained a metal insert blocking the magnetic field and utilized electrodes on the scalp, which delivered a matched somatosensory sensation. Primary outcomes were the daily change in severity of suicidal thinking as measured by the Beck Scale of Suicidal Ideation (SSI) administered at baseline and then daily, as well as subjective visual analog scale measures before and after each TMS session. Mixed model repeated measures (MMRM) analysis was performed on modified intent to treat (mITT) and completer populations. This intense schedule of rTMS with suicidal inpatients was feasible and safe. Minimal side effects occurred, none

  13. Sequence of the Sugar Pine Megagenome

    Science.gov (United States)

    Kristian A. Stevens; Jill L. Wegrzyn; Aleksey Zimin; Daniela Puiu; Marc Crepeau; Charis Cardeno; Robin Paul; Daniel Gonzalez-Ibeas; Maxim Koriabine; Ann E. Holtz-Morris; Pedro J. Martínez-García; Uzay U. Sezen; Guillaume Marçais; Kathie Jermstad; Patrick E. McGuire; Carol A. Loopstra; John M. Davis; Andrew Eckert; Pieter de Jong; James A. Yorke; Steven L. Salzberg; David B. Neale; Charles H. Langley

    2016-01-01

    Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group...

  14. Whole Genome Sequencing of Enterovirus species C Isolates by High-throughput Sequencing: Development of Generic Primers

    Directory of Open Access Journals (Sweden)

    Maël Bessaud

    2016-08-01

    Full Text Available Enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Enterovirus species C (EV-C consists of more than 20 types, among which the 3 serotypes of polioviruses, the etiological agents of poliomyelitis, are included. Biodiversity and evolution of EV-C genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating EV-C strains require the sequencing of different genomic regions.A simple method was developed to sequence quickly the entire genome of EV-C isolates. Four overlapping fragments were produced separately by RT-PCR performed with generic primers. The four amplicons were then pooled and purified prior to be sequenced by high-throughput technique.The method was assessed on a panel of EV-Cs belonging to a wide-range of types. It can be used to determine full-length genome sequences through de novo assembly of thousands of reads. It was also able to discriminate reads from closely related viruses in mixtures.By decreasing the workload compared to classical Sanger-based techniques, this method will serve as a precious tool for sequencing large panels of EV-Cs isolated in cell cultures during environmental surveillance or from patients, including vaccine-derived polioviruses.

  15. Compact high-repetition-rate terahertz source based on difference frequency generation from an efficient 2-μm dual-wavelength KTP OPO

    Science.gov (United States)

    Mei, Jialin; Zhong, Kai; Wang, Maorong; Liu, Pengxiang; Xu, Degang; Wang, Yuye; Shi, Wei; Yao, Jianquan; Norwood, Robert A.; Peyghambarian, Nasser

    2016-11-01

    A compact optical terahertz (THz) source was demonstrated based on an efficient high-repetition-rate doubly resonant optical parametric oscillator (OPO) around 2 μm with two type-II phase-matched KTP crystals in the walk-off compensated configuration. The KTP OPO was intracavity pumped by an acousto-optical (AO) Q-switched Nd:YVO4 laser and emitted two tunable wavelengths near degeneracy. The tuning range extended continuously from 2.068 μm to 2.191 μm with a maximum output power of 3.29 W at 24 kHz, corresponding to an optical-optical conversion efficiency (from 808 nm to 2 μm) of 20.69%. The stable pulsed dual-wavelength operation provided an ideal pump source for generating terahertz wave of micro-watt level by the difference frequency generation (DFG) method. A 7.84-mm-long periodically inverted quasi-phase-matched (QPM) GaAs crystal with 6 periods was used to generate a terahertz wave, the maximum voltage of 180 mV at 1.244 THz was acquired by a 4.2-K Si bolometer, corresponding to average output power of 0.6 μW and DFG conversion efficiency of 4.32×10-7. The acceptance bandwidth was found to be larger than 0.35 THz (FWHM). As to the 15-mm-long GaSe crystal used in the type-II collinear DFG, a tunable THz source ranging from 0.503 THz to 3.63 THz with the maximum output voltage of 268 mV at 1.65 THz had been achieved, and the corresponding average output power and DFG conversion efficiency were 0.9 μW and 5.86×10-7 respectively. This provides a potential practical palm-top tunable THz sources for portable applications.

  16. Manufacturing of High-Strength and High-Ductility Pearlitic Steel Wires Using Noncircular Drawing Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Baek, Hyun Moo; Joo, Ho Seon; Im, Yong-Taek [KAIST, Daejeon (Korea, Republic of); Hwang, Sun Kwang [KITECH, Cheonan (Korea, Republic of); Son, Il-Heon; Bae, Chul Min [POSCO, Pohang (Korea, Republic of)

    2014-07-15

    In this study, a noncircular drawing (NCD) sequence for manufacturing high-strength and high-ductility pearlitic steel wires was investigated. Multipass NCD was conducted up to the 12th pass at room temperature with two processing routes (defined as the NCDA and NCDB), and compared with the wire drawing (WD). During the torsion test, delamination fracture in the drawn wire was observed in the 10th pass of the WD whereas it was not observed until the 12th pass of the NCDB. From X-ray diffraction, the circular texture component that increases the likelihood of delamination fracture of the drawn wire was rarely observed in the NCDB. Thus, the improved ability of the multipass NCDB to manufacture high-strength pearlitic steel wires with high torsional ductility compared to the WD (by reducing the likelihood of delamination fracture) was demonstrated.

  17. Nonword repetition in adults who stutter: The effects of stimuli stress and auditory-orthographic cues.

    Directory of Open Access Journals (Sweden)

    Geoffrey A Coalson

    Full Text Available Adults who stutter (AWS are less accurate in their immediate repetition of novel phonological sequences compared to adults who do not stutter (AWNS. The present study examined whether manipulation of the following two aspects of traditional nonword repetition tasks unmask distinct weaknesses in phonological working memory in AWS: (1 presentation of stimuli with less-frequent stress patterns, and (2 removal of auditory-orthographic cues immediately prior to response.Fifty-two participants (26 AWS, 26 AWNS produced 12 bisyllabic nonwords in the presence of corresponding auditory-orthographic cues (i.e., immediate repetition task, and the absence of auditory-orthographic cues (i.e., short-term recall task. Half of each cohort (13 AWS, 13 AWNS were exposed to the stimuli with high-frequency trochaic stress, and half (13 AWS, 13 AWNS were exposed to identical stimuli with lower-frequency iambic stress.No differences in immediate repetition accuracy for trochaic or iambic nonwords were observed for either group. However, AWS were less accurate when recalling iambic nonwords than trochaic nonwords in the absence of auditory-orthographic cues.Manipulation of two factors which may minimize phonological demand during standard nonword repetition tasks increased the number of errors in AWS compared to AWNS. These findings suggest greater vulnerability in phonological working memory in AWS, even when producing nonwords as short as two syllables.

  18. Highly-efficient 1-GHz-repetition-frequency femtosecond Yb3+:KY(WO42 laser for super-continuum generation

    Directory of Open Access Journals (Sweden)

    Leburn C.G.

    2013-03-01

    Full Text Available We present a 1.024-GHz-repetition-rate femtosecond Yb3+:KY(WO42 laser with 61% optical-to-optical efficiency and 69% slope efficiency, generating a supercontinuum of bandwidth 400 nm in silica photonic-crystal fibre. RIN measurements of the laser yielded values <0.1%.

  19. Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

    Directory of Open Access Journals (Sweden)

    Matthew W. Blair

    2011-11-01

    Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

  20. Deep Mutational Scanning: Library Construction, Functional Selection, and High-Throughput Sequencing.

    Science.gov (United States)

    Starita, Lea M; Fields, Stanley

    2015-08-03

    Deep mutational scanning is a highly parallel method that uses high-throughput sequencing to track changes in >10(5) protein variants before and after selection to measure the effects of mutations on protein function. Here we outline the stages of a deep mutational scanning experiment, focusing on the construction of libraries of protein sequence variants and the preparation of Illumina sequencing libraries. © 2015 Cold Spring Harbor Laboratory Press.

  1. High-throughput sequencing of black pepper root transcriptome

    Directory of Open Access Journals (Sweden)

    Gordo Sheila MC

    2012-09-01

    Full Text Available Abstract Background Black pepper (Piper nigrum L. is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

  2. High-throughput sequencing of black pepper root transcriptome.

    Science.gov (United States)

    Gordo, Sheila M C; Pinheiro, Daniel G; Moreira, Edith C O; Rodrigues, Simone M; Poltronieri, Marli C; de Lemos, Oriel F; da Silva, Israel Tojal; Ramos, Rommel T J; Silva, Artur; Schneider, Horacio; Silva, Wilson A; Sampaio, Iracilda; Darnet, Sylvain

    2012-09-17

    Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

  3. High-throughput sequencing of black pepper root transcriptome

    Science.gov (United States)

    2012-01-01

    Background Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms. PMID:22984782

  4. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

    Science.gov (United States)

    Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

    2017-05-15

    B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

  5. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  6. High-power, narrow-band, high-repetition-rate, 5.9 eV coherent light source using passive optical cavity for laser-based angle-resolved photoelectron spectroscopy.

    Science.gov (United States)

    Omachi, J; Yoshioka, K; Kuwata-Gonokami, M

    2012-10-08

    We demonstrate a scheme for efficient generation of a 5.9 eV coherent light source with an average power of 23 mW, 0.34 meV linewidth, and 73 MHz repetition rate from a Ti: sapphire picosecond mode-locked laser with an output power of 1 W. Second-harmonic light is generated in a passive optical cavity by a BiB(3)O(6) crystal with a conversion efficiency as high as 67%. By focusing the second-harmonic light transmitted from the cavity into a β-BaB(2)O(4) crystal, we obtain fourth-harmonic light at 5.9 eV. This light source offers stable operation for at least a week. We discuss the suitability of the laser light source for high-resolution angle-resolved photoelectron spectroscopy by comparing it with other sources (synchrotron radiation facilities and gas discharge lamp).

  7. The Microsoft Biology Foundation Applications for High-Throughput Sequencing

    Science.gov (United States)

    Mercer, S.

    2010-01-01

    w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

  8. [Derealization and repetition].

    Science.gov (United States)

    Dahmer, H

    1990-02-01

    The psycho-technique of "derealization" helped the majority of the German population that had been loyal to the Hitler regime to escape from their historical responsibility in 1945. The derealization of an historical era of collective history and of the corresponding phases of their individual histories saved these people the work of self transformation and opened the way to an unwitting repetition. In the unending debates around Nazi war criminal and their accomplices, the paramount issue is to refuse the "normality" of this derealization.

  9. INTERACTION OF LASER RADIATION WITH MATTER. LASER PLASMA: Calculation of mass transfer in the remote cutting of metals by radiation of a high-power repetitively pulsed CO2 laser

    Science.gov (United States)

    Gladush, G. G.; Rodionov, N. B.

    2002-01-01

    The mechanism of remote cutting of steel plates by radiation of a high-power repetitively pulsed CO2 laser is theoretically studied. The models of melt removal by the gravity force and the recoil pressure of material vapour are proposed and the sufficient conditions for the initiation of cutting are determined. A numerical model of a thermally thin plate was employed to describe the cutting for large focal spots.

  10. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

    National Research Council Canada - National Science Library

    Yang, Lin; Yang, Hui-lin; Tu, Zong-cai; Wang, Xiao-lan

    2016-01-01

    .... A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla...

  11. Coexistence of noise-like pulse and high repetition rate harmonic mode-locking in a dual-wavelength mode-locked Tm-doped fiber laser.

    Science.gov (United States)

    Wang, Yazhou; Li, Jianfeng; Zhang, Entao; Mo, Kundong; Wang, Yanyan; Liu, Fei; Zhou, Xiaojun; Liu, Yong

    2017-07-24

    Coexistence of harmonic mode-locking (HML) and noise-like pulse (NLP) were experimentally observed in a dual-wavelength mode-locked Tm-doped fiber laser for the first time. The coexistence patterns were self-started and maintained within a wide pump range by appropriately setting the intra-cavity polarization state. The HML was obtained at 1955.3 nm with a varied repetition rate range from 324 MHz to 1.138 GHz which benefits from the dispersion compensation, while the NLP observing at 1983.2 nm can operate at either fundamental repetition rate of 4.765 MHz or second harmonic state. Experimental investigations show that the coexistence patterns are caused by the wavelength-dependent phase delay of the mode-locked fiber cavity. Moreover, dual-wavelength NLP was also observed for the first time at 2 μm spectral region by changing the intra-cavity polarization state.

  12. Recent progress using high-throughput sequencing technologies in plant molecular breeding.

    Science.gov (United States)

    Gao, Qiang; Yue, Guidong; Li, Wenqi; Wang, Junyi; Xu, Jiaohui; Yin, Ye

    2012-04-01

    High-throughput sequencing is a revolutionary technological innovation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi-faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies. © 2012 Institute of Botany, Chinese Academy of Sciences.

  13. Left and right High Frequency repetitive Transcranial Magnetic Stimulation of the dorsolateral prefrontal cortex does not affect mood in female volunteers.

    Science.gov (United States)

    Baeken, C; Leyman, L; De Raedt, R; Vanderhasselt, M A; D'haenen, H

    2008-03-01

    High Frequency repetitive Transcranial Magnetic Stimulation (HF-rTMS) has yielded divergent results concerning its effect on mood in normal volunteers. In a former study, we were unable to demonstrate negative mood effects after one session of HF-rTMS on the left dorsolateral prefrontal cortex (DLPFC) in a large group of healthy female volunteers: researchers had focused mainly on negative mood changes, overlooking a possible positive mood induction, while no studies had yet examined mood effects of HF-rTMS delivered on the right prefrontal cortex. In this study, we have tried to replicate our previous HF-rTMS findings on the left DLPFC in a new (large) group of healthy female subjects, and we focused especially on positive mood changes. We also extended our former research by stimulating the right DLPFC in a different but comparable (large) group of healthy female volunteers with the same HF-rTMS parameters. In this sham-controlled, single blind, crossover HF-rTMS study, stimulus parameters were an exact copy of our previous healthy volunteer study. To exclude individual anatomical differences, the left and right DLPFC were targeted under magnetic resonance (MRI) guidance. To examine subjective mood changes we used Visual Analogue Scales (VAS), the Profile of Mood States (POMS), and the Positive Affect and Negative Affect Schedule (PANAS), the latter to assure assessment of positive emotions. To detect any delayed mood changes, assessments were also re-administered 30min post-HF-rTMS. We were unable to demonstrate immediate or delayed mood changes after one single active HF-rTMS session on the left or right DLPFC. Although we took into account several methodological problems which might have confounded previous rTMS mood induction studies, the hypothesis that one single session of HF-rTMS on the left or on the right DLPFC can influence mood in healthy female volunteers was not supported. One HF-rTMS session has no effect on subjective mood in healthy female

  14. Sources of PCR-induced distortions in high-throughput sequencing data sets

    Science.gov (United States)

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

    PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

  15. Tracking of intercalary DNA sequences integrated into tandem repeat arrays in rye Secale vavilovii

    Directory of Open Access Journals (Sweden)

    Magdalena Achrem

    2017-06-01

    Full Text Available The structure of repetitive sequences of the JNK block present in the pericentromeric region of the 2RL chromosome was studied in Secale vavilovii. Amplification of sequences present between the JNK sequences led to the identification of seven abnormal DNA fragments. Two of these fragments showed high similarity to the glutamate 5-kinase gene and putative alcohol dehydrogenase gene of trypanosomatid from the genus Leishmania, whose presence can be explained by horizontal gene transfer (HGT. Other fragments were similar to mitochondrial gene for ribosomal protein S4 in plants and to the glycoprotein (G gene of the IHNV virus. Presumably, they are pseudogenes inserted into the JNK heterochromatin region. Within this region, also fragments similar to the rye repetitive sequence and chromosome 3B in wheat were found. There is no known mechanism that would explain how foreign sequences were inserted into the block region of tandem repetitive sequences of the JNK family.

  16. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

    Directory of Open Access Journals (Sweden)

    Banfield Jillian F

    2010-03-01

    Full Text Available Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

  17. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  18. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome

    Science.gov (United States)

    Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC)...

  19. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

    Science.gov (United States)

    Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

    2014-08-08

    Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

  20. Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

    DEFF Research Database (Denmark)

    Vinner, Lasse; Mourier, Tobias; Friis-Nielsen, Jens

    2015-01-01

    small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low...... biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material....

  1. Multiple Teaching Approaches, Teaching Sequence and Concept Retention in High School Physics Education

    Science.gov (United States)

    Fogarty, Ian; Geelan, David

    2013-01-01

    Students in 4 Canadian high school physics classes completed instructional sequences in two key physics topics related to motion--Straight Line Motion and Newton's First Law. Different sequences of laboratory investigation, teacher explanation (lecture) and the use of computer-based scientific visualizations (animations and simulations) were…

  2. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

    Science.gov (United States)

    Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is...

  3. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  4. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

    Science.gov (United States)

    Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

    2017-11-13

    A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

  5. High-Throughput Two-Dimensional Infrared (2D IR) Spectroscopy Achieved by Interfacing Microfluidic Technology with a High Repetition Rate 2D IR Spectrometer.

    Science.gov (United States)

    Tracy, Kathryn M; Barich, Michael V; Carver, Christina L; Luther, Bradley M; Krummel, Amber T

    2016-12-01

    The precision control of microfluidic technology was successfully interfaced with a 100 kHz two-dimensional infrared (2D IR) spectrometer to observe the sensitivity of the anion cyanate (OCN-) to the surrounding solvent environment in a high-throughput manner. Producing high-throughput 2D IR spectroscopy measurements allows us to observe the vibrational response of cyanate in mixed solvent environments. Changes in solvation environment around the cyanate ion yield frequency shifts from 2150 to 2165 cm-1 when moving from a pure dimethylformamide solvent environment to a pure methanol environment. 2D IR spectra were captured laterally across microfluidic devices tailored to produce a tunable gradient to observe the OCN- vibrational response to mixed solvent environments. These experiments reveal that there is no preferential solvation of cyanate in this system; instead, a more complex local solvent environment is observed.

  6. Repetitive elements may comprise over two-thirds of the human genome.

    Directory of Open Access Journals (Sweden)

    A P Jason de Koning

    2011-12-01

    Full Text Available Transposable elements (TEs are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds". We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM, to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp. Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.

  7. The Treatment Effect of Grade Repetitions

    Science.gov (United States)

    Mahjoub, Mohamed-Badrane

    2017-01-01

    This paper estimates the treatment effect of grade repetitions in French junior high schools, using a value-added test score as outcome and quarter of birth as instrument. With linear two-stage least squares, local average treatment effect is estimated at around 1.6 times the standard deviation of the achievement gain. With non-linear…

  8. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe

    2005-01-01

    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  9. 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

  10. Effects of loading sequence for notched specimens under high-low two-step fatigue loading

    Science.gov (United States)

    Crews, J. H., Jr.

    1971-01-01

    The effects of loading sequence on crack-initiation period were investigated for notched aluminum-alloy specimens under high-low two-step loading with special emphasis on local cyclic stresses and strains at the notch root. Local stress and strain were determined by a procedure based on an equation proposed by Neuber which relates elastoplastic stress and strain at a notch. Local stress and strain were also measured experimentally to verify the Neuber equation. The effects of initial high load on the crack-initiation periods were demonstrated with notched specimens and were simulated in unnotched specimens fatigue tested with local stress sequences. An analysis of the results indicated that sequence effects were not caused solely by local residual stresses, as is usually assumed; the existence of a damaging effect, resulting from the high local strain cycles, was demonstrated. The sequence effects observed with notched specimens were interpreted as the combined result of residual stresses and high local strain cycles.

  11. The pathophysiology of restricted repetitive behavior.

    Science.gov (United States)

    Lewis, Mark; Kim, Soo-Jeong

    2009-06-01

    Restricted, repetitive behaviors (RRBs) are heterogeneous ranging from stereotypic body movements to rituals to restricted interests. RRBs are most strongly associated with autism but occur in a number of other clinical disorders as well as in typical development. There does not seem to be a category of RRB that is unique or specific to autism and RRB does not seem to be robustly correlated with specific cognitive, sensory or motor abnormalities in autism. Despite its clinical significance, little is known about the pathophysiology of RRB. Both clinical and animal models studies link repetitive behaviors to genetic mutations and a number of specific genetic syndromes have RRBs as part of the clinical phenotype. Genetic risk factors may interact with experiential factors resulting in the extremes in repetitive behavior phenotypic expression that characterize autism. Few studies of individuals with autism have correlated MRI findings and RRBs and no attempt has been made to associate RRB and post-mortem tissue findings. Available clinical and animal models data indicate functional and structural alterations in cortical-basal ganglia circuitry in the expression of RRB, however. Our own studies point to reduced activity of the indirect basal ganglia pathway being associated with high levels of repetitive behavior in an animal model. These findings, if generalizable, suggest specific therapeutic targets. These, and perhaps other, perturbations to cortical basal ganglia circuitry are mediated by specific molecular mechanisms (e.g., altered gene expression) that result in long-term, experience-dependent neuroadaptations that initiate and maintain repetitive behavior. A great deal more research is needed to uncover such mechanisms. Work in areas such as substance abuse, OCD, Tourette syndrome, Parkinson's disease, and dementias promise to provide findings critical for identifying neurobiological mechanisms relevant to RRB in autism. Moreover, basic research in areas such

  12. Highly parallel translation of DNA sequences into small molecules.

    Directory of Open Access Journals (Sweden)

    Rebecca M Weisinger

    Full Text Available A large body of in vitro evolution work establishes the utility of biopolymer libraries comprising 10(10 to 10(15 distinct molecules for the discovery of nanomolar-affinity ligands to proteins. Small-molecule libraries of comparable complexity will likely provide nanomolar-affinity small-molecule ligands. Unlike biopolymers, small molecules can offer the advantages of cell permeability, low immunogenicity, metabolic stability, rapid diffusion and inexpensive mass production. It is thought that such desirable in vivo behavior is correlated with the physical properties of small molecules, specifically a limited number of hydrogen bond donors and acceptors, a defined range of hydrophobicity, and most importantly, molecular weights less than 500 Daltons. Creating a collection of 10(10 to 10(15 small molecules that meet these criteria requires the use of hundreds to thousands of diversity elements per step in a combinatorial synthesis of three to five steps. With this goal in mind, we have reported a set of mesofluidic devices that enable DNA-programmed combinatorial chemistry in a highly parallel 384-well plate format. Here, we demonstrate that these devices can translate DNA genes encoding 384 diversity elements per coding position into corresponding small-molecule gene products. This robust and efficient procedure yields small molecule-DNA conjugates suitable for in vitro evolution experiments.

  13. A Bayesian framework to identify methylcytosines from high-throughput bisulfite sequencing data.

    Directory of Open Access Journals (Sweden)

    Qing Xie

    2014-09-01

    Full Text Available High-throughput bisulfite sequencing technologies have provided a comprehensive and well-fitted way to investigate DNA methylation at single-base resolution. However, there are substantial bioinformatic challenges to distinguish precisely methylcytosines from unconverted cytosines based on bisulfite sequencing data. The challenges arise, at least in part, from cell heterozygosis caused by multicellular sequencing and the still limited number of statistical methods that are available for methylcytosine calling based on bisulfite sequencing data. Here, we present an algorithm, termed Bycom, a new Bayesian model that can perform methylcytosine calling with high accuracy. Bycom considers cell heterozygosis along with sequencing errors and bisulfite conversion efficiency to improve calling accuracy. Bycom performance was compared with the performance of Lister, the method most widely used to identify methylcytosines from bisulfite sequencing data. The results showed that the performance of Bycom was better than that of Lister for data with high methylation levels. Bycom also showed higher sensitivity and specificity for low methylation level samples (<1% than Lister. A validation experiment based on reduced representation bisulfite sequencing data suggested that Bycom had a false positive rate of about 4% while maintaining an accuracy of close to 94%. This study demonstrated that Bycom had a low false calling rate at any methylation level and accurate methylcytosine calling at high methylation levels. Bycom will contribute significantly to studies aimed at recalibrating the methylation level of genomic regions based on the presence of methylcytosines.

  14. A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences.

    Science.gov (United States)

    Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L

    2017-06-19

    An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5'-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5'-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  15. Mixed-frame and stationary-frame repetitive control schemes for compensating typical load and grid harmonics

    DEFF Research Database (Denmark)

    Loh, P.; Tang, Y.; Blaabjerg, Frede

    2011-01-01

    In this study, repetitive current controllers operating in either the mixed or stationary frame are proposed for high-precision reference tracking and disturbance rejection of power converters. Both controllers use a proportional-resonant regulator in the stationary frame for regulating...... the positive- and negative-sequence fundamental currents, which are known to directly influence the flow of active and reactive power in most energy conversion systems. Moreover, for the tracking or compensation of harmonics, the controllers include a repetitive control path in either the synchronous...... or stationary frame, whose inherent feedback and feedforward structure is proven to resemble a bank of resonant filters in either reference frames. Unlike other existing controllers, the proposed repetitive controllers function by introducing multiple resonant peaks at only those harmonic frequencies typically...

  16. A multi-site study using high-resolution HLA genotyping by next generation sequencing.

    Science.gov (United States)

    Holcomb, C L; Höglund, B; Anderson, M W; Blake, L A; Böhme, I; Egholm, M; Ferriola, D; Gabriel, C; Gelber, S E; Goodridge, D; Hawbecker, S; Klein, R; Ladner, M; Lind, C; Monos, D; Pando, M J; Pröll, J; Sayer, D C; Schmitz-Agheguian, G; Simen, B B; Thiele, B; Trachtenberg, E A; Tyan, D B; Wassmuth, R; White, S; Erlich, H A

    2011-03-01

    The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution. © 2011 John Wiley & Sons A/S.

  17. Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads.

    Science.gov (United States)

    Bai, Yu; Ni, Min; Cooper, Blerta; Wei, Yi; Fury, Wen

    2014-05-01

    Accurate HLA typing at amino acid level (four-digit resolution) is critical in hematopoietic and organ transplantations, pathogenesis studies of autoimmune and infectious diseases, as well as the development of immunoncology therapies. With the rapid adoption of genome-wide sequencing in biomedical research, HLA typing based on transcriptome and whole exome/genome sequencing data becomes increasingly attractive due to its high throughput and convenience. However, unlike targeted amplicon sequencing, genome-wide sequencing often employs a reduced read length and coverage that impose great challenges in resolving the highly homologous HLA alleles. Though several algorithms exist and have been applied to four-digit typing, some deliver low to moderate accuracies, some output ambiguous predictions. Moreover, few methods suit diverse read lengths and depths, and both RNA and DNA sequencing inputs. New algorithms are therefore needed to leverage the accuracy and flexibility of HLA typing at high resolution using genome-wide sequencing data. We have developed a new algorithm named PHLAT to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring. Over a comprehensive set of benchmarking data (a total of 768 HLA alleles) from both RNA and DNA sequencing and with a broad range of read lengths and coverage, PHLAT consistently achieves a high accuracy at four-digit (92%-95%) and two-digit resolutions (96%-99%), outcompeting most of the existing methods. It also supports targeted amplicon sequencing data from Illumina Miseq. PHLAT significantly leverages the accuracy and flexibility of high resolution HLA typing based on genome-wide sequencing data. It may benefit both basic and applied research in immunology and related fields as well as numerous clinical applications.

  18. The promise and challenge of high-throughput sequencing of the antibody repertoire

    Science.gov (United States)

    Georgiou, George; Ippolito, Gregory C; Beausang, John; Busse, Christian E; Wardemann, Hedda; Quake, Stephen R

    2014-01-01

    Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories. PMID:24441474

  19. Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Jeffrey R Johansen

    Full Text Available A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%. The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%, and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.

  20. A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Aditi Sengupta

    2016-03-01

    Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

  1. Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing.

    Directory of Open Access Journals (Sweden)

    Sivan Osenberg

    Full Text Available Adenosine to Inosine (A-to-I RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3'UTRs, 5'UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs. We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions.

  2. The repetitive component of the sunflower genome

    Directory of Open Access Journals (Sweden)

    T. Giordani

    2014-08-01

    Full Text Available The sunflower (Helianthus annuus and species belonging to the genus Helianthus are emerging as a model species and genus for a number of studies on genome evolution. In this review, we report on the repetitive component of the H. annuus genome at the biochemical, molecular, cytological, and genomic levels. Recent work on sunflower genome composition is described, with emphasis on different types of repeat sequences, especially LTR-retrotransposons, of which we report on isolation, characterisation, cytological localisation, transcription, dynamics of proliferation, and comparative analyses within the genus Helianthus.

  3. A high repetition rate TEA CO II laser operating at λ=9.3-μm for the rapid and conservative ablation and modification of dental hard tissues

    Science.gov (United States)

    Fan, Kenneth; Fried, Daniel

    2006-02-01

    TEA CO II lasers tuned to the strong mineral absorption of hydroxyapatite near λ=9-μm are ideally suited for the efficient ablation of dental hard tissues if the laser-pulse is stretched to greater than 5-10-μs to avoid plasma shielding phenomena. Such CO II lasers are capable of operating at high repetition rates for the rapid removal of dental hard tissues. An Impact 2500 TEA CO II laser system from GSI Lumonics (Rugby, UK) custom modified by LightMachinery (Ottawa, Canada) with a repetition rate of 0-500 Hz was used for rapid tissue removal. The single pulse ablation rates through enamel were determined for incident fluence ranging from (1-160 J/cm2). Lateral incisions using a computer controlled scanning stage and water spray were produced and the crater morphology and chemical composition were measured using optical microscopy and high-resolution synchrotron radiation infrared spectromicroscopy. The transmission through 2-meter length 300, 500, 750 and 1000-μm silica hollow waveguides was measured and 80% transmission was achieved with 40-mJ per pulse. The λ=9.3-μm laser pulses efficiently removed dental enamel at rates exceeding 15-μm per pulses with minimal heat accumulation. The residual energy remaining in tooth samples was measured to be 30-40% without water cooling, significantly lower than for longer CO II laser pulses. These results suggest that high repetition rate TEA CO II laser systems operating at λ=9.3-μm with pulse durations of 10-20-μs are ideally suited for dental application.

  4. Finding sRNA generative locales from high-throughput sequencing data with NiBLS

    Directory of Open Access Journals (Sweden)

    Moulton Vincent

    2010-02-01

    Full Text Available Abstract Background Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales. Results We describe and implement an algorithm that can determine small RNA generative locales from high-throughput sequencing data. The algorithm creates a network, or graph, of the small RNAs by creating links between them depending on their proximity on the target genome. For each of the sub-networks in the resulting graph the clustering coefficient, a measure of the interconnectedness of the subnetwork, is used to identify the generative locales. We test the algorithm over a wide range of parameters using RFAM sequences as positive controls and demonstrate that the algorithm has good sensitivity and specificity in a range of Arabidopsis and mouse small RNA sequence sets and that the locales it generates are robust to differences in the choice of parameters. Conclusions NiBLS is a fast, reliable and sensitive method for determining small RNA locales in high-throughput sequence data that is generally applicable to all classes of small RNA.

  5. High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus

    2016-01-01

    Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards...... with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates...... automation of DNA sequencing....

  6. 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.

  7. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

    OpenAIRE

    Althammer, Sonja Daniela; González-Vallinas Rostes, Juan, 1983-; Ballaré, Cecilia Julia; Beato, Miguel; Eyras Jiménez, Eduardo

    2011-01-01

    Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein?DNA and protein?RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or b...

  8. Retirement Sequences of Older Americans: Moderately Destandardized and Highly Stratified Across Gender, Class, and Race.

    Science.gov (United States)

    Calvo, Esteban; Madero-Cabib, Ignacio; Staudinger, Ursula M

    2017-06-06

    A destandardization of labor-force patterns revolving around retirement has been observed in recent literature. It is unclear, however, to which degree and of which kind. This study looked at sequences rather than individual statuses or transitions and argued that differentiating older Americans' retirement sequences by type, order, and timing and considering gender, class, and race differences yields a less destandardized picture. Sequence analysis was employed to analyze panel data from the Health and Retirement Study (HRS) for 7,881 individuals observed 6 consecutive times between ages 60-61 and 70-71. As expected, types of retirement sequences were identified that cannot be subsumed under the conventional model of complete retirement from full-time employment around age 65. However, these retirement sequences were not entirely destandardized, as some irreversibility and age-grading persisted. Further, the degree of destandardization varied along gender, class, and race. Unconventional sequences were archetypal for middle-level educated individuals and Blacks. Also, sequences for women and individuals with lower education showed more unemployment and part-time jobs, and less age-grading. A sequence-analytic approach that models group differences uncovers misjudgments about the degree of destandardization of retirement sequences. When a continuous process is represented as individual transitions, the overall pattern of retirement sequences gets lost and appears destandardized. These patterns get further complicated by differences in social structures by gender, class, and race in ways that seem to reproduce advantages that men, more highly educated individuals, and Whites enjoy in numerous areas over the life course.

  9. The application of the high throughput sequencing technology in the transposable elements.

    Science.gov (United States)

    Liu, Zhen; Xu, Jian-hong

    2015-09-01

    High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

  10. Circadian modulation of sequence learning under high and low sleep pressure conditions.

    Science.gov (United States)

    Cajochen, Christian; Knoblauch, Vera; Wirz-Justice, Anna; Kräuchi, Kurt; Graw, Peter; Wallach, Dieter

    2004-05-05

    Humans are able to learn complex sequences even without conscious awareness. We have studied the repercussions of circadian phase and sleep pressure on the ability to learn structured sequences using a serial reaction time task (SRT). Sixteen young healthy volunteers were studied in a 40-h "constant posture protocol" under high sleep pressure (i.e. sleep deprivation) and low sleep pressure conditions (i.e. sleep satiation attained by multiple naps). Here we show that learning of different sequence structures improved after multiple naps, in particular after naps that followed the circadian peak of rapid-eye-movement (REM) sleep. This situation following sleep contrasted with the lack of learning without sleep. We have evidenced that the observed amelioration of learning new sequences came about by memorizing short sub-fragments ("chunks") of the sequence train. However, SRT performance did not deteriorate under high sleep pressure, despite the high level of sleepiness. Our data indicate that sequence learning is modulated by circadian phase, and the neurophysiological medium required for this type of learning is related to sleep. Copyright 2003 Elsevier B.V.

  11. 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.

  12. Strongly structured DNA sequences as targets for genosensing: sensing phase design and coupling to PCR amplification for a highly specific 33-mer gliadin DNA fragment.

    Science.gov (United States)

    Martín-Fernández, Begoña; Miranda-Ordieres, Arturo J; Lobo-Castañón, María Jesús; Frutos-Cabanillas, Gloria; de-los-Santos-Álvarez, Noemí; López-Ruiz, Beatriz

    2014-10-15

    Electrochemical genosensors are becoming cost-effective miniaturizable alternatives to real-time PCR (RT-PCR) methods for the detection of sequence-specific DNA fragments. We report on the rapid detection of PCR amplicons without the need of purification or strand separation. A challenging target sequence for both PCR amplification and electrochemical detection allowed us to address some difficulties associated to hybridization on electrode surfaces. The target was a highly specific oligonucleotide sequence of wheat encoding the most immunogenic peptide of gliadin that triggers the immune response of celiac disease (CD), the 33-mer. With a sandwich assay format and a rational design of the capture and tagged-signaling probes the problems posed by the strong secondary structure of the target and complementary probes were alleviated. Using a binary self-assembled monolayer and enzymatic amplification, a limit of detection of 0.3 nM was obtained. The genosensor did not respond to other gluten-containing cereals such as rye and barley. Coupling to PCR to analyze wheat flour samples required tailoring both the capture and signaling probes. This is the first time that deleterious steric hindrance from long single-stranded regions adjacent to the electrode surface is reported for relatively short amplicons (less than 200 bp). The importance of the location of the recognition site within the DNA sequence is discussed. Since the selected gene fragment contains several repetitions of short sequences, a careful optimization of the PCR conditions had to be performed to circumvent the amplification of non-specific fragments from wheat flour. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Exome sequencing generates high quality data in non-target regions

    Directory of Open Access Journals (Sweden)

    Guo Yan

    2012-05-01

    Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

  14. DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis

    Science.gov (United States)

    Erlich, Yaniv; Chang, Kenneth; Gordon, Assaf; Ronen, Roy; Navon, Oron; Rooks, Michelle; Hannon, Gregory J.

    2009-01-01

    Next-generation sequencers have sufficient power to analyze simultaneously DNAs from many different specimens, a practice known as multiplexing. Such schemes rely on the ability to associate each sequence read with the specimen from which it was derived. The current practice of appending molecular barcodes prior to pooling is practical for parallel analysis of up to many dozen samples. Here, we report a strategy that permits simultaneous analysis of tens of thousands of specimens. Our approach relies on the use of combinatorial pooling strategies in which pools rather than individual specimens are assigned barcodes. Thus, the identity of each specimen is encoded within the pooling pattern rather than by its association with a particular sequence tag. Decoding the pattern allows the sequence of an original specimen to be inferred with high confidence. We verified the ability of our encoding and decoding strategies to accurately report the sequence of individual samples within a large number of mixed specimens in two ways. First, we simulated data both from a clone library and from a human population in which a sequence variant associated with cystic fibrosis was present. Second, we actually pooled, sequenced, and decoded identities within two sets of 40,000 bacterial clones comprising approximately 20,000 different artificial microRNAs targeting Arabidopsis or human genes. We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals. PMID:19447965

  15. Note: An avalanche transistor-based nanosecond pulse generator with 25 MHz repetition rate.

    Science.gov (United States)

    Beev, Nikolai; Keller, Jonas; Mehlstäubler, Tanja E

    2017-12-01

    We have developed an avalanche transistor-based pulse generator for driving the photocathode of an image intensifier, which comprises a mainly capacitive load on the order of 100 pF. The circuit produces flat-top pulses with a rise time of 2 ns, a FWHM of 10 ns, and an amplitude of tens of V at a high repetition rate in the range of tens of MHz. The generator is built of identical avalanche transistor sections connected in parallel and triggered in a sequence, synchronized to a reference rf signal. The described circuit and mode of operation overcome the power dissipation limit of avalanche transistor generators and enable a significant increase of pulse repetition rates. Our approach is naturally suited for synchronized imaging applications at low light levels.

  16. Note: An avalanche transistor-based nanosecond pulse generator with 25 MHz repetition rate

    Science.gov (United States)

    Beev, Nikolai; Keller, Jonas; Mehlstäubler, Tanja E.

    2017-12-01

    We have developed an avalanche transistor-based pulse generator for driving the photocathode of an image intensifier, which comprises a mainly capacitive load on the order of 100 pF. The circuit produces flat-top pulses with a rise time of 2 ns, a FWHM of 10 ns, and an amplitude of tens of V at a high repetition rate in the range of tens of MHz. The generator is built of identical avalanche transistor sections connected in parallel and triggered in a sequence, synchronized to a reference rf signal. The described circuit and mode of operation overcome the power dissipation limit of avalanche transistor generators and enable a significant increase of pulse repetition rates. Our approach is naturally suited for synchronized imaging applications at low light levels.

  17. On the optimal trimming of high-throughput mRNA sequence data

    Directory of Open Access Journals (Sweden)

    Matthew D MacManes

    2014-01-01

    Full Text Available The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score < 2 or < 5, is optimal for most studies across a wide variety of metrics.

  18. New Tools For Understanding Microbial Diversity Using High-throughput Sequence Data

    Science.gov (United States)

    Knight, R.; Hamady, M.; Liu, Z.; Lozupone, C.

    2007-12-01

    High-throughput sequencing techniques such as 454 are straining the limits of tools traditionally used to build trees, choose OTUs, and perform other essential sequencing tasks. We have developed a workflow for phylogenetic analysis of large-scale sequence data sets that combines existing tools, such as the Arb phylogeny package and the NAST multiple sequence alignment tool, with new methods for choosing and clustering OTUs and for performing phylogenetic community analysis with UniFrac. This talk discusses the cyberinfrastructure we are developing to support the human microbiome project, and the application of these workflows to analyze very large data sets that contrast the gut microbiota with a range of physical environments. These tools will ultimately help to define core and peripheral microbiomes in a range of environments, and will allow us to understand the physical and biotic factors that contribute most to differences in microbial diversity.

  19. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.

    Science.gov (United States)

    Dias, Elaine Silva; Hatt, Clémence; Hamon, Serge; Hamon, Perla; Rigoreau, Michel; Crouzillat, Dominique; Carareto, Claudia Marcia Aparecida; de Kochko, Alexandre; Guyot, Romain

    2015-09-01

    Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.

  20. The Role Of Rejuvenation In Shaping The High-Mass End Of The Main Sequence

    Science.gov (United States)

    Mancini, Chiara

    2017-06-01

    We investigate the nature of star forming galaxies with reduced specific SFRs and high stellar masses, those that seemingly cause the so-called bending of the main sequence. The fact that such objects host large bulges recently lead some to suggest that the internal formation of the bulges, via compaction or disk instabilities, was the late event that induced sSFRs of massive galaxies to drop in a slow downfall and thus the main sequence to bend. We have studied in detail a sample of 16 galaxies at 0.5hosted in these systems 'below main sequence' are virtually all maximally old, with ages approaching the age of the Universe at the time of observation, while disks are very young (t50 1-2 Gyr). We conclude that the bending of the main sequence is likely due to rejuvenation, disfavouring mechanisms that postulate the internal formation of bulges at late times.

  1. Kaleidaseq: a Web-based tool to monitor data flow in a high throughput sequencing facility.

    Science.gov (United States)

    Dedhia, N N; McCombie, W R

    1998-03-01

    Tracking data flow in high throughput sequencing is important in maintaining a consistent number of successfully sequenced samples, making decisions on scheduling the flow of sequencing steps, resolving problems at various steps and tracking the status of different projects. This is especially critical when the laboratory is handling a multitude of projects. We have built a Web-based data flow tracking package, called Kaleidaseq, which allows us to monitor the flow and quality of sequencing samples through the steps of preparation of library plates, plaque-picking, preparation of templates, conducting sequencing reactions, loading of samples on gels, base-calling the traces, and calculating the quality of the sequenced samples. Kaleidaseq's suite of displays allows for outstanding monitoring of the production sequencing process. The online display of current information that Kaleidaseq provides on both project status and process queues sorted by project enables accurate real-time assessment of the necessary samples that must be processed to complete the project. This information allows the process manager to allocate future resources optimally and schedule tasks according to scientific priorities. Quality of the sequenced samples can be tracked on a daily basis, which allows the sequencing laboratory to maintain a steady performance level and quickly resolve dips in quality. Kaleidaseq has a simple easy-to-use interface that allows access to all major functions and process queues from one Web page. This software package is modular and designed to allow additional processing steps and new monitoring variables to be added and tracked with ease. Access to the underlying relational database is through the Perl DBI interface, which allows for the use of different relational databases. Kaleidaseq is available for free use by the academic community from http://www.cshl.org/kaleidaseq.

  2. Chromosomal mapping of repetitive DNAs in Triportheus trifurcatus (Characidae, Characiformes: insights into the differentiation of the Z and W chromosomes.

    Directory of Open Access Journals (Sweden)

    Cassia Fernanda Yano

    Full Text Available Repetitive DNA sequences play an important role in the structural and functional organization of chromosomes, especially in sex chromosome differentiation. The genus Triportheus represents an interesting model for such studies because all of its species analyzed so far contain a ZZ/ZW sex chromosome system. A close relationship has been found between the differentiation of the W chromosome and heterochromatinization, with the involvement of different types of repetitive DNA in this process. This study investigated several aspects of this association in the W chromosome of Triportheus trifurcatus (2 n = 52 chromosomes, including the cytogenetic mapping of repetitive DNAs such as telomeric sequences (TTAGGGn, microsatellites and retrotransposons. A remarkable heterochromatic segment on the W chromosome was observed with a preferential accumulation of (CAC10, (CAG10, (CGG10, (GAA10 and (TA15. The retrotransposons Rex1 and Rex3 showed a general distribution pattern in the chromosomes, and Rex6 showed a different distribution on the W chromosome. The telomeric repeat (TTAGGGn was highly evident in both telomeres of all chromosomes without the occurrence of ITS. Thus, the differentiation of the W chromosome of T. trifurcatus is clearly associated with the formation of heterochromatin and different types of repetitive DNA, suggesting that these elements had a prominent role in this evolutionary process.

  3. Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

    Science.gov (United States)

    Dilernia, Dario A.; Chien, Jung-Ting; Monaco, Daniela C.; Brown, Michael P.S.; Ende, Zachary; Deymier, Martin J.; Yue, Ling; Paxinos, Ellen E.; Allen, Susan; Tirado-Ramos, Alfredo; Hunter, Eric

    2015-01-01

    Single Molecule, Real-Time (SMRT®) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution. PMID:26101252

  4. Nonword Repetition in Children and Adults: Effects on Movement Coordination

    Science.gov (United States)

    Sasisekaran, Jayanthi; Smith, Anne; Sadagopan, Neeraja; Weber-Fox, Christine

    2010-01-01

    Hearing and repeating novel phonetic sequences, or novel nonwords, is a task that taps many levels of processing, including auditory decoding, phonological processing, working memory, speech motor planning and execution. Investigations of nonword repetition abilities have been framed within models of psycholinguistic processing, while the motor…

  5. Development of a compact and reliable repetitively pulsed Xe Cl ...

    Indian Academy of Sciences (India)

    ionized XeCl(Xenon Chloride) excimer laser is described. The laser uses discharge pumped C–C charge transfer excitation. A compact gas circulation loop was adopted to achieve high repetition rate operation. The laser generates optical ...

  6. Versatile high-repetition-rate phase-locked chopper system for fast timing experiments in the vacuum ultraviolet and x-ray spectral region.

    Science.gov (United States)

    Plogmaker, Stefan; Linusson, Per; Eland, John H D; Baker, Neville; Johansson, Erik M J; Rensmo, Håkan; Feifel, Raimund; Siegbahn, Hans

    2012-01-01

    A novel light chopper system for fast timing experiments in the vacuum-ultraviolet (VUV) and x-ray spectral region has been developed. It can be phase-locked and synchronized with a synchrotron radiation storage ring, accommodating repetition rates in the range of ~8 to ~120 kHz by choosing different sets of apertures and subharmonics of the ring frequency (MHz range). Also the opening time of the system can be varied from some nanoseconds to several microseconds to meet the needs of a broad range of applications. Adjusting these parameters, the device can be used either for the generation of single light pulses or pulse packages from a microwave driven, continuous He gas discharge lamp or from storage rings which are otherwise often considered as quasi-continuous light sources. This chopper can be utilized for many different kinds of experiments enabling, for example, unambiguous time-of-flight (TOF) multi-electron coincidence studies of atoms and molecules excited by a single light pulse as well as time-resolved visible laser pump x-ray probe electron spectroscopy of condensed matter in the valence and core level region.

  7. Versatile high-repetition-rate phase-locked chopper system for fast timing experiments in the vacuum ultraviolet and x-ray spectral region

    Energy Technology Data Exchange (ETDEWEB)

    Plogmaker, Stefan; Johansson, Erik M. J.; Rensmo, Haakan; Feifel, Raimund; Siegbahn, Hans [Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala (Sweden); Linusson, Per [Department of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm (Sweden); Eland, John H. D. [Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala (Sweden); Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ (United Kingdom); Baker, Neville [Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ (United Kingdom)

    2012-01-15

    A novel light chopper system for fast timing experiments in the vacuum-ultraviolet (VUV) and x-ray spectral region has been developed. It can be phase-locked and synchronized with a synchrotron radiation storage ring, accommodating repetition rates in the range of {approx}8 to {approx}120 kHz by choosing different sets of apertures and subharmonics of the ring frequency (MHz range). Also the opening time of the system can be varied from some nanoseconds to several microseconds to meet the needs of a broad range of applications. Adjusting these parameters, the device can be used either for the generation of single light pulses or pulse packages from a microwave driven, continuous He gas discharge lamp or from storage rings which are otherwise often considered as quasi-continuous light sources. This chopper can be utilized for many different kinds of experiments enabling, for example, unambiguous time-of-flight (TOF) multi-electron coincidence studies of atoms and molecules excited by a single light pulse as well as time-resolved visible laser pump x-ray probe electron spectroscopy of condensed matter in the valence and core level region.

  8. Emotional arousal enhances word repetition priming

    OpenAIRE

    Thomas, Laura A.; LaBar, Kevin S.

    2005-01-01

    Three experiments were conducted to determine if emotional content increases repetition priming magnitude. In the study phase of Experiment 1, participants rated high-arousing negative (taboo) words and neutral words for concreteness. In the test phase, they made lexical decision judgements for the studied words intermixed with novel words (half taboo, half neutral) and pseudowords. In Experiment 2, low-arousing negative (LAN) words were substituted for the taboo words, and in Experiment 3 al...

  9. Communicating the Benefits of a Full Sequence of High School Science Courses

    Science.gov (United States)

    Nicholas, Catherine Marie

    High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit in the STEM degree production rate needed to fill the demand of the current job market and remain competitive as a nation. The purpose of the study was to make a difference in the number of students who have access to information about the benefits of completing a full sequence of science courses. This dissertation study employed qualitative research methodology to gain a broad perspective of staff through a questionnaire and document review and then a deeper understanding through semi-structured interview protocol. The data revealed that a universal sequence of science courses in the high school district did not exist. It also showed that not all students had access to all science courses; students were sorted and tracked according to prerequisites that did not necessarily match the skill set needed for the courses. In addition, the study showed a desire for more support and direction from the district office. It was also apparent that there was a disconnect that existed between who staff members believed should enroll in a full sequence of science courses and who actually enrolled. Finally, communication about science was shown to occur mainly through counseling and peers. A common science sequence, detracking of science courses, increased communication about the postsecondary and academic benefits of a science education, increased district direction and realistic mathematics alignment were all discussed as solutions to the problem.

  10. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Bellgard Matthew

    2010-06-01

    Full Text Available Abstract Background The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing. Results The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing. Conclusion Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database.

  11. A Highly Dense Genetic Map for Ginkgo biloba Constructed Using Sequence-Based Markers

    Directory of Open Access Journals (Sweden)

    Hailin Liu

    2017-06-01

    Full Text Available Ginkgo biloba L. is a well-known living gymnosperm fossil that has medicinal and ornamental value. In this study, a high density genetic map was constructed with megagametophytes of 94 seeds from a single Ginkgo tree by employing the specific-locus amplified fragment (SLAF sequencing technique. The average sequencing depth was 11.20×, which yielded 538,031 high-quality SLAFs. Among these SLAFs, 204,361 were heterozygous in the maternal tree and segregated in the progeny. The established map contained 12,263 SLAFs that were assigned to 12 linkage groups (LGs. The number of LGs on this map equaled the number of chromosomes in Ginkgo. The total map length was 1,671.77 cM, with an average distance of 0.89 cM between adjacent marker bins. Map evaluation based on the haplotype map and the heat map validated the high quality of the established map. Because Ginkgo is an economically and biologically important tree, strenuous efforts have been exerted to sequence its genome. This new map, built using sequence-based markers, will serve in the future as a fundamental platform for anchoring sequence assemblies along Ginkgo chromosomes. This map also provides a desirable platform for various genetic studies of Ginkgo, including gene/quantitative trait locus mapping and marker-aided selection.

  12. Comprehensive molecular diagnosis of Bardet-Biedl syndrome by high-throughput targeted exome sequencing.

    Directory of Open Access Journals (Sweden)

    Dong-Jun Xing

    Full Text Available Bardet-Biedl syndrome (BBS is an autosomal recessive disorder with significant genetic heterogeneity. BBS is linked to mutations in 17 genes, which contain more than 200 coding exons. Currently, BBS is diagnosed by direct DNA sequencing for mutations in these genes, which because of the large genomic screening region is both time-consuming and expensive. In order to develop a practical method for the clinic diagnosis of BBS, we have developed a high-throughput targeted exome sequencing (TES for genetic diagnosis. Five typical BBS patients were recruited and screened for mutations in a total of 144 known genes responsible for inherited retinal diseases, a hallmark symptom of BBS. The genomic DNA of these patients and their families were subjected to high-throughput DNA re-sequencing. Deep bioinformatics analysis was carried out to filter the massive sequencing data, which were further confirmed through co-segregation analysis. TES successfully revealed mutations in BBS genes in each patient and family member. Six pathological mutations, including five novel mutations, were revealed in the genes BBS2, MKKS, ARL6, MKS1. This study represents the first report of targeted exome sequencing in BBS patients and demonstrates that high-throughput TES is an accurate and rapid method for the genetic diagnosis of BBS.

  13. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  14. 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

  15. High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

    Directory of Open Access Journals (Sweden)

    Bus Anja

    2012-06-01

    Full Text Available Abstract Background The complex genome of rapeseed (Brassica napus is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD fragments for polymorphism detection and genotyping. Results More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the Brassica rapa reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the B. rapa chromosomes, which suggests that there might be an equal distribution over the Brassica oleracea chromosomes, too. The representation of Gene Ontology (GO terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category. Conclusions Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as B. napus.

  16. Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).

    Science.gov (United States)

    Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong

    2006-08-01

    Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

  17. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data

    Science.gov (United States)

    Zomer, Aldert; Burghout, Peter; Bootsma, Hester J.; Hermans, Peter W. M.; van Hijum, Sacha A. F. T.

    2012-01-01

    High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality. PMID:22900082

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

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

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

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

    Directory of Open Access Journals (Sweden)

    Zhao Patrick X

    2011-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Christian M. Tobias

    2008-11-01

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

  1. High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

    Science.gov (United States)

    Wang, Wenqin; Messing, Joachim

    2011-01-01

    Background Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. Methods We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs) using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. Conclusions This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power. PMID:21931804

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

    Directory of Open Access Journals (Sweden)

    Wenqin Wang

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

  3. Longitudinal patterns of repetitive behavior in toddlers with autism.

    Science.gov (United States)

    Wolff, Jason J; Botteron, Kelly N; Dager, Stephen R; Elison, Jed T; Estes, Annette M; Gu, Hongbin; Hazlett, Heather C; Pandey, Juhi; Paterson, Sarah J; Schultz, Robert T; Zwaigenbaum, Lonnie; Piven, Joseph

    2014-08-01

    Recent evidence suggests that restricted and repetitive behaviors may differentiate children who develop autism spectrum disorder (ASD) by late infancy. How these core symptoms manifest early in life, particularly among infants at high risk for the disorder, is not well characterized. Prospective, longitudinal parent-report data (Repetitive Behavior Scales-Revised) were collected for 190 high-risk toddlers and 60 low-risk controls from 12 to 24 months of age. Forty-one high-risk children were classified with ASD at age 2. Profiles of repetitive behavior were compared between groups using generalized estimating equations. Longitudinal profiles for children diagnosed with ASD differed significantly from high- and low-risk children without the disorder on all measures of repetitive behavior. High-risk toddlers without ASD were intermediate to low risk and ASD positive counterparts. Toddlers with ASD showed significantly higher rates of repetitive behavior across subtypes at the 12-month time point. Repetitive behaviors were significantly correlated with adaptive behavior and socialization scores among children with ASD at 24 months of age, but were largely unrelated to measures of general cognitive ability. These findings suggest that as early as 12 months of age, a broad range of repetitive behaviors are highly elevated in children who go on to develop ASD. While some degree of repetitive behavior is elemental to typical early development, the extent of these behaviors among children who develop ASD appears highly atypical. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

  4. Semi-automated library preparation for high-throughput DNA sequencing platforms.

    Science.gov (United States)

    Farias-Hesson, Eveline; Erikson, Jonathan; Atkins, Alexander; Shen, Peidong; Davis, Ronald W; Scharfe, Curt; Pourmand, Nader

    2010-01-01

    Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.

  5. A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.

    Science.gov (United States)

    Yus, Eva; Yang, Jae-Seong; Sogues, Adrià; Serrano, Luis

    2017-08-28

    Quantitative analysis of the sequence determinants of transcription and translation regulation is relevant for systems and synthetic biology. To identify these determinants, researchers have developed different methods of screening random libraries using fluorescent reporters or antibiotic resistance genes. Here, we have implemented a generic approach called ELM-seq (expression level monitoring by DNA methylation) that overcomes the technical limitations of such classic reporters. ELM-seq uses DamID (Escherichia coli DNA adenine methylase as a reporter coupled with methylation-sensitive restriction enzyme digestion and high-throughput sequencing) to enable in vivo quantitative analyses of upstream regulatory sequences. Using the genome-reduced bacterium Mycoplasma pneumoniae, we show that ELM-seq has a large dynamic range and causes minimal toxicity. We use ELM-seq to determine key sequences (known and putatively novel) of promoter and untranslated regions that influence transcription and translation efficiency. Applying ELM-seq to other organisms will help us to further understand gene expression and guide synthetic biology.Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5'-UTR regions.

  6. Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation.

    Science.gov (United States)

    Zhang, Hangxiao; Luo, Qibin; Sun, Jing; Liu, Fei; Wu, Gang; Yu, Jun; Wang, Weiwei

    2013-05-01

    Brine shrimps, Artemia (Crustacea, Anostraca), inhabit hypersaline environments and have a broad geographical distribution from sea level to high plateaus. Artemia therefore possess significant genetic diversity, which gives them their outstanding adaptability. To understand this remarkable plasticity, we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia, A. franciscana. We compared the ratio of the rate of nonsynonymous (Ka) and synonymous (Ks) substitutions (Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of A. franciscana with either A. tibetiana or A. urmiana and that atp6 had the highest Ka/Ks ratio between A. tibetiana and A. urmiana. Atp6 may have experienced strong selective pressure for high-altitude adaptation because although A. tibetiana and A. urmiana are closely related they live at different altitudes. We identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial genomes. We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

  7. Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

    Directory of Open Access Journals (Sweden)

    Tu Jing

    2012-01-01

    Full Text Available Abstract Background The multiplexing becomes the major limitation of the next-generation sequencing (NGS in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples. Results Here we introduce pair-barcode sequencing (PBS, an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc., 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid. Conclusions By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.

  8. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data.

    NARCIS (Netherlands)

    Zomer, A.L.; Burghout, P.J.; Bootsma, H.J.; Hermans, P.W.M.; Hijum, S.A.F.T. van

    2012-01-01

    High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon

  9. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

    Science.gov (United States)

    D. Lee Taylor; Michael G. Booth; Jack W. McFarland; Ian C. Herriott; Niall J. Lennon; Chad Nusbaum; Thomas G. Marr

    2008-01-01

    High throughput sequencing methods are widely used in analyses of microbial diversity but are generally applied to small numbers of samples, which precludes charaterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to...

  10. The Importance of Agriculture Science Course Sequencing in High Schools: A View from Collegiate Agriculture Students

    Science.gov (United States)

    Wheelus, Robin P.

    2009-01-01

    The objective of this study was to investigate the importance of Agriculture Science course sequencing in high schools, as a preparatory factor for students enrolled in collegiate agriculture classes. With the variety of courses listed in the Texas Essential Knowledge and Skills (TEKS) for Agriculture Science, it has been possible for counselors,…

  11. Emotional arousal enhances word repetition priming

    Science.gov (United States)

    Thomas, Laura A.; LaBar, Kevin S.

    2012-01-01

    Three experiments were conducted to determine if emotional content increases repetition priming magnitude. In the study phase of Experiment 1, participants rated high-arousing negative (taboo) words and neutral words for concreteness. In the test phase, they made lexical decision judgements for the studied words intermixed with novel words (half taboo, half neutral) and pseudowords. In Experiment 2, low-arousing negative (LAN) words were substituted for the taboo words, and in Experiment 3 all three word types were used. Results showed significant priming in all experiments, as indicated by faster reaction times for studied words than for novel words. A priming × emotion interaction was found in Experiments 1 and 3, with greater priming for taboo relative to neutral words. The LAN words in Experiments 2 and 3 showed no difference in priming magnitude relative to the other word types. These results show selective enhancement of word repetition priming by emotional arousal. PMID:26321783

  12. Emotional arousal enhances word repetition priming.

    Science.gov (United States)

    Thomas, Laura A; LaBar, Kevin S

    Three experiments were conducted to determine if emotional content increases repetition priming magnitude. In the study phase of Experiment 1, participants rated high-arousing negative (taboo) words and neutral words for concreteness. In the test phase, they made lexical decision judgements for the studied words intermixed with novel words (half taboo, half neutral) and pseudowords. In Experiment 2, low-arousing negative (LAN) words were substituted for the taboo words, and in Experiment 3 all three word types were used. Results showed significant priming in all experiments, as indicated by faster reaction times for studied words than for novel words. A priming × emotion interaction was found in Experiments 1 and 3, with greater priming for taboo relative to neutral words. The LAN words in Experiments 2 and 3 showed no difference in priming magnitude relative to the other word types. These results show selective enhancement of word repetition priming by emotional arousal.

  13. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.

    Directory of Open Access Journals (Sweden)

    Riccardo Velasco

    Full Text Available BACKGROUND: Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. PRINCIPAL FINDINGS: We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs. The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before. CONCLUSIONS: Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS, together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps. SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.

  14. A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

    Science.gov (United States)

    Cartwright, Dustin A.; Cestaro, Alessandro; Pruss, Dmitry; Pindo, Massimo; FitzGerald, Lisa M.; Vezzulli, Silvia; Reid, Julia; Malacarne, Giulia; Iliev, Diana; Coppola, Giuseppina; Wardell, Bryan; Micheletti, Diego; Macalma, Teresita; Facci, Marco; Mitchell, Jeff T.; Perazzolli, Michele; Eldredge, Glenn; Gatto, Pamela; Oyzerski, Rozan; Moretto, Marco; Gutin, Natalia; Stefanini, Marco; Chen, Yang; Segala, Cinzia; Davenport, Christine; Demattè, Lorenzo; Mraz, Amy; Battilana, Juri; Stormo, Keith; Costa, Fabrizio; Tao, Quanzhou; Si-Ammour, Azeddine; Harkins, Tim; Lackey, Angie; Perbost, Clotilde; Taillon, Bruce; Stella, Alessandra; Solovyev, Victor; Fawcett, Jeffrey A.; Sterck, Lieven; Vandepoele, Klaas; Grando, Stella M.; Toppo, Stefano; Moser, Claudio; Lanchbury, Jerry; Bogden, Robert; Skolnick, Mark; Sgaramella, Vittorio; Bhatnagar, Satish K.; Fontana, Paolo; Gutin, Alexander; Van de Peer, Yves; Salamini, Francesco; Viola, Roberto

    2007-01-01

    Background Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape. PMID:18094749

  15. Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data

    Directory of Open Access Journals (Sweden)

    Junttila Sini

    2012-10-01

    Full Text Available Abstract Background Lichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to survive in a dehydrated molecular dormant state for decades at a time. Genetic resources have been established in lichen species for the study of molecular systematics and their taxonomic classification. No lichen species have been characterised yet using genomics and the molecular mechanisms underlying the lichen symbiosis and the fundamentals of desiccation tolerance remain undescribed. We report the characterisation of a transcriptome of the grey reindeer lichen, Cladonia rangiferina, using high-throughput next-generation transcriptome sequencing and traditional Sanger EST sequencing data. Results Altogether 243,729 high quality sequence reads were de novo assembled into 16,204 contigs and 49,587 singletons. The genome of origin for the sequences produced was predicted using Eclat with sequences derived from the axenically grown symbiotic partners used as training sequences for the classification model. 62.8% of the sequences were classified as being of fungal origin while the remaining 37.2% were predicted as being of algal origin. The assembled sequences were annotated by BLASTX comparison against a non-redundant protein sequence database with 34.4% of the sequences having a BLAST match. 29.3% of the sequences had a Gene Ontology term match and 27.9% of the sequences had a domain or structural match following an InterPro search. 60 KEGG pathways with more than 10 associated sequences were identified. Conclusions Our results present a first transcriptome sequencing and de novo assembly for a lichen species and describe the ongoing molecular processes and the most active pathways in C. rangiferina. This brings a meaningful contribution to publicly available lichen sequence information. These data provide a first

  16. Improving High-Throughput Sequencing Approaches for Reconstructing the Evolutionary Dynamics of Upper Paleolithic Human Groups

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine

    the development and testing of innovative molecular approaches aiming at improving the amount of informative HTS data one can recover from ancient DNA extracts. We have characterized important ligation and amplification biases in the sequencing library building and enrichment steps, which can impede further...... been mainly driven by the development of High-Throughput DNA Sequencing (HTS) technologies but also by the implementation of novel molecular tools tailored to the manipulation of ultra short and damaged DNA molecules. Our ability to retrieve traces of genetic material has tremendously improved, pushing...

  17. Whole-genome sequencing of the Mycobacterium tuberculosis Manila sublineage results in less clustering and better resolution than mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping.

    Science.gov (United States)

    Jamieson, F B; Teatero, S; Guthrie, J L; Neemuchwala, A; Fittipaldi, N; Mehaffy, C

    2014-10-01

    Mycobacterium tuberculosis isolates of the Manila sublineage are genetically homogeneous. In this study, we used whole-genome sequencing (WGS) to type a collection of 36 M. tuberculosis isolates of the Manila family. WGS enabled the subtyping of these 36 isolates into at least 10 distinct clusters. Our results indicate that WGS is a powerful approach to determining the relatedness of Manila family M. tuberculosis isolates. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  18. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

    2007-01-01

    to the correct source once sequencing anomalies are accounted for (miss-assignment ratebias in the distribution of the differently tagged...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

  19. Biosynthesis and characterization of a non-repetitive polypeptide derived from silk fibroin heavy chain

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Gaoqiang; Wu, Mingyang; Yi, Honggen; Wang, Jiannan, E-mail: wangjn@suda.edu.cn

    2016-02-01

    Silk fibroin heavy chain is the major protein component of Bombyx mori silk fibroin and is composed of 12 repetitive and 11 non-repetitive regions, with the non-repetitive domain consisting of a hydrophilic polypeptide chain. In order to determine the biomedical function of the non-repetitive domain or potentially use it to modify hydrophobic biomaterials, high-purity isolation is necessary. Previously, we cloned and extended a gene motif (f(1)) encoding the non-repetitive domain. Here, this motif and its multimers are inserted into a glutathione S-transferase (GST)-tagged fusion-protein expression vector. Motif f(1) and multimers f(4) and f(8) were expressed in Escherichia coli BL21 cells following isopropyl β-D-1-thiogalactopyranoside induction, purified by GST-affinity chromatography, and single bands of purified fusion proteins GST-F(1), GST-F(4), and GST-F(8), were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Target polypeptides F(1), F(4), and F(8), were cleaved clearly from the GST-fusion tag following thrombin digestion. Mass spectrometry results indicate that the molecular weights associated with fusion proteins GST-F(1), GST-F(4), and GST-F(8) are 31.5, 43.8, and 59.0 kDa, respectively, and with the cleaved polypeptides F(1), F(4), and F(8) are 4.8, 16.8, and 32.8 kDa, respectively. The F(1), F(4), and F(8) polypeptide chains are negatively charged with isoelectric points (pI) of 3.3, 3.2, and 3.0, respectively. The molecular weight and pI values of the polypeptide chains are consistent with the predicted values and the amino acid compositions similar to predicted sequences. FTIR and CD results show the molecular conformation of F(1) was mainly random coil, and more stable α-helix structure formed in longer molecular chain. - Highlights: • A non-repetitive domain and its multimers of silk fibroin were expressed by E. coli. • The corresponding target polypeptides F(1), F(4) and F(8) were cleaved clearly. • Their

  20. Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361(T).

    Science.gov (United States)

    Jung, Ji Young; Ahn, Youngbeom; Kweon, Ohgew; LiPuma, John J; Hussong, David; Marasa, Bernard S; Cerniglia, Carl E

    2017-04-20

    Burkholderia contaminans LMG 23361 is the type strain of the species isolated from the milk of a dairy sheep with mastitis. Some pharmaceutical products contain disinfectants such as benzalkonium chloride (BZK) and previously we reported that B. contaminans LMG 23361(T) possesses the ability to inactivate BZK with high biodegradation rates. Here, we report an improved high-quality draft genome sequence of this strain. Copyright © 2017 Jung et al.

  1. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

    Directory of Open Access Journals (Sweden)

    Craig W. Herbold

    2015-07-01

    Full Text Available High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse and high quality sets of amplicon sequence data for modern studies in microbial ecology.

  2. SAMQA: error classification and validation of high-throughput sequenced read data

    Directory of Open Access Journals (Sweden)

    Bressler Ryan

    2011-08-01

    Full Text Available Abstract Background The advances in high-throughput sequencing technologies and growth in data sizes has highlighted the need for scalable tools to perform quality assurance testing. These tests are necessary to ensure that data is of a minimum necessary standard for use in downstream analysis. In this paper we present the SAMQA tool to rapidly and robustly identify errors in population-scale sequence data. Results SAMQA has been used on samples from three separate sets of cancer genome data from The Cancer Genome Atlas (TCGA project. Using technical standards provided by the SAM specification and biological standards defined by researchers, we have classified errors in these sequence data sets relative to individual reads within a sample. Due to an observed linearithmic speedup through the use of a high-performance computing (HPC framework for the majority of tasks, poor quality data was identified prior to secondary analysis in significantly less time on the HPC framework than the same data run using alternative parallelization strategies on a single server. Conclusions The SAMQA toolset validates a minimum set of data quality standards across whole-genome and exome sequences. It is tuned to run on a high-performance computational framework, enabling QA across hundreds gigabytes of samples regardless of coverage or sample type.

  3. A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing.

    Science.gov (United States)

    Fraser, James; Ethier, Sylvain D; Miura, Hisashi; Dostie, Josée

    2012-01-01

    The study of three-dimensional genome organization is an exciting research area, which has benefited from the rapid development of high-resolution molecular mapping techniques over the past decade. These methods are derived from the chromosome conformation capture (3C) technique and are each aimed at improving some aspect of 3C. All 3C technologies use formaldehyde fixation and proximity-based ligation to capture chromatin contacts in cell populations and consider in vivo spatial proximity more or less inversely proportional to the frequency of measured interactions. The 3C-carbon copy (5C) method is among the most quantitative of these approaches. 5C is extremely robust and can be used to study chromatin organization at various scales. Here, we present a modified 5C analysis protocol adapted for sequencing with an Ion Torrent Personal Genome Machine™ (PGM™). We explain how Torrent 5C libraries are produced and sequenced. We also describe the statistical and computational methods we developed to normalize and analyze raw Torrent 5C sequence data. The Torrent 5C protocol should facilitate the study of in vivo chromatin architecture at high resolution because it benefits from high accuracy, greater speed, low running costs, and the flexibility of in-house next-generation sequencing. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. 454 sequencing put to the test using the complex genome of barley

    Directory of Open Access Journals (Sweden)

    Keller Beat

    2006-10-01

    Full Text Available Abstract Background During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing", promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. Results To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. Conclusion Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing

  5. On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution

    Science.gov (United States)

    Rabadan, Raul; Bhanot, Gyan; Marsilio, Sonia; Chiorazzi, Nicholas; Pasqualucci, Laura; Khiabanian, Hossein

    2017-12-01

    One cause of cancer mortality is tumor evolution to therapy-resistant disease. First line therapy often targets the dominant clone, and drug resistance can emerge from preexisting clones that gain fitness through therapy-induced natural selection. Such mutations may be identified using targeted sequencing assays by analysis of noise in high-depth data. Here, we develop a comprehensive, unbiased model for sequencing error background. We find that noise in sufficiently deep DNA sequencing data can be approximated by aggregating negative binomial distributions. Mutations with frequencies above noise may have prognostic value. We evaluate our model with simulated exponentially expanded populations as well as data from cell line and patient sample dilution experiments, demonstrating its utility in prognosticating tumor progression. Our results may have the potential to identify significant mutations that can cause recurrence. These results are relevant in the pretreatment clinical setting to determine appropriate therapy and prepare for potential recurrence pretreatment.

  6. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

    DEFF Research Database (Denmark)

    Gamba, Cristina; Hanghøj, Kristian Ebbesen; Gaunitz, Charleen

    2016-01-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs...... of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning...... a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules...

  7. High sequence variability among hemocyte-specific Kazal-type proteinase inhibitors in decapod crustaceans.

    Science.gov (United States)

    Cerenius, Lage; Liu, Haipeng; Zhang, Yanjiao; Rimphanitchayakit, Vichien; Tassanakajon, Anchalee; Gunnar Andersson, M; Söderhäll, Kenneth; Söderhäll, Irene

    2010-01-01

    Crustacean hemocytes were found to produce a large number of transcripts coding for Kazal-type proteinase inhibitors (KPIs). A detailed study performed with the crayfish Pacifastacus leniusculus and the shrimp Penaeus monodon revealed the presence of at least 26 and 20 different Kazal domains from the hemocyte KPIs, respectively. Comparisons with KPIs from other taxa indicate that the sequences of these domains evolve rapidly. A few conserved positions, e.g. six invariant cysteines were present in all domain sequences whereas the position of P1 amino acid, a determinant for substrate specificity, varied highly. A study with a single crayfish animal suggested that even at the individual level considerable sequence variability among hemocyte KPIs produced exist. Expression analysis of four crayfish KPI transcripts in hematopoietic tissue cells and different hemocyte types suggest that some of these KPIs are likely to be involved in hematopoiesis or hemocyte release as they were produced in particular hemocyte types or maturation stages only.

  8. High Sequence Variations in Mitochondrial DNA Control Region among Worldwide Populations of Flathead Mullet Mugil cephalus

    Directory of Open Access Journals (Sweden)

    Brian Wade Jamandre

    2014-01-01

    Full Text Available The sequence and structure of the complete mtDNA control region (CR of M. cephalus from African, Pacific, and Atlantic populations are presented in this study to assess its usefulness in phylogeographic studies of this species. The mtDNA CR sequence variations among M. cephalus populations largely exceeded intraspecific polymorphisms that are generally observed in other vertebrates. The length of CR sequence varied among M. cephalus populations due to the presence of indels and variable number of tandem repeats at the 3′ hypervariable domain. The high evolutionary rate of the CR in this species probably originated from these mutations. However, no excessive homoplasic mutations were noticed. Finally, the star shaped tree inferred from the CR polymorphism stresses a rapid radiation worldwide, in this species. The CR still appears as a good marker for phylogeographic investigations and additional worldwide samples are warranted to further investigate the genetic structure and evolution in M. cephalus.

  9. Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

    Directory of Open Access Journals (Sweden)

    William H Thiel

    2016-01-01

    Full Text Available Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment. High-throughput sequencing (HTS revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs.

  10. Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data.

    Science.gov (United States)

    Thiel, William H

    2016-01-01

    Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). High-throughput sequencing (HTS) revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs. Copyright © 2016 Official journal of the American Society of Gene & Cell Therapy. Published by Elsevier Inc. All rights reserved.

  11. Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.

    Science.gov (United States)

    Cai, Qingle; Qian, Xiaoju; Lang, Yongshan; Luo, Yadan; Xu, Jiaohui; Pan, Shengkai; Hui, Yuanyuan; Gou, Caiyun; Cai, Yue; Hao, Meirong; Zhao, Jinyang; Wang, Songbo; Wang, Zhaobao; Zhang, Xinming; He, Rongjun; Liu, Jinchao; Luo, Longhai; Li, Yingrui; Wang, Jun

    2013-03-28

    The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.

  12. Anomaly Detection in Large Sets of High-Dimensional Symbol Sequences

    Science.gov (United States)

    Budalakoti, Suratna; Srivastava, Ashok N.; Akella, Ram; Turkov, Eugene

    2006-01-01

    This paper addresses the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. The approach taken uses unsupervised clustering of sequences using the normalized longest common subsequence (LCS) as a similarity measure, followed by detailed analysis of outliers to detect anomalies. As the LCS measure is expensive to compute, the first part of the paper discusses existing algorithms, such as the Hunt-Szymanski algorithm, that have low time-complexity. We then discuss why these algorithms often do not work well in practice and present a new hybrid algorithm for computing the LCS that, in our tests, outperforms the Hunt-Szymanski algorithm by a factor of five. The second part of the paper presents new algorithms for outlier analysis that provide comprehensible indicators as to why a particular sequence was deemed to be an outlier. The algorithms provide a coherent description to an analyst of the anomalies in the sequence, compared to more normal sequences. The algorithms we present are general and domain-independent, so we discuss applications in related areas such as anomaly detection.

  13. Analysis of 4,664 high-quality sequence-finished poplar full-length

    Energy Technology Data Exchange (ETDEWEB)

    Ralph, S. [University of British Columbia, Vancouver; Gunter, Lee E [ORNL; Tuskan, Gerald A [ORNL; Douglas, Carl [University of British Columbia, Vancouver; Holt, Robert A. [Genome Sciences Centre, Vancouver, BC, Canada; Jones, Steven [Genome Sciences Centre, Vancouver, BC, Canada; Marra, Marco [Genome Sciences Centre, Vancouver, BC, Canada; Bohlmann, J. [University of British Columbia, Vancouver

    2008-01-01

    The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa x P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in

  14. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+".

    Directory of Open Access Journals (Sweden)

    Markus H Antwerpen

    Full Text Available The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  15. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+").

    Science.gov (United States)

    Antwerpen, Markus H; Prior, Karola; Mellmann, Alexander; Höppner, Sebastian; Splettstoesser, Wolf D; Harmsen, Dag

    2015-01-01

    The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  16. Suicide attempts: prevention of repetition.

    Science.gov (United States)

    Daigle, Marc S; Pouliot, Louise; Chagnon, François; Greenfield, Brian; Mishara, Brian

    2011-10-01

    To present an overview of promising strategies to prevent repetition of suicidal behaviours. This literature review on tertiary preventive interventions of suicide attempts was produced using the computerized databases PubMed and PsycINFO from January 1966 to September 2010, using French- and English-language limits and the key words: suicid* or deliberate self-harm and treatment* or therapy or intervention* or management. Thirteen of the 35 included studies showed statistically significant effects of fewer repeated attempts or suicides in the experimental condition. Overall, 22 studies focused on more traditional approaches, that is, pharmacological or psychological approaches. Only 2 of the 6 pharmacological treatments proved significantly superior to a placebo- a study of lithium with depression and flupenthixol with personality disorders. Eight out of 16 psychological treatments proved superior to treatment as usual or another approach: cognitive-behavioural therapy (CBT) (n = 4), (including dialectical behaviour therapy [n = 2]); psychodynamic therapy (n = 2); mixed (CBT plus psychodynamic therapy [n = 1]); and motivational approach and change in therapist (n = 1). Among the 8 studies using visit, postal, or telephone contact or green-token emergency card provision, 2 were significant: one involving telephone follow-up and the other telephone follow-up or visits. Hospitalization was not related to fewer attempts, and 1 of the 4 outreach approaches had significant results: a program involving individualized biweekly treatment. The rationale behind these single or multiple approaches still needs to be clarified. There were methodological flaws in many studies and some had very specific limited samples. There is a need for more research addressing the problem in definitions of outcomes and measurement of the dependent variables, gender-specific effects, and inclusion of high-risk groups. There is a need for the development and evaluation of new approaches that

  17. Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger.

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    Bastiaan A van den Berg

    Full Text Available Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing protein production and secretion could be employed to improve enzyme production levels in industrial bioprocesses via protein engineering. A large set, over 600 homologous and nearly 2,000 heterologous fungal genes, were overexpressed in Aspergillus niger using a standardized expression cassette and scored for high versus no production. Subsequently, sequence-based machine learning techniques were applied for identifying relevant DNA and protein sequence features. T