WorldWideScience

Sample records for repeatedly perform sequences

  1. Performance and physiological responses to repeated-sprint and jump sequences.

    Science.gov (United States)

    Buchheit, Martin

    2010-11-01

    In this study, the performance and selected physiological responses to team-sport specific repeated-sprint and jump sequence were investigated. On four occasions, 13 team-sport players (22 ± 3 year) performed alternatively six repeated maximal straight-line or shuttle-sprints interspersed with a jump ([RS(+j), 6 × 25 m] or [RSS(+j), 6 × (2 × 12.5 m)]) or not ([RS, 6 × 25 m] or [RSS, 6 × (2 × 12.5 m)]) within each recovery period. Mean running time, rate of perceived exertion (RPE), pulmonary oxygen uptake (V(O)₂), blood lactate ([La](b)), and vastus lateralis deoxygenation ([HHb]) were obtained for each condition. Mean sprint times were greater for RS(+j) versus RS (4.14 ± 0.17 vs. 4.09 ± 0.16 s, with the qualitative analysis revealing a 82% chance of RS(+j) times to be greater than RS) and for RSS(+j) versus RSS (5.43 ± 0.18 vs. 5.29 ± 0.17 s; 99% chance of RSS(+j) to be >RSS). The correlation between sprint and jump abilities were large-to-very-large, but below 0.71 for RSSs. Jumps increased RPE (Cohen's d ± 90% CL: +0.7 ± 0.5; 95% chance for RS(+j) > RS and +0.7 ± 0.5; 96% for RSS(+j) > RSS), V(O)₂(+0.4 ± 0.5; 80% for RS(+j) > RS and +0.5 ± 0.5; 86% for RSS(+j) > RSS), [La](b) (+0.5 ± 0.5; 59% for RS(+j) > RS and +0.2 ± 0.5; unclear for RSS(+j) > RSS), and [HHb] (+0.5 ± 0.5; 86% for RS(+j) > RS and +0.5 ± 0.5; 85% for RSS(+j) > RSS). To conclude, repeated- sprint and jump abilities could be considered as specific qualities. The addition of a jump within the recovery periods during repeated-sprint running sequences impairs sprinting performance and might be an effective training practice for eliciting both greater systemic and vastus lateralis physiological loads.

  2. 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.

  3. Mining of simple sequence repeats in the Genome of Gentianaceae

    Directory of Open Access Journals (Sweden)

    R Sathishkumar

    2011-01-01

    Full Text Available Simple sequence repeats (SSRs or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI. Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16% among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

  4. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Vattipally B Sreenu; Pankaj Kumar; Javaregowda Nagaraju; Hampapathalu A Nagarajaram

    2007-01-01

    Simple sequence repeats (SSRs) or microsatellites are the repetitive nucleotide sequences of motifs of length 1–6 bp. They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes. Microsatellites undergo mutations in the form of insertions and deletions (INDELS) of their repeat units with some bias towards insertions that lead to microsatellite tract expansion. Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these enzymes and as a null hypothesis one could expect these genomes to harbour many long tracts. It is therefore interesting to analyse the mycobacterial genomes for distribution and abundance of microsatellites tracts and to look for potentially polymorphic microsatellites. Available mycobacterial genomes, Mycobacterium avium, M. leprae, M. bovis and the two strains of M. tuberculosis (CDC1551 and H37Rv) were analysed for frequencies and abundance of SSRs. Our analysis revealed that the SSRs are distributed throughout the mycobacterial genomes at an average of 220–230 SSR tracts per kb. All the mycobacterial genomes contain few regions that are conspicuously denser or poorer in microsatellites compared to their expected genome averages. The genomes distinctly show scarcity of long microsatellites despite the absence of a post-replicative DNA repair system. Such severe scarcity of long microsatellites could arise as a result of strong selection pressures operating against long and unstable sequences although influence of GC-content and role of point mutations in arresting microsatellite expansions can not be ruled out. Nonetheless, the long tracts occasionally found in coding as well as non-coding regions may account for limited genome plasticity in these genomes.

  5. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.

    Directory of Open Access Journals (Sweden)

    Chong Chu

    Full Text Available Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo.

  6. Steganalytic method based on short and repeated sequence distance statistics

    Institute of Scientific and Technical Information of China (English)

    WANG GuoXin; PING XiJian; XU ManKun; ZHANG Tao; BAO XiRui

    2008-01-01

    According to the distribution characteristics of short and repeated sequence (SRS),a steganalytic method based on the correlation of image bit planes is proposed.Firstly,we provide the conception of SRS distance statistics and deduce its statistical distribution.Because the SRS distance statistics can effectively reflect the correlation of the sequence,SRS has statistical features when the image bit plane sequence equals the image width.Using this characteristic,the steganalytic method is fulfilled by the distinct test of Poisson distribution.Experimental results show a good performance for detecting LSB matching steganographic method in still images.By the way,the proposed method is not designed for specific steganographic algorithms and has good generality.

  7. Highly Informative Simple Sequence Repeat (SSR) Markers for Fingerprinting Hazelnut

    Science.gov (United States)

    Simple sequence repeat (SSR) or microsatellite markers have many applications in breeding and genetic studies of plants, including fingerprinting of cultivars and investigations of genetic diversity, and therefore provide information for better management of germplasm collections. They are repeatab...

  8. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    Aug 28, 2012 ... In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 ... mean (UPGMA) with each cluster representing a particular Vigna species. ..... were reported to be more frequent than the compound.

  9. Study of simple sequence repeat (SSR) polymorphism for biotic ...

    African Journals Online (AJOL)

    home

    2013-10-02

    Oct 2, 2013 ... back cross breeding; SSRs, simple sequence repeats; PIC, polymorphism ..... PIC values were reported in barley wheat and rice (Gu et ... doubled-haploid rice population. Theor. ... Grover A, Aishwarya V, Sharma PC (2007).

  10. Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes

    Institute of Scientific and Technical Information of China (English)

    Neng-zhi Jin; Zi-xian Liu; Yan-jiao Qi; Wen-yuan Qiu

    2009-01-01

    On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.

  11. Survey of simple sequence repeats in woodland strawberry (Fragaria vesca).

    Science.gov (United States)

    Guan, L; Huang, J F; Feng, G Q; Wang, X W; Wang, Y; Chen, B Y; Qiao, Y S

    2013-07-30

    The use of simple sequence repeats (SSRs), or microsatellites, as genetic markers has become popular due to their abundance and variation in length among individuals. In this study, we investigated linkage groups (LGs) in the woodland strawberry (Fragaria vesca) and demonstrated variation in the abundances, densities, and relative densities of mononucleotide, dinucleotide, and trinucleotide repeats. Mononucleotide, dinucleotide, and trinucleotide repeats were more common than longer repeats in all LGs examined. Perfect SSRs were the predominant SSR type found and their abundance was extremely stable among LGs and chloroplasts. Abundances of mononucleotide, dinucleotide, and trinucleotide repeats were positively correlated with LG size, whereas those of tetranucleotide and hexanucleotide SSRs were not. Generally, in each LG, the abundance, relative abundance, relative density, and the proportion of each unique SSR all declined rapidly as the repeated unit increased. Furthermore, the lengths and frequencies of SSRs varied among different LGs.

  12. Analysis of Simple Sequence Repeats in Genomes of Rhizobia

    Institute of Scientific and Technical Information of China (English)

    GAO Ya-mei; HAN Yi-qiang; TANG Hui; SUN Dong-mei; WANG Yan-jie; WANG Wei-dong

    2008-01-01

    Simple sequence repeats (SSRs) or microsatellites, as genetic markers, are ubiquitous in genomes of various organisms. The analysis of SSR in rhizobia genome provides useful information for a variety of applications in population genetics of rhizobia. We analyzed the occurrences, relative abundance, and relative density of SSRs, the most common in Bradyrhizobium japonicum, Mesorhizobium loti, and Sinorhizobium meliloti genomes se-quenced in the microorganisms tandem repeats database, and SSRs in the three species genomes were compared with each other. The result showed that there were 1 410, 859, and 638 SSRs in B. japonicum, M. loti, and 5. meliloti genomes, respectively. In the genomes of B. japonicum, M. loti, and 5. meliloti, tetranucleotide, pentanucleotide, and hexanucleotide repeats were more abundant and indicated higher mutation rates in these species. The least abundance was mononucleotide repeat. The SSRs type and distribution were similar among these species.

  13. Coevolution between simple sequence repeats (SSRs and virus genome size

    Directory of Open Access Journals (Sweden)

    Zhao Xiangyan

    2012-08-01

    Full Text Available Abstract Background Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. Results In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome  Conclusions We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree.

  14. Cloning, characterization, and properties of seven triplet repeat DNA sequences.

    Science.gov (United States)

    Ohshima, K; Kang, S; Larson, J E; Wells, R D

    1996-07-12

    Several neuromuscular and neurodegenerative diseases are caused by genetically unstable triplet repeat sequences (CTG.CAG, CGG.CCG, or AAG.CTT) in or near the responsible genes. We implemented novel cloning strategies with chemically synthesized oligonucleotides to clone seven of the triplet repeat sequences (GTA.TAC, GAT.ATC, GTT.AAC, CAC.GTG, AGG.CCT, TCG.CGA, and AAG.CTT), and the adjoining paper (Ohshima, K., Kang, S., Larson, J. E., and Wells, R. D.(1996) J. Biol. Chem. 271, 16784-16791) describes studies on TTA.TAA. This approach in conjunction with in vivo expansion studies in Escherichia coli enabled the preparation of at least 81 plasmids containing the repeat sequences with lengths of approximately 16 up to 158 triplets in both orientations with varying extents of polymorphisms. The inserts were characterized by DNA sequencing as well as DNA polymerase pausings, two-dimensional agarose gel electrophoresis, and chemical probe analyses to evaluate the capacity to adopt negative supercoil induced non-B DNA conformations. AAG.CTT and AGG.CCT form intramolecular triplexes, and the other five repeat sequences do not form any previously characterized non-B structures. However, long tracts of TCG.CGA showed strong inhibition of DNA synthesis at specific loci in the repeats as seen in the cases of CTG.CAG and CGG.CCG (Kang, S., Ohshima, K., Shimizu, M., Amirhaeri, S., and Wells, R. D.(1995) J. Biol. Chem. 270, 27014-27021). This work along with other studies (Wells, R. D.(1996) J. Biol. Chem. 271, 2875-2878) on CTG.CAG, CGG.CCG, and TTA.TAA makes available long inserts of all 10 triplet repeat sequences for a variety of physical, molecular biological, genetic, and medical investigations. A model to explain the reduction in mRNA abundance in Friedreich's ataxia based on intermolecular triplex formation is proposed.

  15. Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai).

    Science.gov (United States)

    Jarret, R L; Merrick, L C; Holms, T; Evans, J; Aradhya, M K

    1997-08-01

    Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.

  16. Repeat-based Sequence Typing of Carnobacterium maltaromaticum.

    Science.gov (United States)

    Rahman, Abdur; El Kheir, Sara M; Back, Alexandre; Mangavel, Cécile; Revol-Junelles, Anne-Marie; Borges, Frédéric

    2016-06-01

    Carnobacterium maltaromaticum is a Lactic Acid Bacterium (LAB) of technological interest for the food industry, especially the dairy as bioprotection and ripening flora. The industrial use of this LAB requires accurate and resolutive typing tools. A new typing method for C. maltaromaticum inspired from MLVA analysis and called Repeat-based Sequence Typing (RST) is described. Rather than electrophoresis analysis, our RST method is based on sequence analysis of multiple loci containing Variable-Number Tandem-Repeats (VNTRs). The method described here for C. maltaromaticum relies on the analysis of three VNTR loci, and was applied to a collection of 24 strains. For each strain, a PCR product corresponding to the amplification of each VNTR loci was sequenced. Sequence analysis allowed delineating 11, 11, and 12 alleles for loci VNTR-A, VNTR-B, and VNTR-C, respectively. Considering the allele combination exhibited by each strain allowed defining 15 genotypes, ending in a discriminatory index of 0.94. Comparison with MLST revealed that both methods were complementary for strain typing in C. maltaromaticum.

  17. A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers

    Science.gov (United States)

    A blackberry (Rubus L.) expressed sequence tag (EST) library was produced for developing simple sequence repeat (SSR) markers from the tetraploid blackberry cultivar, Merton Thornless, the source of the thornless trait in commercial cultivars. RNA was extracted from young expanding leaves and used f...

  18. Repeatability of locomotor performance and morphology-locomotor performance relationships.

    Science.gov (United States)

    Conradsen, Cara; Walker, Jeffrey A; Perna, Catherine; McGuigan, Katrina

    2016-09-15

    There is good evidence that natural selection drives the evolution of locomotor performance, but the processes that generate the among-individual variation for selection to act on are relatively poorly understood. We measured prolonged swimming performance, Ucrit, and morphology in a large cohort (n=461) of wild-type zebrafish (Danio rerio) at ∼6 months and again at ∼9 months. Using mixed-model analyses to estimate repeatability as the intraclass correlation coefficient, we determined that Ucrit was significantly repeatable (r=0.55; 95% CI: 0.45-0.64). Performance differences between the sexes (males 12% faster than females) and changes with age (decreasing 0.07% per day) both contributed to variation in Ucrit and, therefore, the repeatability estimate. Accounting for mean differences between sexes within the model decreased the estimate of Ucrit repeatability to 21% below the naïve estimate, while fitting age in the models increased the estimate to 14% above the naïve estimate. Greater consideration of factors such as age and sex is therefore necessary for the interpretation of performance repeatability in wild populations. Body shape significantly predicted Ucrit in both sexes in both assays, with the morphology-performance relationship significantly repeatable at the population level. However, morphology was more strongly predicative of performance in older fish, suggesting a change in the contribution of morphology relative to other factors such as physiology and behaviour. The morphology-performance relationship changed with age to a greater extent in males than females.

  19. Characterization of simple sequence repeats (SSRs from Phlebotomus papatasi (Diptera: Psychodidae expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Hamarsheh Omar

    2011-09-01

    Full Text Available Abstract Background Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. Results Simple sequence repeats (SSRs were characterized in P. papatasi expressed sequence tags (ESTs derived from a public database, National Center for Biotechnology Information (NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. Conclusion The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

  20. Diversity Analysis in Cannabis sativa Based on Large-Scale Development of Expressed Sequence Tag-Derived Simple Sequence Repeat Markers

    OpenAIRE

    Chunsheng Gao; Pengfei Xin; Chaohua Cheng; Qing Tang; Ping Chen; Changbiao Wang; Gonggu Zang; Lining Zhao

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SS...

  1. Simple sequence repeat map of the sunflower genome.

    Science.gov (United States)

    Tang, S.; Yu, J.-K.; Slabaugh, B.; Shintani, K.; Knapp, J.

    2002-12-01

    Several independent molecular genetic linkage maps of varying density and completeness have been constructed for cultivated sunflower ( Helianthus annuus L.). Because of the dearth of sequence and probe-specific DNA markers in the public domain, the various genetic maps of sunflower have not been integrated and a single reference map has not emerged. Moreover, comparisons between maps have been confounded by multiple linkage group nomenclatures and the lack of common DNA markers. The goal of the present research was to construct a dense molecular genetic linkage map for sunflower using simple sequence repeat (SSR) markers. First, 879 SSR markers were developed by identifying 1,093 unique SSR sequences in the DNA sequences of 2,033 clones isolated from genomic DNA libraries enriched for (AC)(n) or (AG)(n) and screening 1,000 SSR primer pairs; 579 of the newly developed SSR markers (65.9% of the total) were polymorphic among four elite inbred lines (RHA280, RHA801, PHA and PHB). The genetic map was constructed using 94 RHA280 x RHA801 F(7) recombinant inbred lines (RILs) and 408 polymorphic SSR markers (462 SSR marker loci segregated in the mapping population). Of the latter, 459 coalesced into 17 linkage groups presumably corresponding to the 17 chromosomes in the haploid sunflower genome ( x = 17). The map was 1,368.3-cM long and had a mean density of 3.1 cM per locus. The SSR markers described herein supply a critical mass of DNA markers for constructing genetic maps of sunflower and create the basis for unifying and cross-referencing the multitude of genetic maps developed for wild and cultivated sunflowers.

  2. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.).

    Science.gov (United States)

    Zhu, H; Senalik, D; McCown, B H; Zeldin, E L; Speers, J; Hyman, J; Bassil, N; Hummer, K; Simon, P W; Zalapa, J E

    2012-01-01

    The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar 'HyRed'. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540-590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2-15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

  3. Analysis of simple sequence repeats markers derived from Phytophthora sojae expressed sequence tags

    Institute of Scientific and Technical Information of China (English)

    ZHU Zhendong; HUO Yunlong; WANG Xiaoming; HUANG Junbin; WU Xiaofei

    2004-01-01

    Five thousand and eight hundred publicly available expressed sequence tags (ESTs) of Phytophthora sojae were electronically searched and 415 simple sequence repeats (SSRs) were identified in 369 ESTs. The average density of SSRs was one SSR per 8.9 kb of EST sequence screened. The most frequent repeats were trinucleotide repeats (50.1%) and the least frequent were tetranucleotide repeats (8.2%). Forty primer pairs were designed and tested on 5 strains of P. sojae. Thirty-three primer pairs had successful PCR amplifications. Of the 33 functional primer pairs, 28 primer pairs produced characteristic SSR bands of the expected size, and 15 primer pairs (45.5%) detected polymorphism among 5 tested strains of P. sojae. Based on the polymorphisms detected with 20 EST-SSR markers, the 5 tested strains of P. sojae were clustered into 3 groups. In this study, the SSR markers of P. sojae were developed for the first time. These markers could be useful for identification, genetic variation study, and molecular mapping of P. sojae and its relative species.

  4. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes

    OpenAIRE

    Kumar, Pankaj; Chaitanya, Pasumarthy S.; Nagarajaram, Hampapathalu A

    2010-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1–6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in s...

  5. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.

    2010-07-12

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  6. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Matt J Cahill

    Full Text Available BACKGROUND: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL FINDINGS: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. CONCLUSIONS: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

  7. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2004-01-01

    Full Text Available Abstract Background Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison. Results In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors. Conclusions We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at http://minisatellites.u-psud.fr now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial

  8. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.

    Directory of Open Access Journals (Sweden)

    Simon Philipp W

    2010-10-01

    Full Text Available Abstract Background Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although

  9. Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

    Directory of Open Access Journals (Sweden)

    Stéphanie Barthe

    Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  10. The Cipher Code of Simple Sequence Repeats in "Vampire Pathogens".

    Science.gov (United States)

    Zou, Geng; Bello-Orti, Bernardo; Aragon, Virginia; Tucker, Alexander W; Luo, Rui; Ren, Pinxing; Bi, Dingren; Zhou, Rui; Jin, Hui

    2015-07-28

    Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like "vampire pathogens" (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales, and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3, and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

  11. Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats

    Directory of Open Access Journals (Sweden)

    Everaldo G. de Barros

    2000-06-01

    Full Text Available The genetic basis of cultivated soybean is rather narrow. This observation has been confirmed by analysis of agronomic traits among different genotypes, and more recently by the use of molecular markers. During the construction of an RFLP soybean map (Glycine soja x Glycine max the two progenitors were analyzed with over 2,000 probes, of which 25% were polymorphic. Among the probes that revealed polymorphisms, a small proportion, about 0.5%, hybridized to regions that were highly polymorphic. Here we report the sequencing and analysis of five of these probes. Three of the five contain segments that encode leucine-rich repeat (LRR sequence homologous to known disease resistance genes in plants. Two other probes are relatively AT-rich and contain segments of (An/(Tn. DNA segments corresponding to one of the probes (A45-10 were amplified from nine soybean genotypes. Partial sequencing of these amplicons suggests that deletions and/or insertions are responsible for the extensive polymorphism observed. We propose that genes encoding LRR proteins and simple sequence repeat region prone to slippage are some of the most hypervariable regions of the soybean genome.A base genética da soja cultivada é relativamente estreita. Essa observação foi confirmada por análises de características agronômicas entre diferentes genótipos e, mais recentemente, pelo uso de marcadores moleculares. Durante a construção de um mapa de RFLP da soja (Glycine soja x Glycine max, os dois progenitores foram analisados com mais de 2000 sondas, das quais 25% eram polimórficas. Entre as sondas que revelaram polimorfismos, uma pequena proporção, cerca de 0,5%, hibridizou com regiões que eram altamente polimórficas. Neste trabalho, são apresentados o seqüenciamento e análise de cinco dessas sondas. Três dessas sondas contêm segmentos que codificam repetições ricas em leucina que são homólogas a genes de resistência a doenças já conhecidos em plantas. As duas

  12. Assembly of Repeat Content Using Next Generation Sequencing Data

    Energy Technology Data Exchange (ETDEWEB)

    labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

    2014-03-17

    Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

  13. Exact Tandem Repeats Analyzer (E-TRA): A new program for DNA sequence mining

    Indian Academy of Sciences (India)

    Mehmet Karaca; Mehmet Bilgen; A. Naci Onus; Ayse Gul Ince; Safinaz Y. Elmasulu

    2005-04-01

    Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as ‘organs’, ‘tissues’, ‘cell lines’ and ‘development stages’ for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.

  14. Repeated-Sprint Sequences During Female Soccer Matches Using Fixed and Individual Speed Thresholds.

    Science.gov (United States)

    Nakamura, Fábio Y; Pereira, Lucas A; Loturco, Irineu; Rosseti, Marcelo; Moura, Felipe A; Bradley, Paul S

    2017-07-01

    Nakamura, FY, Pereira, LA, Loturco, I, Rosseti, M, Moura, FA, and Bradley, PS. Repeated-sprint sequences during female soccer matches using fixed and individual speed thresholds. J Strength Cond Res 31(7): 1802-1810, 2017-The main objective of this study was to characterize the occurrence of single sprint and repeated-sprint sequences (RSS) during elite female soccer matches, using fixed (20 km·h) and individually based speed thresholds (>90% of the mean speed from a 20-m sprint test). Eleven elite female soccer players from the same team participated in the study. All players performed a 20-m linear sprint test, and were assessed in up to 10 official matches using Global Positioning System technology. Magnitude-based inferences were used to test for meaningful differences. Results revealed that irrespective of adopting fixed or individual speed thresholds, female players produced only a few RSS during matches (2.3 ± 2.4 sequences using the fixed threshold and 3.3 ± 3.0 sequences using the individually based threshold), with most sequences composing of just 2 sprints. Additionally, central defenders performed fewer sprints (10.2 ± 4.1) than other positions (fullbacks: 28.1 ± 5.5; midfielders: 21.9 ± 10.5; forwards: 31.9 ± 11.1; with the differences being likely to almost certainly associated with effect sizes ranging from 1.65 to 2.72), and sprinting ability declined in the second half. The data do not support the notion that RSS occurs frequently during soccer matches in female players, irrespective of using fixed or individual speed thresholds to define sprint occurrence. However, repeated-sprint ability development cannot be ruled out from soccer training programs because of its association with match-related performance.

  15. A blackberry (Rubus L. expressed sequence tag library for the development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Main Dorrie S

    2008-06-01

    Full Text Available Abstract Background The recent development of novel repeat-fruiting types of blackberry (Rubus L. cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR, and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars. Results A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products. Conclusion This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.

  16. Methods for sequencing GC-rich and CCT repeat DNA templates

    Science.gov (United States)

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  17. Who Repeats Algebra, and How Does Initial Performance Relate to Improvement When the Course Is Repeated?

    Science.gov (United States)

    Fong, Anthony; Jaquet, Karina; Finkelstein, Neal

    2016-01-01

    The information provided in this report shows how students perform when they repeat algebra I and how the level of improvement varies depending on initial course performance and the academic measure (course grades or CST scores). This information can help inform decisions and policies regarding whether and under what circumstances students should…

  18. 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.

  19. Large cryptic internal sequence repeats in protein structures from Homo sapiens

    Indian Academy of Sciences (India)

    R Sarani; N A Udayaprakash; R Subashini; P Mridula; T Yamane; K Sekar

    2009-03-01

    Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensuring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats – be it structure, function or evolution – would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

  20. Localization of a new highly repeated DNA sequence of Lemur cafta (Lemuridae, Strepsirhini).

    Science.gov (United States)

    Boniotto, Michele; Ventura, Mario; Cardone, Maria Francesca; Boaretto, Francesca; Archidiacono, Nicoletta; Rocchi, Mariano; Crovella, Sergio

    2002-10-01

    We have isolated and cloned an 800-bp highly repeated DNA (HRDNA) sequence from Lemur catta (LCA) and described its localization on LCA chromosomes. Lemur catta HRDNA sequences were localized by performing FISH experiments on standard and elongated metaphasic chromosomes using an LCA HRDNA probe (LCASAT). A complex hybridization pattern was detected. A strong pericentromeric hybridization signal was observed on most LCA chromosomes. Chromosomes 7 and 13 were lit in pericentromeric regions, as well as in the interspersed heterochromatin. Chromosomes 1, 3, 4, 17, 19, X, and microchromosomes (20, 25, 26, and 27) showed no signals in the pericentromeric region, but chromosomes 3 and 4 showed a positive hybridization in heterochromatic regions. The 800-bp L catta HRDNA was species specific. We performed FISH experiments with the LCASAT probe on Eulemur macaco macaco (EMA) and Eulemur fulvus fulvus (EFU) metaphases and no positive signal of hybridization was detected. These findings were also confirmed by Southern blot analysis and PCR.

  1. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    Directory of Open Access Journals (Sweden)

    David H. Warshauer

    2015-08-01

    Full Text Available Massively parallel sequencing (MPS technology is capable of determining the sizes of short tandem repeat (STR alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics. The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

  2. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    Institute of Scientific and Technical Information of China (English)

    David H Warshauer; Jennifer D Churchill; Nicole Novroski; Jonathan L King; Bruce Budowle

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

  3. Differential distribution and association of repeat DNA sequences in the lateral element of the synaptonemal complex in rat spermatocytes.

    Science.gov (United States)

    Hernández-Hernández, Abrahan; Rincón-Arano, Héctor; Recillas-Targa, Félix; Ortiz, Rosario; Valdes-Quezada, Christian; Echeverría, Olga M; Benavente, Ricardo; Vázquez-Nin, Gerardo H

    2008-02-01

    The synaptonemal complex (SC) is an evolutionarily conserved structure that mediates synapsis of homologous chromosomes during meiotic prophase I. Previous studies have established that the chromatin of homologous chromosomes is organized in loops that are attached to the lateral elements (LEs) of the SC. The characterization of the genomic sequences associated with LEs of the SC represents an important step toward understanding meiotic chromosome organization and function. To isolate these genomic sequences, we performed chromatin immunoprecipitation assays in rat spermatocytes using an antibody against SYCP3, a major structural component of the LEs of the SC. Our results demonstrated the reproducible and exclusive isolation of repeat deoxyribonucleic acid (DNA) sequences, in particular long interspersed elements, short interspersed elements, long terminal direct repeats, satellite, and simple repeats. The association of these repeat sequences to the LEs of the SC was confirmed by in situ hybridization of meiotic nuclei shown by both light and electron microscopy. Signals were also detected over the chromatin surrounding SCs and in small loops protruding from the lateral elements into the SC central region. We propose that genomic repeat DNA sequences play a key role in anchoring the chromosome to the protein scaffold of the SC.

  4. Spectroscopic investigation on the telomeric DNA base sequence repeat

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Telomeres are protein-DNA complexes at the terminals of linear chromosomes, which protect chromosomal integrity and maintain cellular replicative capacity.From single-cell organisms to advanced animals and plants,structures and functions of telomeres are both very conservative. In cells of human and vertebral animals, telomeric DNA base sequences all are (TTAGGG)n. In the present work, we have obtained absorption and fluorescence spectra measured from seven synthesized oligonucleotides to simulate the telomeric DNA system and calculated their relative fluorescence quantum yields on which not only telomeric DNA characteristics are predicted but also possibly the shortened telomeric sequences during cell division are imrelative fluorescence quantum yield and remarkable excitation energy innerconversion, which tallies with the telomeric sequence of (TTAGGG)n. This result shows that telomeric DNA has a strong non-radiative or innerconvertible capability.``

  5. Plasmid P1 replication: negative control by repeated DNA sequences.

    OpenAIRE

    Chattoraj, D; Cordes, K.; Abeles, A

    1984-01-01

    The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

  6. Recombination frequency in plasmid DNA containing direct repeats--predictive correlation with repeat and intervening sequence length.

    Science.gov (United States)

    Oliveira, Pedro H; Lemos, Francisco; Monteiro, Gabriel A; Prazeres, Duarte M F

    2008-09-01

    In this study, a simple non-linear mathematical function is proposed to accurately predict recombination frequencies in bacterial plasmid DNA harbouring directly repeated sequences. The mathematical function, which was developed on the basis of published data on deletion-formation in multicopy plasmids containing direct-repeats (14-856 bp) and intervening sequences (0-3872 bp), also accounts for the strain genotype in terms of its recA function. A bootstrap resampling technique was used to estimate confidence intervals for the correlation parameters. More than 92% of the predicted values were found to be within a pre-established +/-5-fold interval of deviation from experimental data. The correlation does not only provide a way to predict, with good accuracy, the recombination frequency, but also opens the way to improve insight into these processes.

  7. Sequencing analysis of the spinal bulbar muscular atrophy CAG expansion reveals absence of repeat interruptions.

    Science.gov (United States)

    Fratta, Pietro; Collins, Toby; Pemble, Sally; Nethisinghe, Suran; Devoy, Anny; Giunti, Paola; Sweeney, Mary G; Hanna, Michael G; Fisher, Elizabeth M C

    2014-02-01

    Trinucleotide repeat disorders are a heterogeneous group of diseases caused by the expansion, beyond a pathogenic threshold, of unstable DNA tracts in different genes. Sequence interruptions in the repeats have been described in the majority of these disorders and may influence disease phenotype and heritability. Spinal bulbar muscular atrophy (SBMA) is a motor neuron disease caused by a CAG trinucleotide expansion in the androgen receptor (AR) gene. Diagnostic testing and previous research have relied on fragment analysis polymerase chain reaction to determine the AR CAG repeat size, and have therefore not been able to assess the presence of interruptions. We here report a sequencing study of the AR CAG repeat in a cohort of SBMA patients and control subjects in the United Kingdom. We found no repeat interruptions to be present, and we describe differences between sequencing and traditional sizing methods.

  8. Applications of inter simple sequence repeat (ISSR) rDNA in ...

    African Journals Online (AJOL)

    Applications of inter simple sequence repeat (ISSR) rDNA in detecting ... and phylogenetic relationships between Lymnaea natalensis collected from Giza, ... in water samples of all tested governorates with different significant differences.

  9. RePS: a sequence assembler that masks exact repeats identified from the shotgun data

    DEFF Research Database (Denmark)

    Wang, Jun; Wong, Gane Ka-Shu; Ni, Peixiang;

    2002-01-01

    We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing i...

  10. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.

    Directory of Open Access Journals (Sweden)

    Michael J McDonald

    2011-06-01

    Full Text Available The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution.

  11. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.

    Science.gov (United States)

    McDonald, Michael J; Wang, Wei-Chi; Huang, Hsien-Da; Leu, Jun-Yi

    2011-06-01

    The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels) with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution.

  12. Characterization of a highly repeated DNA sequence family in five species of the genus Eulemur.

    Science.gov (United States)

    Ventura, M; Boniotto, M; Cardone, M F; Fulizio, L; Archidiacono, N; Rocchi, M; Crovella, S

    2001-09-19

    The karyotypes of Eulemur species exhibit a high degree of variation, as a consequence of the Robertsonian fusion and/or centromere fission. Centromeric and pericentromeric heterochromatin of eulemurs is constituted by highly repeated DNA sequences (including some telomeric TTAGGG repeats) which have so far been investigated and used for the study of the systematic relationships of the different species of the genus Eulemur. In our study, we have cloned a set of repetitive pericentromeric sequences of five Eulemur species: E. fulvus fulvus (EFU), E. mongoz (EMO), E. macaco (EMA), E. rubriventer (ERU), and E. coronatus (ECO). We have characterized these clones by sequence comparison and by comparative fluorescence in situ hybridization analysis in EMA and EFU. Our results showed a high degree of sequence similarity among Eulemur species, indicating a strong conservation, within the five species, of these pericentromeric highly repeated DNA sequences.

  13. Repeat Associated Non-AUG Translation (RAN Translation Dependent on Sequence Downstream of the ATXN2 CAG Repeat.

    Directory of Open Access Journals (Sweden)

    Daniel R Scoles

    Full Text Available Spinocerebellar ataxia type 2 (SCA2 is a progressive autosomal dominant disorder caused by the expansion of a CAG tract in the ATXN2 gene. The SCA2 disease phenotype is characterized by cerebellar atrophy, gait ataxia, and slow saccades. ATXN2 mutation causes gains of toxic and normal functions of the ATXN2 gene product, ataxin-2, and abnormally slow Purkinje cell firing frequency. Previously we investigated features of ATXN2 controlling expression and noted expression differences for ATXN2 constructs with varying CAG lengths, suggestive of repeat associated non-AUG translation (RAN translation. To determine whether RAN translation occurs for ATXN2 we assembled various ATXN2 constructs with ATXN2 tagged by luciferase, HA or FLAG tags, driven by the CMV promoter or the ATXN2 promoter. Luciferase expression from ATXN2-luciferase constructs lacking the ATXN2 start codon was weak vs AUG translation, regardless of promoter type, and did not increase with longer CAG repeat lengths. RAN translation was detected on western blots by the anti-polyglutamine antibody 1C2 for constructs driven by the CMV promoter but not the ATXN2 promoter, and was weaker than AUG translation. Strong RAN translation was also observed when driving the ATXN2 sequence with the CMV promoter with ATXN2 sequence downstream of the CAG repeat truncated to 18 bp in the polyglutamine frame but not in the polyserine or polyalanine frames. Our data demonstrate that ATXN2 RAN translation is weak compared to AUG translation and is dependent on ATXN2 sequences flanking the CAG repeat.

  14. TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2007-01-01

    Full Text Available Abstract Background Solenoid repeat proteins of the Tetratrico Peptide Repeat (TPR family are involved as scaffolds in a broad range of protein-protein interactions. Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units. Results We have developed TPRpred, a profile-based method which uses a P-value-dependent score offset to include divergent repeat units and which exploits the tendency of repeats to occur in tandem. TPRpred detects not only TPR-like repeats, but also the related Pentatrico Peptide Repeats (PPRs and SEL1-like repeats. The corresponding profiles were generated through iterative searches, by varying the threshold parameters for inclusion of repeat units into the profiles, and the best profiles were selected based on their performance on proteins of known structure. We benchmarked the performance of TPRpred in detecting TPR-containing proteins and in delineating the individual repeats therein, against currently available resources. Conclusion TPRpred performs significantly better in detecting divergent repeats in TPR-containing proteins, and finds more individual repeats than the existing methods. The web server is available at http://tprpred.tuebingen.mpg.de, and the C++ and Perl sources of TPRpred along with the profiles can be downloaded from ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/.

  15. Hypoxic Repeat Sprint Training Improves Rugby Player's Repeated Sprint but Not Endurance Performance.

    Science.gov (United States)

    Hamlin, Michael J; Olsen, Peter D; Marshall, Helen C; Lizamore, Catherine A; Elliot, Catherine A

    2017-01-01

    This study aims to investigate the performance changes in 19 well-trained male rugby players after repeat-sprint training (six sessions of four sets of 5 × 5 s sprints with 25 s and 5 min of active recovery between reps and sets, respectively) in either normobaric hypoxia (HYP; n = 9; FIO2 = 14.5%) or normobaric normoxia (NORM; n = 10; FIO2 = 20.9%). Three weeks after the intervention, 2 additional repeat-sprint training sessions in hypoxia (FIO2 = 14.5%) was investigated in both groups to gauge the efficacy of using "top-up" sessions for previously hypoxic-trained subjects and whether a small hypoxic dose would be beneficial for the previously normoxic-trained group. Repeated sprint (8 × 20 m) and Yo-Yo Intermittent Recovery Level 1 (YYIR1) performances were tested twice at baseline (Pre 1 and Pre 2) and weekly after (Post 1-3) the initial intervention (intervention 1) and again weekly after the second "top-up" intervention (Post 4-5). After each training set, heart rate, oxygen saturation, and rate of perceived exertion were recorded. Compared to baseline (mean of Pre 1 and Pre 2), both the hypoxic and normoxic groups similarly lowered fatigue over the 8 sprints 1 week after the intervention (Post 1: -1.8 ± 1.6%, -1.5 ± 1.4%, mean change ± 90% CI in HYP and NORM groups, respectively). However, from Post 2 onwards, only the hypoxic group maintained the performance improvement compared to baseline (Post 2: -2.1 ± 1.8%, Post 3: -2.3 ± 1.7%, Post 4: -1.9 ± 1.8%, and Post 5: -1.2 ± 1.7%). Compared to the normoxic group, the hypoxic group was likely to have substantially less fatigue at Post 3-5 (-2.0 ± 2.4%, -2.2 ± 2.4%, -1.6 ± 2.4% Post 3, Post 4, Post 5, respectively). YYIR1 performances improved throughout the recovery period in both groups (13-37% compared to baseline) with unclear differences found between groups. The addition of two sessions of "top-up" training after intervention 1, had little effect on either group. Repeat-sprint training in

  16. Hypoxic Repeat Sprint Training Improves Rugby Player's Repeated Sprint but Not Endurance Performance

    Science.gov (United States)

    Hamlin, Michael J.; Olsen, Peter D.; Marshall, Helen C.; Lizamore, Catherine A.; Elliot, Catherine A.

    2017-01-01

    This study aims to investigate the performance changes in 19 well-trained male rugby players after repeat-sprint training (six sessions of four sets of 5 × 5 s sprints with 25 s and 5 min of active recovery between reps and sets, respectively) in either normobaric hypoxia (HYP; n = 9; FIO2 = 14.5%) or normobaric normoxia (NORM; n = 10; FIO2 = 20.9%). Three weeks after the intervention, 2 additional repeat-sprint training sessions in hypoxia (FIO2 = 14.5%) was investigated in both groups to gauge the efficacy of using “top-up” sessions for previously hypoxic-trained subjects and whether a small hypoxic dose would be beneficial for the previously normoxic-trained group. Repeated sprint (8 × 20 m) and Yo-Yo Intermittent Recovery Level 1 (YYIR1) performances were tested twice at baseline (Pre 1 and Pre 2) and weekly after (Post 1–3) the initial intervention (intervention 1) and again weekly after the second “top-up” intervention (Post 4–5). After each training set, heart rate, oxygen saturation, and rate of perceived exertion were recorded. Compared to baseline (mean of Pre 1 and Pre 2), both the hypoxic and normoxic groups similarly lowered fatigue over the 8 sprints 1 week after the intervention (Post 1: −1.8 ± 1.6%, −1.5 ± 1.4%, mean change ± 90% CI in HYP and NORM groups, respectively). However, from Post 2 onwards, only the hypoxic group maintained the performance improvement compared to baseline (Post 2: −2.1 ± 1.8%, Post 3: −2.3 ± 1.7%, Post 4: −1.9 ± 1.8%, and Post 5: −1.2 ± 1.7%). Compared to the normoxic group, the hypoxic group was likely to have substantially less fatigue at Post 3–5 (−2.0 ± 2.4%, −2.2 ± 2.4%, −1.6 ± 2.4% Post 3, Post 4, Post 5, respectively). YYIR1 performances improved throughout the recovery period in both groups (13–37% compared to baseline) with unclear differences found between groups. The addition of two sessions of “top-up” training after intervention 1, had little effect on either

  17. 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.

  18. Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species

    Science.gov (United States)

    Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n=384) harbored various SSR motifs. After eliminating the redundant seq...

  19. An ancient repeat sequence in the ATP synthase beta-subunit gene of forcipulate sea stars.

    Science.gov (United States)

    Foltz, David W

    2007-11-01

    A novel repeat sequence with a conserved secondary structure is described from two nonadjacent introns of the ATP synthase beta-subunit gene in sea stars of the order Forcipulatida (Echinodermata: Asteroidea). The repeat is present in both introns of all forcipulate sea stars examined, which suggests that it is an ancient feature of this gene (with an approximate age of 200 Mya). Both stem and loop regions show high levels of sequence constraint when compared to flanking nonrepetitive intronic regions. The repeat was also detected in (1) the family Pterasteridae, order Velatida and (2) the family Korethrasteridae, order Velatida. The repeat was not detected in (1) the family Echinasteridae, order Spinulosida, (2) the family Astropectinidae, order Paxillosida, (3) the family Solasteridae, order Velatida, or (4) the family Goniasteridae, order Valvatida. The repeat lacks similarity to published sequences in unrestricted GenBank searches, and there are no significant open reading frames in the repeat or in the flanking intron sequences. Comparison via parametric bootstrapping to a published phylogeny based on 4.2 kb of nuclear and mitochondrial sequence for a subset of these species allowed the null hypothesis of a congruent phylogeny to be rejected for each repeat, when compared separately to the published phylogeny. In contrast, the flanking nonrepetitive sequences in each intron yielded separate phylogenies that were each congruent with the published phylogeny. In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion.

  20. A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

    Science.gov (United States)

    Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

    1997-06-01

    In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

  1. Archery performance level and repeatability of event-related EMG.

    Science.gov (United States)

    Soylu, A R; Ertan, H; Korkusuz, F

    2006-12-01

    The purpose of the current study was to compare the repeatability of electromyographic linear envelopes (LE) of archery groups. Surface electromyography (EMG) signals of musculus flexor digitorum superficialis (MFDS) and extensor digitorum (MED) of 23 participants (seven skilled, six beginner archers and ten non-archers) were recorded during archery shooting. Two-second periods (clicker falls at first second) of 12 shots' EMG data were recorded, full-wave rectified and filtered (60 ms moving-average filter) for each participant's drawing arm. Repeatability was investigated by using a statistical criterion, variance ratio (VR). Archers' performances were evaluated in terms of FITA scores. The results showed that FITA scores were significantly correlated to the VRs of MFDS and MED. EMG LEs were more repeatable among archers than non-archers. Therefore, we inferred that VRs of MFDS and MED might be important variables for (a) assessing shooting techniques, (b) evaluation of archers' progress, and (c) selection of talented archers.

  2. Novel multiplex format of an extended multilocus variable-number-tandem-repeat analysis of Clostridium difficile correlates with tandem repeat sequence typing.

    Science.gov (United States)

    Jensen, Mie Birgitte Frid; Engberg, Jørgen; Larsson, Jonas T; Olsen, Katharina E P; Torpdahl, Mia

    2015-03-01

    Subtyping of Clostridium difficile is crucial for outbreak investigations. An extended multilocus variable-number tandem-repeat analysis (eMLVA) of 14 variable number tandem repeat (VNTR) loci was validated in multiplex format compatible with a routine typing laboratory and showed excellent concordance with tandem repeat sequence typing (TRST) and high discriminatory power.

  3. Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

    Science.gov (United States)

    Passos, Marco A. N.; de Oliveira Cruz, Viviane; Emediato, Flavia L.; de Camargo Teixeira, Cristiane; Souza, Manoel T.; Matsumoto, Takashi; Rennó Azevedo, Vânia C.; Ferreira, Claudia F.; Amorim, Edson P.; de Alencar Figueiredo, Lucio Flavio; Martins, Natalia F.; de Jesus Barbosa Cavalcante, Maria; Baurens, Franc-Christophe; da Silva, Orzenil Bonfim; Pappas, Georgios J.; Pignolet, Luc; Abadie, Catherine; Ciampi, Ana Y.; Piffanelli, Pietro; Miller, Robert N. G.

    2012-01-01

    Background and aims Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana–Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement. Methodology cDNA libraries were constructed from in vitro-infected leaves from BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5′-end Sanger sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs), with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases. Principal results A total of 9333 high-quality ESTs were obtained for MAC4 and 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed homology to genes encoding proteins with known or putative function, and 266 to genes encoding proteins with unknown function. Gene ontology (GO) classification identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes pathways. A total of 624 SSR loci were identified, with trinucleotide repeat motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across M. acuminata accessions was observed with 75 markers. Alleles per polymorphic locus ranged from 2 to 8, totalling 289. The polymorphism information content ranged from 0.08 to 0.81. Conclusions This EST collection offers a resource for studying functional genes, including

  4. The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats

    Institute of Scientific and Technical Information of China (English)

    Thomas Simonet; Elena Giulotto; Frederique Magdinier; Béatrice Horard; Pascal Barbry; Rainer Waldmann; Eric Gison; Laure-Emmanuelle Zaragosi; Claude Philippe; Kevin Lebrigand; Clémentine Schouteden; Adeline Augereau; Serge Bauwens; Jing Ye; Marco Santagostino

    2011-01-01

    The study of the proteins that bind to telomeric DNA in mammals has provided a deep understanding of the mech anisms involved in chromosome-end protection. However, very little is known on the binding of these proteins to nontelomeric DNA sequences. The TTAGGG DNA repeat proteins 1 and 2 (TRF1 and TRF2) bind to mammalian telomeres as part of the shelterin complex and are essential for maintaining chromosome end stability. In this study, we combined chromatin immunoprecipitation with high-throughput sequencing to map at high sensitivity and resolution the human chromosomal sites to which TRF1 and TRF2 bind. While most of the identified sequences correspond to telomeric regions, we showed that these two proteins also bind to extratelomeric sites. The vast majority of these extratelomeric sites contains interstitial telomeric sequences (or ITSs). However, we also identified non-iTS sites, which correspond to centromeric and pericentromeric satellite DNA. Interestingly, the TRF-binding sites are often located in the proximity of genes or within introns. We propose that TRF1 and TRF2 couple the functional state of telomeres to the long-range organization of chromosomes and gene regulation networks by binding to extratelomeric sequences.

  5. Spatio-temporal Variations of Characteristic Repeating Earthquake Sequences along the Middle America Trench in Mexico

    Science.gov (United States)

    Dominguez, L. A.; Taira, T.; Hjorleifsdottir, V.; Santoyo, M. A.

    2015-12-01

    Repeating earthquake sequences are sets of events that are thought to rupture the same area on the plate interface and thus provide nearly identical waveforms. We systematically analyzed seismic records from 2001 through 2014 to identify repeating earthquakes with highly correlated waveforms occurring along the subduction zone of the Cocos plate. Using the correlation coefficient (cc) and spectral coherency (coh) of the vertical components as selection criteria, we found a set of 214 sequences whose waveforms exceed cc≥95% and coh≥95%. Spatial clustering along the trench shows large variations in repeating earthquakes activity. Particularly, the rupture zone of the M8.1, 1985 earthquake shows an almost absence of characteristic repeating earthquakes, whereas the Guerrero Gap zone and the segment of the trench close to the Guerrero-Oaxaca border shows a significantly larger number of repeating earthquakes sequences. Furthermore, temporal variations associated to stress changes due to major shows episodes of unlocking and healing of the interface. Understanding the different components that control the location and recurrence time of characteristic repeating sequences is a key factor to pinpoint areas where large megathrust earthquakes may nucleate and consequently to improve the seismic hazard assessment.

  6. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae inferred from genomic in situ hybridization.

    Directory of Open Access Journals (Sweden)

    Sebastian Pita

    Full Text Available The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.

  7. Significance of satellite DNA revealed by conservation of a widespread repeat DNA sequence among angiosperms.

    Science.gov (United States)

    Mehrotra, Shweta; Goel, Shailendra; Raina, Soom Nath; Rajpal, Vijay Rani

    2014-08-01

    The analysis of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of plant nuclear DNA. In the present study, we analyzed the nature of pCtKpnI-I and pCtKpnI-II tandem repeated sequences, reported earlier in Carthamus tinctorius. Interestingly, homolog of pCtKpnI-I repeat sequence was also found to be present in widely divergent families of angiosperms. pCtKpnI-I showed high sequence similarity but low copy number among various taxa of different families of angiosperms analyzed. In comparison, pCtKpnI-II was specific to the genus Carthamus and was not present in any other taxa analyzed. The molecular structure of pCtKpnI-I was analyzed in various unrelated taxa of angiosperms to decipher the evolutionary conserved nature of the sequence and its possible functional role.

  8. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

    Science.gov (United States)

    Background: Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed S...

  9. Unstable microsatellite repeats facilitate rapid evolution of coding and regulatory sequences.

    Science.gov (United States)

    Jansen, A; Gemayel, R; Verstrepen, K J

    2012-01-01

    Tandem repeats are intrinsically highly variable sequences since repeat units are often lost or gained during replication or following unequal recombination events. Because of their low complexity and their instability, these repeats, which are also called satellite repeats, are often considered to be useless 'junk' DNA. However, recent findings show that tandem repeats are frequently found within promoters of stress-induced genes and within the coding regions of genes encoding cell-surface and regulatory proteins. Interestingly, frequent changes in these repeats often confer phenotypic variability. Examples include variation in the microbial cell surface, rapid tuning of internal molecular clocks in flies, and enhanced morphological plasticity in mammals. This suggests that instead of being useless junk DNA, some variable tandem repeats are useful functional elements that confer 'evolvability', facilitating swift evolution and rapid adaptation to changing environments. Since changes in repeats are frequent and reversible, repeats provide a unique type of mutation that bridges the gap between rare genetic mutations, such as single nucleotide polymorphisms, and highly unstable but reversible epigenetic inheritance.

  10. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  11. Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus.

    Science.gov (United States)

    Wei, Yunzhou; Chesne, Megan T; Terns, Rebecca M; Terns, Michael P

    2015-02-18

    CRISPR-Cas systems are RNA-based immune systems that protect prokaryotes from invaders such as phages and plasmids. In adaptation, the initial phase of the immune response, short foreign DNA fragments are captured and integrated into host CRISPR loci to provide heritable defense against encountered foreign nucleic acids. Each CRISPR contains a ∼100-500 bp leader element that typically includes a transcription promoter, followed by an array of captured ∼35 bp sequences (spacers) sandwiched between copies of an identical ∼35 bp direct repeat sequence. New spacers are added immediately downstream of the leader. Here, we have analyzed adaptation to phage infection in Streptococcus thermophilus at the CRISPR1 locus to identify cis-acting elements essential for the process. We show that the leader and a single repeat of the CRISPR locus are sufficient for adaptation in this system. Moreover, we identified a leader sequence element capable of stimulating adaptation at a dormant repeat. We found that sequences within 10 bp of the site of integration, in both the leader and repeat of the CRISPR, are required for the process. Our results indicate that information at the CRISPR leader-repeat junction is critical for adaptation in this Type II-A system and likely other CRISPR-Cas systems.

  12. Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease.

    Science.gov (United States)

    Wang, Yuh-Hwa

    2007-05-01

    In eukaryotic cells, chromatin structure organizes genomic DNA in a dynamic fashion, and results in regulation of many DNA metabolic processes. The CTG/CAG and CGG/CCG repeating sequences involved in several neuromuscular degenerative diseases display differential abilities for the binding of histone octamers. The effect of the repeating DNA on nucleosome assembly could be amplified as the number of repeats increases. Also, CpG methylation, and sequence interruptions within the triplet repeats exert an impact on the formation of nucleosomes along these repeating DNAs. The two most common triplet expansion human diseases, myotonic dystrophy 1 and fragile X syndrome, are caused by the expanded CTG/CAG and CGG/CCG repeats, respectively. In addition to the expanded repeats and CpG methylation, histone modifications, chromatin remodeling factors, and noncoding RNA have been shown to coordinate the chromatin structure at both myotonic dystrophy 1 and fragile X loci. Alterations in chromatin structure at these two loci can affect transcription of these disease-causing genes, leading to disease symptoms. These observations have brought a new appreciation that a full understanding of disease gene expression requires a knowledge of the structure of the chromatin domain within which the gene resides.

  13. A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Ravi Gupta

    2007-03-01

    Full Text Available The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period P or its multiple (i.e., 2P, 3P, etc., and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of O(NLw logLw, where N is the length of DNA sequence and Lw is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach.

  14. Characterisation data of simple sequence repeats of phages closely related to T7M

    Directory of Open Access Journals (Sweden)

    Tiao-Yin Lin

    2016-09-01

    Full Text Available Coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2 share high homology in genomic sequences. Simple sequence repeats (SSRs are found in their genomes and variations of SSRs among these phages are observed. Analyses on regions of sequences in T7M and T3 genomes that are likely derived from phage recombination, as well as the counterparts in ϕYeO3-12 and ϕSG-JL2, have been discussed by Lin in “Simple sequence repeat variations expedite phage divergence: mechanisms of indels and gene mutations” [1]. These regions are referred to as recombinant regions. The focus here is on SSRs in the whole genome and regions of sequences outside the recombinant regions, referred to as non-recombinant regions. This article provides SSR counts, relative abundance, relative density, and GC contents in the complete genome and non-recombinant regions of these phages. SSR period sizes and motifs in the non-recombinant regions of phage genomes are plotted. Genomic sequence changes between T7M and T3 due to insertions, deletions, and substitutions are also illustrated. SSRs and nearby sequences of T7M in the non-recombinant regions are compared to the sequences of ϕYeO3-12 and ϕSG-JL2 in the corresponding positions. The sequence variations of SSRs due to vertical evolution are classified into four categories and tabulated: (1 insertion/deletion of SSR units, (2 expansion/contraction of SSRs without alteration of genome length, (3 changes of repeat motifs, and (4 generation/loss of repeats.

  15. Effects of Hypohydration on Repeated 40-yd Sprint Performance.

    Science.gov (United States)

    Gann, Joshua J; Green, James M; OʼNeal, Eric K; Renfroe, Lee G; Andre, Thomas L

    2016-04-01

    This study examined the effects of hypohydration on repeated 40-yd sprint performance. Anaerobically fit current and former Division II male athletes (n = 12) completed 2 bouts of 10 × 40-yd sprints followed by an agility test, dehydrated (∼3% body weight [DT]), or hydrated trial (HT). Statistical analysis of group means indicated that hypohydration had little effect on sprint times for either the first (DT= 5.38 ± 0.37; HT = 5.35 ± 0.34) or second (DT = 5.47 ± 0.39; HT = 5.42 ± 0.39) bout of 10 sprints with only sprint number 2, 5, and 6 of bout 2 reaching statistical significance. However, when individual sprint performance was considered, a greater effect was seen. In all, 83% (10 of 12) of subjects experienced a meaningful change (≥0.1 seconds) (positive or negative) in mean sprint time (DT vs. HT) for one or more bout of 10 sprints. Ratings of perceived exertion was significantly higher (∼1 unit on a 10 point scale) for DT in all sprints during bout 1 and the first 2 sprints of bout 2. These results indicate that the effect of hypohydration on repeated sprint performance varies among individuals. Some improved performance with hypohydration, while others experienced detrimental effects. Hypohydration also resulted in a particularly notable negative impact on perceptual measures of exertion even when performance was similar.

  16. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  17. Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc..

    Directory of Open Access Journals (Sweden)

    Lidan Sun

    Full Text Available Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc. has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca, and apple (Malus×domestica genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb and almost twice as high as that of apple (398 SSR/Mb. Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs, with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.

  18. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

    Science.gov (United States)

    Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

    2011-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

  19. Tandem repeats and G-rich sequences are enriched at human CNV breakpoints.

    Directory of Open Access Journals (Sweden)

    Promita Bose

    Full Text Available Chromosome breakage in germline and somatic genomes gives rise to copy number variation (CNV responsible for genomic disorders and tumorigenesis. DNA sequence is known to play an important role in breakage at chromosome fragile sites; however, the sequences susceptible to double-strand breaks (DSBs underlying CNV formation are largely unknown. Here we analyze 140 germline CNV breakpoints from 116 individuals to identify DNA sequences enriched at breakpoint loci compared to 2800 simulated control regions. We find that, overall, CNV breakpoints are enriched in tandem repeats and sequences predicted to form G-quadruplexes. G-rich repeats are overrepresented at terminal deletion breakpoints, which may be important for the addition of a new telomere. Interstitial deletions and duplication breakpoints are enriched in Alu repeats that in some cases mediate non-allelic homologous recombination (NAHR between the two sides of the rearrangement. CNV breakpoints are enriched in certain classes of repeats that may play a role in DNA secondary structure, DSB susceptibility and/or DNA replication errors.

  20. Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans

    NARCIS (Netherlands)

    Li, Y.; Cooke, D.E.L.; Jacobsen, E.; Lee, van der T.A.J.

    2013-01-01

    Genotyping is fundamental to population analysis. To accommodate fast, accurate and cost-effective genotyping, a one-step multiplex PCR method employing twelve simple sequence repeat (SSR) markers was developed for high-throughput screening of Phytophthora infestans populations worldwide. The SSR

  1. The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers

    Directory of Open Access Journals (Sweden)

    Soraya Mousavi

    2017-07-01

    Full Text Available Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG, established in the years’ 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries. In the present study, a set of 370 olive trees previously uncharacterized was screened with 10 standard simple sequence repeats (SSRs and nine new EST-SSR markers, to correctly and thoroughly identify all genotypes, verify their representativeness of the entire cultivated olive variation, and validate the effectiveness of new markers in comparison to standard genotyping tools. The SSR analysis revealed the presence of 59 genotypes, corresponding to 72 well known cultivars, 13 of them resulting exclusively present in this collection. The new EST-SSRs have shown values of diversity parameters quite similar to those of best standard SSRs. When compared to hundreds of Mediterranean cultivars, the UNIPG olive accessions were splitted into the three main populations (East, Center and West Mediterranean, confirming that the collection has a good representativeness of the entire olive variability. Furthermore, Bayesian analysis, performed on the 59 genotypes of the collection by the use of both sets of markers, have demonstrated their splitting into four clusters, with a well balanced membership obtained by EST respect to standard SSRs. The new OLEST (Olea expressed sequence tags SSR markers resulted as effective as the best standard markers. The information obtained from this study represents a high valuable tool for ex situ conservation and management of olive genetic resources, useful to build a common database from worldwide olive

  2. Estimating thermal performance curves from repeated field observations

    Science.gov (United States)

    Childress, Evan; Letcher, Benjamin H.

    2017-01-01

    Estimating thermal performance of organisms is critical for understanding population distributions and dynamics and predicting responses to climate change. Typically, performance curves are estimated using laboratory studies to isolate temperature effects, but other abiotic and biotic factors influence temperature-performance relationships in nature reducing these models' predictive ability. We present a model for estimating thermal performance curves from repeated field observations that includes environmental and individual variation. We fit the model in a Bayesian framework using MCMC sampling, which allowed for estimation of unobserved latent growth while propagating uncertainty. Fitting the model to simulated data varying in sampling design and parameter values demonstrated that the parameter estimates were accurate, precise, and unbiased. Fitting the model to individual growth data from wild trout revealed high out-of-sample predictive ability relative to laboratory-derived models, which produced more biased predictions for field performance. The field-based estimates of thermal maxima were lower than those based on laboratory studies. Under warming temperature scenarios, field-derived performance models predicted stronger declines in body size than laboratory-derived models, suggesting that laboratory-based models may underestimate climate change effects. The presented model estimates true, realized field performance, avoiding assumptions required for applying laboratory-based models to field performance, which should improve estimates of performance under climate change and advance thermal ecology.

  3. Estimating thermal performance curves from repeated field observations.

    Science.gov (United States)

    Childress, Evan S; Letcher, Benjamin H

    2017-03-08

    Estimating thermal performance of organisms is critical for understanding population distributions and dynamics and predicting responses to climate change. Typically, performance curves are estimated using laboratory studies to isolate temperature effects, but other abiotic and biotic factors influence temperature-performance relationships in nature reducing these models' predictive ability. We present a model for estimating thermal performance curves from repeated field observations that includes environmental and individual variation. We fit the model in a Bayesian framework using MCMC sampling, which allowed for estimation of unobserved latent growth while propagating uncertainty. Fitting the model to simulated data varying in sampling design and parameter values demonstrated that the parameter estimates were accurate, precise, and unbiased. Fitting the model to individual growth data from wild trout revealed high out-of-sample predictive ability relative to laboratory-derived models, which produced more biased predictions for field performance. The field-based estimates of thermal maxima were lower than those based on laboratory studies. Under warming temperature scenarios, field-derived performance models predicted stronger declines in body size than laboratory-derived models, suggesting that laboratory-based models may underestimate climate change effects. The presented model estimates true, realized field performance, avoiding assumptions required for applying laboratory-based models to field performance, which should improve estimates of performance under climate change and advance thermal ecology. This article is protected by copyright. All rights reserved.

  4. Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

    Science.gov (United States)

    Tozaki, T; Inoue, S; Mashima, S; Ohta, M; Miura, N; Tomita, M

    2000-04-01

    Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

  5. Role of the striatum, cerebellum and frontal lobes in the automatization of a repeated visuomotor sequence of movements.

    Science.gov (United States)

    Doyon, J; Laforce, R; Bouchard, G; Gaudreau, D; Roy, J; Poirier, M; Bédard, P J; Bédard, F; Bouchard, J P

    1998-07-01

    Recently, Doyon et al. [20] demonstrated that lesions to both the striatum and to the cerebellum in humans produce a similar deficit in the learning of a repeated visuomotor sequence, which occurs late in the acquisition process. We now report the results of two experiments that were designed to examine whether this impairment was due to a lack of automatization of the repeating sequence of finger movements by using a dual-task paradigm and by testing for long-term retention of this skill. In Experiment 1, the performance of groups of patients with Parkinson's disease, or with damage to the cerebellum or to the frontal lobes, was compared to that of matched control subjects on the Repeated Sequence Test (primary task) and the Brooks' Matrices Test (secondary task). These two tests were administered concomitantly in both early and late learning phases of the visuomotor sequence. Overall, the groups did not differ in their ability to execute the primary task. By contrast, in accordance with the predictions, patients in Stages 2-3 of Parkinson's disease or with a cerebellar lesion failed to reveal the expected increase in performance on the secondary task seen with learning, suggesting that the latter groups of patients did not have access to the same level of residual cognitive resources to complete the matrices compared to controls. In Experiment 2, the same groups of patients and control subjects were retested again 10-18 months later. They were given four blocks of 100 trials each of the repeating sequence task, followed by a questionnaire and a self-generation task that measured their declarative knowledge of that sequence. The results revealed a long-term retention impairment only in patients who changed from Stage I to Stage II of the disease (suggesting further striatal degeneration) during the one-year interval, or who had a cerebellar lesion. By contrast, performance of the three clinical groups did not differ from controls on declarative memory tests. These

  6. Flexibility of Expressive Timing in Repeated Musical Performances

    Directory of Open Access Journals (Sweden)

    Alexander Pantelis Demos

    2016-10-01

    Full Text Available Performances by soloists in the Western classical tradition are normally highly prepared, yet must sound fresh and spontaneous. How do musicians manage this? We tested the hypothesis that they achieve the necessary spontaneity by varying the musical gestures that express their interpretation of a piece. We examined the tempo arches produced by final slowing at the ends of phrases in performances of J.S. Bach’s No. 6 (Prelude for solo cello (12 performances and the Italian Concerto (Presto for solo piano (8 performances. The performances were given by two experienced concert soloists during a short time period (3½ months for the Prelude, 2 weeks for the Presto after completing their preparations for public performance. We measured the tempo of each bar or half-bar, and the stability of tempo across performances (difference of the tempo of each bar/half bar from each of the other performances. There were phrase arches for both tempo and stability with slower, less stable tempi at beginnings and ends of phrases and faster, more stable tempi mid-phrase. The effects of practice were complex. Tempo decreased overall with practice, while stability increased in some bars and decreased in others. One effect of practice may be to imbue well-learned, automatic motor sequences with freshness and spontaneity through cognitive control at phrase boundaries where slower tempi and decreased stability provide opportunities for slower cognitive processes to modulate rapid automatic motor sequences.

  7. Flexibility of Expressive Timing in Repeated Musical Performances

    Science.gov (United States)

    Demos, Alexander P.; Lisboa, Tânia; Chaffin, Roger

    2016-01-01

    Performances by soloists in the Western classical tradition are normally highly prepared, yet must sound fresh and spontaneous. How do musicians manage this? We tested the hypothesis that they achieve the necessary spontaneity by varying the musical gestures that express their interpretation of a piece. We examined the tempo arches produced by final slowing at the ends of phrases in performances of J. S. Bach’s No. 6 (Prelude) for solo cello (12 performances) and the Italian Concerto (Presto) for solo piano (eight performances). The performances were given by two experienced concert soloists during a short time period (3½ months for the Prelude, 2 weeks for the Presto) after completing their preparations for public performance. We measured the tempo of each bar or half-bar, and the stability of tempo across performances (difference of the tempo of each bar/half bar from each of the other performances). There were phrase arches for both tempo and stability with slower, less stable tempi at beginnings and ends of phrases and faster, more stable tempi mid-phrase. The effects of practice were complex. Tempo decreased overall with practice, while stability increased in some bars and decreased in others. One effect of practice may be to imbue well-learned, automatic motor sequences with freshness and spontaneity through cognitive control at phrase boundaries where slower tempi and decreased stability provide opportunities for slower cognitive processes to modulate rapid automatic motor sequences. PMID:27757089

  8. Neck-cooling improves repeated sprint performance in the heat

    Directory of Open Access Journals (Sweden)

    Caroline eSunderland

    2015-11-01

    Full Text Available The present study evaluated the effect of neck-cooling during exercise on repeated sprint ability in a hot environment. Seven team-sport playing males completed two experimental trials involving repeated sprint exercise (5 x 6 s before and after two 45 min bouts of a football specific intermittent treadmill protocol in the heat (33.0  0.2 ºC; 53 ± 2% relative humidity. Participants wore a neck-cooling collar in one of the trials (CC. Mean power output and peak power output declined over time in both trials but were higher in CC (540 ± 99 v 507 ± 122W, d = 0.32; 719 ± 158 v 680 ± 182 W, d = 0.24 respectively. The improved power output was particularly pronounced (d = 0.51 – 0.88 after the 2nd 45 min bout but the CC had no effect on % fatigue. The collar lowered neck temperature and the thermal sensation of the neck (P 0.05. There were no trial differences but interaction effects were demonstrated for prolactin concentration and rating of perceived exertion (RPE. Prolactin concentration was initially higher in the collar cold trial and then was lower from 45 minutes onwards (interaction trial x time P=0.04. RPE was lower during the football intermittent treadmill protocol in the collar cold trial (interaction trial x time P = 0.01. Neck-cooling during exercise improves repeated sprint performance in a hot environment without altering physiological or neuroendocrinological responses. RPE is reduced and may partially explain the performance improvement.

  9. Carbohydrate mouth rinse does not improve repeated sprint performance

    Directory of Open Access Journals (Sweden)

    Leandro Ricardo Altimari

    2013-09-01

    Full Text Available The objective of this study was to evaluate the effect of a carbohydrate mouth rinse on the repeated sprint ability (RSA of young soccer players. Nine youth soccer players (15.0 ± 1.5 years; 60.7 ± 4.84 kg; 1.72 ± 0.05 m; 20.5 ± 1.25 kg/m2 were selected. The athletes were submitted to an RSA test consisting of six sprints of 40 m (going/return = 20 m + 20 m, separated by 20 s of passive recovery, under three experimental conditions: carbohydrate mouth rinse (CHO or placebo (PLA and control (CON. The mouth rinses containing CHO or PLA were administered 5 min and immediately before the beginning of the test in doses of 100 mL. The best sprint time (RSAbest, mean sprint time (RSAmean, and drop-off in sprint performance (fatigue index were determined for the different treatments. One-not identify significant differences (p> 0.05 in RSAbest (CHO way ANOVA for repeated measures did = 7.30 ± 0.31 s; PLA = 7.30 ± 0.30 s; CON = 7.26 ±0.16 s, RSA mean (CHO = 7.71 ± 0.30 s; PLA = 7.71 ± 0.25 s; CON = 7.66 ± 0.24s, or fatigue index (CHO = 5.58 ± 2.16%; PLA = 5.77 ± 3.04%; CON = 5.55 ±3.72%. The results suggest that a carbohydrate mouth rinse does not improve the repeated sprint performance of young soccer players.

  10. Expressed sequence tags (ESTs and simple sequence repeat (SSR markers from octoploid strawberry (Fragaria × ananassa

    Directory of Open Access Journals (Sweden)

    Bies Dawn H

    2005-06-01

    Full Text Available Abstract Background Cultivated strawberry (Fragaria × ananassa represents one of the most valued fruit crops in the United States. Despite its economic importance, the octoploid genome presents a formidable barrier to efficient study of genome structure and molecular mechanisms that underlie agriculturally-relevant traits. Many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases. As a first step to remedy this discrepancy a cDNA library has been developed from salicylate-treated, whole-plant tissues and over 1800 expressed sequence tags (EST's have been sequenced and analyzed. Results A putative unigene set of 1304 sequences – 133 contigs and 1171 singlets – has been developed, and the transcripts have been functionally annotated. Homology searches indicate that 89.5% of sequences share significant similarity to known/putative proteins or Rosaceae ESTs. The ESTs have been functionally characterized and genes relevant to specific physiological processes of economic importance have been identified. A set of tools useful for SSR development and mapping is presented. Conclusion Sequences derived from this effort may be used to speed gene discovery efforts in Fragaria and the Rosaceae in general and also open avenues of comparative mapping. This report represents a first step in expanding molecular-genetic analyses in strawberry and demonstrates how computational tools can be used to optimally mine a large body of useful information from a relatively small data set.

  11. Elevations in core and muscle temperature impairs repeated sprint performance

    DEFF Research Database (Denmark)

    Drust, B.; Rasmussen, P.; Mohr, Magni

    2005-01-01

    following the hyperthermic sprints compared to control. CONCLUSION: Although an elevated muscle temperature is expected to promote sprint performance, power output during the repeated sprints was reduced by hyperthermia. The impaired performance does not seem to relate to the accumulation of recognized...... on a cycle ergometer in normal (approximately 20 degrees C, control) and hot (40 degrees C, hyperthermia) environments. RESULTS: Completion of the intermittent protocol in the heat elevated core and muscle temperatures (39.5 +/- 0.2 degrees C; 40.2 +/- 0.4 degrees C), heart rate (178 +/- 11 beats min(-1......)), rating of perceived exertion (RPE) (18 +/- 1) and noradrenaline (38.9 +/- 13.2 micromol l(-1)) (all P power output were similar across the environmental conditions. However, mean power over the last four sprints declined to a larger extent...

  12. Repeated training with augmentative vibrotactile feedback increases object manipulation performance.

    Directory of Open Access Journals (Sweden)

    Cara E Stepp

    Full Text Available Most users of prosthetic hands must rely on visual feedback alone, which requires visual attention and cognitive resources. Providing haptic feedback of variables relevant to manipulation, such as contact force, may thus improve the usability of prosthetic hands for tasks of daily living. Vibrotactile stimulation was explored as a feedback modality in ten unimpaired participants across eight sessions in a two-week period. Participants used their right index finger to perform a virtual object manipulation task with both visual and augmentative vibrotactile feedback related to force. Through repeated training, participants were able to learn to use the vibrotactile feedback to significantly improve object manipulation. Removal of vibrotactile feedback in session 8 significantly reduced task performance. These results suggest that vibrotactile feedback paired with training may enhance the manipulation ability of prosthetic hand users without the need for more invasive strategies.

  13. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Science.gov (United States)

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  14. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Directory of Open Access Journals (Sweden)

    Chunsheng Gao

    Full Text Available Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.. Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99% were the most abundant, followed by hexanucleotide (25.13%, dinucleotide (16.34%, tetranucloetide (3.8%, and pentanucleotide (3.74% repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96% was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31% were successfully amplified and 87 (74.36% were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  15. Chromosomal localization of a tandemly repeated DNA sequence in Trifilium repens L.

    Institute of Scientific and Technical Information of China (English)

    ZHUJM; NWELLISON; 等

    1996-01-01

    A karyotype of Trifolium repens constructed from mitotic cells revealed 13 pairs of metacentric and 3 pairs of submetacentric chromosomes including a pair of satellites located at the end of the short arm of chromosome 16.C-bands were identified around the centromeric regions of 8 pairs of chromosomes.A 350 bp tandemly repeated DNAsequence from T.repens labelled with digoxygenin hybridized to the proximal centromeric regions of 12 chromosome pairs.Some correlation between the distribution of the repeat sequence and the distribution of C-banding was demonstrated.

  16. Application of inter simple sequence repeat (ISSR) markers to plant genetics.

    Science.gov (United States)

    Godwin, I D; Aitken, E A; Smith, L W

    1997-08-01

    Microsatellites or simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Single-locus SSR markers have been developed for a number of species, although there is a major bottleneck in developing SSR markers whereby flanking sequences must be known to design 5'-anchors for polymerase chain reaction (PCR) primers. Inter SSR (ISSR) fingerprinting was developed such that no sequence knowledge was required. Primers based on a repeat sequence, such as (CA)n, can be made with a degenerate 3'-anchor, such as (CA)8RG or (AGC)6TY. The resultant PCR reaction amplifies the sequence between two SSRs, yielding a multilocus marker system useful for fingerprinting, diversity analysis and genome mapping. PCR products are radiolabelled with 32P or 33P via end-labelling or PCR incorporation, and separated on a polyacrylamide sequencing gel prior to autoradiographic visualisation. A typical reaction yields 20-100 bands per lane depending on the species and primer. We have used ISSR fingerprinting in a number of plant species, and report here some results on two important tropical species, sorghum and banana. Previous investigators have demonstrated that ISSR analysis usually detects a higher level of polymorphism than that detected with restriction fragment length polymorphism (RFLP) or random amplified polymorphic DNA (RAPD) analyses. Our data indicate that this is not a result of greater polymorphism genetically, but rather technical reasons related to the detection methodology used for ISSR analysis.

  17. Linkage of congenital isolated adrenocorticotropic hormone deficiency to the corticotropin releasing hormone locus using simple sequence repeat polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Kyllo, J.H.; Collins, M.M.; Vetter, K.L. [Univ. of Iowa College of Medicine, Iowa City, IA (United States)] [and others

    1996-03-29

    Genetic screening techniques using simple sequence repeat polymorphisms were applied to investigate the molecular nature of congenital isolated adrenocorticotropic hormone (ACTH) deficiency. We hypothesize that this rare cause of hypocortisolism shared by a brother and sister with two unaffected sibs and unaffected parents is inherited as an autosomal recessive single gene mutation. Genes involved in the hypothalamic-pituitary axis controlling cortisol sufficiency were investigated for a causal role in this disorder. Southern blotting showed no detectable mutations of the gene encoding pro-opiomelanocortin (POMC), the ACTH precursor. Other candidate genes subsequently considered were those encoding neuroendocrine convertase-1, and neuroendocrine convertase-2 (NEC-1, NEC-2), and corticotropin releasing hormone (CRH). Tests for linkage were performed using polymorphic di- and tetranucleotide simple sequence repeat markers flanking the reported map locations for POMC, NEC-1, NEC-2, and CRH. The chromosomal haplotypes determined by the markers flanking the loci for POMC, NEC-1, and NEC-2 were not compatible with linkage. However, 22 individual markers defining the chromosomal haplotypes flanking CRH were compatible with linkage of the disorder to the immediate area of this gene of chromosome 8. Based on these data, we hypothesize that the ACTH deficiency in this family is due to an abnormality of CRH gene structure or expression. These results illustrate the useful application of high density genetic maps constructed with simple sequence repeat markers for inclusion/exclusion studies of candidate genes in even very small nuclear families segregating for unusual phenotypes. 25 refs., 5 figs., 2 tabs.

  18. Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers.

    Science.gov (United States)

    Batley, Jacqueline; Jewell, Erica; Edwards, David

    2007-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

  19. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

    Science.gov (United States)

    de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

    2015-11-16

    Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.

  20. Genotyping of simple sequence repeats--factors implicated in shadow band generation revisited.

    Science.gov (United States)

    Olejniczak, Marta; Krzyzosiak, Wlodzimierz J

    2006-10-01

    PCR amplification of microsatellite sequences generates, besides the main product corresponding to allele size, also additional, undesired products usually shorter by multiples of the repeated unit. These extra products known as shadow bands or stutter products may complicate genotyping. The mechanism by which these artifacts are formed is not well understood and so no effective remedy has been found to cope with these spurious products. In this study, using the DNA templates containing the CAG/CTG repeats flanked by gene-specific sequences and universal priming sites, we analyzed the effects of many PCR variables on the shadow band generation. The most important result was that at the decreased temperature of the denaturation step during PCR cycling the shadow bands were either not formed or were strongly suppressed. Several possible sources of this effect are discussed.

  1. In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

    Directory of Open Access Journals (Sweden)

    Evandro Vagner Tambarussi

    2009-01-01

    Full Text Available The availability of chloroplast genome (cpDNA sequences of Atropa belladonna, Nicotiana sylvestris, N.tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species,allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs incpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than geniccpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, pentaandhexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification ofnucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastomedatabase can be exploited for phylogenetic analysis and biotechnological approaches.

  2. Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

    Science.gov (United States)

    Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

    2011-01-01

    Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

  3. Comparison of highly repeated DNA sequences in some Lemuridae and taxonomic implications.

    Science.gov (United States)

    Montagnon, D; Crovella, S; Rumpler, Y

    1993-01-01

    Highly repeated DNA sequences of Eulemur fulvus mayottensis, E. coronatus, Lemur catta, and Hapalemur griseus griseus have been identified and compared. Sequence analysis of highly repeated DNA fragments isolated from L. catta and Hapalemur showed a high percentage of similarity (nearly 95%), as did fragments isolated from the two very close Eulemur species, whereas comparison of the DNA fragments isolated from the two Eulemur species and the L. catta/Hapalemur group showed a very low percentage (approximately 40%) of identity, as might be expected for distant species. These results confirm our previous data, obtained by Southern blot hybridization techniques on the same species, and strongly support the existence of a common trunk between L. catta and Hapalemur, but different from the leading to the Eulemur species.

  4. Cytogenetic analysis of Populus trichocarpa--ribosomal DNA, telomere repeat sequence, and marker-selected BACs.

    Science.gov (United States)

    Islam-Faridi, M N; Nelson, C D; DiFazio, S P; Gunter, L E; Tuskan, G A

    2009-01-01

    The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequence assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.

  5. Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

    Energy Technology Data Exchange (ETDEWEB)

    Tuskan, Gerald A [ORNL; Gunter, Lee E [ORNL; DiFazio, Stephen P [West Virginia University

    2009-01-01

    The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis -type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequence assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.

  6. Genetic Diversity Assessment and Identification of New Sour Cherry Genotypes Using Intersimple Sequence Repeat Markers

    OpenAIRE

    Roghayeh Najafzadeh; Kazem Arzani; Naser Bouzari; Ali Saei

    2014-01-01

    Iran is one of the chief origins of subgenus Cerasus germplasm. In this study, the genetic variation of new Iranian sour cherries (which had such superior growth characteristics and fruit quality as to be considered for the introduction of new cultivars) was investigated and identified using 23 intersimple sequence repeat (ISSR) markers. Results indicated a high level of polymorphism of the genotypes based on these markers. According to these results, primers tested in this study specially IS...

  7. Inter simple sequence repeat fingerprints for assess genetic diversity of tunisian garlic populations

    OpenAIRE

    Jabbes, Naouel; Geoffriau, Emmanuel; Le Clerc, Valérie; Dridi, Boutheina; Hannechi, Chérif

    2011-01-01

    Garlic (Allium sativum L.) that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR) genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used to detect diversity in garlic. ...

  8. Development and characterization of simple sequence repeats for Bipolaris sorokiniana and cross transferability to related species.

    Science.gov (United States)

    Fajolu, Oluseyi L; Wadl, Phillip A; Vu, Andrea L; Gwinn, Kimberly D; Scheffler, Brian E; Trigiano, Robert N; Ownley, Bonnie H

    2013-01-01

    Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n = 384) harbored SSR motifs. After eliminating redundant sequences, 196 SSR loci were identified, of which 84.7% were dinucleotide repeats and 9.7% and 5.6% were tri- and tetra-nucleotide repeats, respectively. Primer pairs were designed for 105 loci and 85 successfully amplified loci. Sixteen polymorphic loci were characterized with 15 B. sorokiniana isolates obtained from infected switchgrass plant materials collected from five states in USA. These loci successfully cross-amplified isolates from at least one related species, including Bipolaris oryzae, Bipolaris spicifera and Bipolaris victoriae, that causes leaf spot on switchgrass. Haploid gene diversity per locus across all isolates studied varied 0.633-0.861. Principal component analysis of SSR data clustered isolates according to their respective species. These SSR markers will be a valuable tool for genetic variability and population studies of B. sorokiniana and related species that are pathogenic on switchgrass and other host plants. In addition, these markers are potential diagnostic tools for species in the genus Bipolaris.

  9. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  10. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  11. Long CAG repeat sequence and protein expression of androgen receptor considered as prognostic indicators in male breast carcinoma.

    Directory of Open Access Journals (Sweden)

    Yan-Ni Song

    Full Text Available BACKGROUND: The androgen receptor (AR expression and the CAG repeat length within the AR gene appear to be involved in the carcinogenesis of male breast carcinoma (MBC. Although phenotypic differences have been observed between MBC and normal control group in AR gene, there is lack of correlation analysis between AR expression and CAG repeat length in MBC. The purpose of the study was to investigate the prognostic value of CAG repeat lengths and AR protein expression. METHODS: 81 tumor tissues were used for immunostaining for AR expression and CAG repeat length determination and 80 normal controls were analyzed with CAG repeat length in AR gene. The CAG repeat length and AR expression were analyzed in relation to clinicopathological factors and prognostic indicators. RESULTS: AR gene in many MBCs has long CAG repeat sequence compared with that in control group (P = 0.001 and controls are more likely to exhibit short CAG repeat sequence than MBCs. There was statistically significant difference in long CAG repeat sequence between AR status for MBC patients (P = 0.004. The presence of long CAG repeat sequence and AR-positive expression were associated with shorter survival of MBC patients (CAG repeat: P = 0.050 for 5y-OS; P = 0.035 for 5y-DFS AR status: P = 0.048 for 5y-OS; P = 0.029 for 5y-DFS, respectively. CONCLUSION: The CAG repeat length within the AR gene might be one useful molecular biomarker to identify males at increased risk of breast cancer development. The presence of long CAG repeat sequence and AR protein expression were in relation to survival of MBC patients. The CAG repeat length and AR expression were two independent prognostic indicators in MBC patients.

  12. Cytogenetic diversity of simple sequences repeats in morphotypes of Brassica rapa ssp. chinensis

    Directory of Open Access Journals (Sweden)

    Jinshuang Zheng

    2016-07-01

    Full Text Available A significant fraction of the nuclear DNA of all eukaryotes is occupied by simple sequence repeats (SSRs. Although thesis sequences have sparked great interest as a means of studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. This paper report the long-range organization of all possible classes of mono-, di- and tri-nucleotide SSRs in Brassica rapa. Fluorescence in situ hybridization (FISH was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphtypes of B. rapa, with trinucleotide SSRs more prevalent in the genome of B. rapa ssp. chinensis. The chromosomal characterizations of mono-, di- and tri-nucleotide repeats have been acquired. The data has revealed the non-random and motif-dependent chromosome distribution of SSRs in different morphtypes, and allowed the relative variability characterized by SSRs amount and similar chromosomal distribution in centromeric/peri-centromeric heterochromatin. The differences of SSRs in the abundance and distribution indicated the driving force of SSRs in relationship with the evolution of B. rapa species. The results provided a comprehensive view on the SSR sequence distribution and evolution for comparison among morphtypes B. rapa ssp. chinensis.

  13. Effective DNA fragmentation technique for simple sequence repeat detection with a microsatellite-enriched library and high-throughput sequencing.

    Science.gov (United States)

    Tanaka, Keisuke; Ohtake, Rumi; Yoshida, Saki; Shinohara, Takashi

    2017-04-01

    Two different techniques for genomic DNA fragmentation before microsatellite-enriched library construction-restriction enzyme (NlaIII and MseI) digestion and sonication-were compared to examine their effects on simple sequence repeat (SSR) detection using high-throughput sequencing. Tens of thousands of SSR regions from 5 species of the plant family Myrtaceae were detected when the output of individual samples was >1 million paired-end reads. Comparison of the two DNA fragmentation techniques showed that restriction enzyme digestion was superior to sonication for identification of heterozygous genotypes, whereas sonication was superior for detection of various SSR flanking regions with both species-specific and common characteristics. Therefore, choosing the most suitable DNA fragmentation method depends on the type of analysis that is planned.

  14. Simple Sequence Repeat Polymorphisms (SSRPs for Evaluation of Molecular Diversity and Germplasm Classification of Minor Crops

    Directory of Open Access Journals (Sweden)

    Nam-Soo Kim

    2009-11-01

    Full Text Available Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the protocols that facilitate the assessment of molecular diversity, SSRPs (simple sequence repeat polymorphisms or microsatellite variation is the preferred system since it detects a large number of DNA polymorphisms with relatively simple technical complexity. The paucity of information on DNA sequences has limited their widespread utilization in the assessment of genetic diversity of minor or neglected crop species. However, recent advancements in DNA sequencing and PCR technologies in conjunction with sophisticated computer software have facilitated the development of SSRP markers in minor crops. This review examines the development and molecular nature of SSR markers, and their utilization in many aspects of plant genetics and ecology.

  15. Genomic and polyploid evolution in genus Avena as revealed by RFLPs of repeated DNA sequences.

    Science.gov (United States)

    Morikawa, Toshinobu; Nishihara, Miho

    2009-06-01

    Phylogenetic relationships and genome affinities were investigated by utilizing all the biological Avena species consisting of 11 diploid species (15 accessions), 8 tetraploid species (9 accessions) and 4 hexaploid species (5 accessions). Genomic DNA regions of As120a, avenin, and globulin were amplified by PCR. A total of 130 polymorphic fragments were detected out of 156 fragments generated by digesting the PCR-amplified fragments with 11 restriction enzymes. The number of fragments generated by PCR-amplification followed by digestion with restriction enzymes was almost the same as those among the three repeated DNA sequences. A high level of genetic distance was detected between A. damascena (Ad) and A. canariensis (Ac) genomes, which reflected their different morphology and reproductive isolation. The A. longiglumis (Al) and A. prostrata (Ap) genomes were closely related to the As genome group. The AB genome species formed a cluster with the AsAs genome artificial autotetraploid and the As genome diploids indicating near-autotetraploid origin. The A. macrostachya is an outbreeding autotetraploid closely related with the C genome diploid and the AC genome tetraploid species. The differences of genetic distances estimated from the repeated DNA sequence divergence among the Avena species were consistent with genome divergences and it was possible to compare the genetic intra- and inter-ploidy relationships produced by RFLPs. These results suggested that the PCR-mediated analysis of repeated DNA polymorphism can be used as a tool to examine genomic relationships of polyploidy species.

  16. Isolation, characterization and amplification of simple sequence repeat loci in coffee

    Directory of Open Access Journals (Sweden)

    Marco-Aurelio Cristancho

    2008-01-01

    Full Text Available Simple sequence repeat (microsatellite loci in coffee were identified in clones isolated from enriched andrandom genomic libraries. It was shown that coffee is a plant species with low microsatellite frequency. However, the averagedistance between two loci, estimated at 127kb for poly (AG, is one of the shortest of all plant genomes. In contrast, thedistance between two poly (AC loci, estimated at 769kb, is one of the largest in plant genomes. Coffee (ACn microsatellites arefrequently associated with other microsatellites, mainly (ATn motifs, while (AGn microsatellites are not normally associatedwith other microsatellites and have a higher number of perfect motifs. Dinucleotide repeats (AG and (AC were found in ATrichregions in coffee. Sequence analysis of (ACn microsatellites identified in coffee revealed the possible association of theserepeated elements with miniature inverted-repeat transposable elements (MITEs. In addition, some of the evaluated SSRmarkers produced transposon-like amplification patterns in tetraploid genotypes. Of 12 SSR markers developed, nine werepolymorphic in diploid genotypes while 5 were polymorphic in tetraploid genotypes, confirming a greater genetic diversity indiploid species.

  17. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

    2013-04-01

    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  18. Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.

    Directory of Open Access Journals (Sweden)

    Eun Soo Seong

    2015-01-01

    Full Text Available Perilla frutescens is valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses of P. frutescens are limited due to a lack of gene annotations and characterization. A full-length cDNA library from P. frutescens leaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST homology searches and annotated Gene Ontology (GO. A total of 18 simple sequence repeats (SSRs were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers from P. frutescens will help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.

  19. Nuclear Receptor HNF4α Binding Sequences are Widespread in Alu Repeats

    Directory of Open Access Journals (Sweden)

    Bolotin Eugene

    2011-11-01

    Full Text Available Abstract Background Alu repeats, which account for ~10% of the human genome, were originally considered to be junk DNA. Recent studies, however, suggest that they may contain transcription factor binding sites and hence possibly play a role in regulating gene expression. Results Here, we show that binding sites for a highly conserved member of the nuclear receptor superfamily of ligand-dependent transcription factors, hepatocyte nuclear factor 4alpha (HNF4α, NR2A1, are highly prevalent in Alu repeats. We employ high throughput protein binding microarrays (PBMs to show that HNF4α binds > 66 unique sequences in Alu repeats that are present in ~1.2 million locations in the human genome. We use chromatin immunoprecipitation (ChIP to demonstrate that HNF4α binds Alu elements in the promoters of target genes (ABCC3, APOA4, APOM, ATPIF1, CANX, FEMT1A, GSTM4, IL32, IP6K2, PRLR, PRODH2, SOCS2, TTR and luciferase assays to show that at least some of those Alu elements can modulate HNF4α-mediated transactivation in vivo (APOM, PRODH2, TTR, APOA4. HNF4α-Alu elements are enriched in promoters of genes involved in RNA processing and a sizeable fraction are in regions of accessible chromatin. Comparative genomics analysis suggests that there may have been a gain in HNF4α binding sites in Alu elements during evolution and that non Alu repeats, such as Tiggers, also contain HNF4α sites. Conclusions Our findings suggest that HNF4α, in addition to regulating gene expression via high affinity binding sites, may also modulate transcription via low affinity sites in Alu repeats.

  20. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

    Science.gov (United States)

    Bahr, A; Thompson, J D; Thierry, J C; Poch, O

    2001-01-01

    BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg. fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2 /.

  1. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  2. Inter-simple sequence repeat (ISSR) loci mapping in the genome of perennial ryegrass

    DEFF Research Database (Denmark)

    Pivorienė, O; Pašakinskienė, I; Brazauskas, G;

    2008-01-01

    The aim of this study was to identify and characterize new ISSR markers and their loci in the genome of perennial ryegrass. A subsample of the VrnA F2 mapping family of perennial ryegrass comprising 92 individuals was used to develop a linkage map including inter-simple sequence repeat markers...... demonstrated a 70% similarity to the Hordeum vulgare germin gene GerA. Inter-SSR mapping will provide useful information for gene targeting, quantitative trait loci mapping and marker-assisted selection in perennial ryegrass....

  3. Behavior of Repeating Earthquake Sequences in Central California and the Implications for Subsurface Fault Creep

    Energy Technology Data Exchange (ETDEWEB)

    Templeton, D C; Nadeau, R; Burgmann, R

    2007-07-09

    Repeating earthquakes (REs) are sequences of events that have nearly identical waveforms and are interpreted to represent fault asperities driven to failure by loading from aseismic creep on the surrounding fault surface at depth. We investigate the occurrence of these REs along faults in central California to determine which faults exhibit creep and the spatio-temporal distribution of this creep. At the juncture of the San Andreas and southern Calaveras-Paicines faults, both faults as well as a smaller secondary fault, the Quien Sabe fault, are observed to produce REs over the observation period of March 1984-May 2005. REs in this area reflect a heterogeneous creep distribution along the fault plane with significant variations in time. Cumulative slip over the observation period at individual sequence locations is determined to range from 5.5-58.2 cm on the San Andreas fault, 4.8-14.1 cm on the southern Calaveras-Paicines fault, and 4.9-24.8 cm on the Quien Sabe fault. Creep at depth appears to mimic the behaviors seen of creep on the surface in that evidence of steady slip, triggered slip, and episodic slip phenomena are also observed in the RE sequences. For comparison, we investigate the occurrence of REs west of the San Andreas fault within the southern Coast Range. Events within these RE sequences only occurred minutes to weeks apart from each other and then did not repeat again over the observation period, suggesting that REs in this area are not produced by steady aseismic creep of the surrounding fault surface.

  4. Target genes of microsatellite sequences in head and neck squamous cell carcinoma: mononucleotide repeats are not detected.

    Science.gov (United States)

    Wang, Yimin; Liu, Xuejuan; Li, Yulin

    2012-09-10

    Microsatellite instability (MSI) is detected in a wide variety of tumors. It is thought that mismatch repair gene mutation or inactivation is the major cause of MSI. Microsatellite sequences are predominantly distributed in intergenic or intronic DNA. However, MSI is found in the exonic sequences of some genes, causing their inactivation. In this report, we searched GenBank for candidate genes containing potential MSI sequences in exonic regions. Twenty seven target genes were selected for MSI analysis. Instability was found in 70% of these genes (14/20) with head and neck squamous cell carcinoma (HNSCC). Interestingly, no instability was detected in mononucleotide repeats in genes or in intergenic sequences. We conclude that instability of mononucleotide repeats is a rare event in HNSCC. High MSI phenotype in young HNSCC patients is limited to noncoding regions only. MSI percentage in HNSCC tumor is closely related to the repeat type, repeat location and patient's age.

  5. The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiying; Zheng, Han; Preamplume, Gan; Shao, Yaming; Li, Hong [FSU

    2012-03-15

    The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of a noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.

  6. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

    Science.gov (United States)

    Wei, Xin; Wang, Linhai; Zhang, Yanxin; Qi, Xiaoqiong; Wang, Xiaoling; Ding, Xia; Zhang, Jing; Zhang, Xiurong

    2014-04-22

    Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

  7. Sequence alignment status and amplicon size difference affecting EST-SSR primer performance and polymorphism

    Science.gov (United States)

    Little attention has been given to failed, poorly-performing, and non-polymorphic expressed sequence tag (EST) simple sequence repeat (SSR) primers. This is due in part to a lack of interest and value in reporting them but also because of the difficulty in addressing the causes of failure on a prime...

  8. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

    Directory of Open Access Journals (Sweden)

    Park Jongsun

    2008-01-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs. Results We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST, which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations. Conclusion Taking our computational, statistical and experimental data together, we conclude that 1 the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2 the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3 there are different levels of evolutionary forces in variation of amino acid repeats, and 4 SSRs are stable molecular markers for genetic studies in N. crassa.

  9. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

    Indian Academy of Sciences (India)

    D. E. Jarvis; O. R. Kopp; E. N. Jellen; M. A. Mallory; J. Pattee; A. Bonifacio; C. E. Coleman; M. R. Stevens; D. J. Fairbanks; P. J. Maughan

    2008-04-01

    Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

  10. Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock.

    Directory of Open Access Journals (Sweden)

    Todd P Michael

    Full Text Available BACKGROUND: WHITE COLLAR-1 (WC-1 mediates interactions between the circadian clock and the environment by acting as both a core clock component and as a blue light photoreceptor in Neurospora crassa. Loss of the amino-terminal polyglutamine (NpolyQ domain in WC-1 results in an arrhythmic circadian clock; this data is consistent with this simple sequence repeat (SSR being essential for clock function. METHODOLOGY/PRINCIPAL FINDINGS: Since SSRs are often polymorphic in length across natural populations, we reasoned that investigating natural variation of the WC-1 NpolyQ may provide insight into its role in the circadian clock. We observed significant phenotypic variation in the period, phase and temperature compensation of circadian regulated asexual conidiation across 143 N. crassa accessions. In addition to the NpolyQ, we identified two other simple sequence repeats in WC-1. The sizes of all three WC-1 SSRs correlated with polymorphisms in other clock genes, latitude and circadian period length. Furthermore, in a cross between two N. crassa accessions, the WC-1 NpolyQ co-segregated with period length. CONCLUSIONS/SIGNIFICANCE: Natural variation of the WC-1 NpolyQ suggests a mechanism by which period length can be varied and selected for by the local environment that does not deleteriously affect WC-1 activity. Understanding natural variation in the N.crassa circadian clock will facilitate an understanding of how fungi exploit their environments.

  11. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.).

    Science.gov (United States)

    Jarvis, D E; Kopp, O R; Jellen, E N; Mallory, M A; Pattee, J; Bonifacio, A; Coleman, C E; Stevens, M R; Fairbanks, D J; Maughan, P J

    2008-04-01

    Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

  12. Molecular characterization of long terminal repeat sequences from Brazilian human immunodeficiency virus type 1 isolates.

    Science.gov (United States)

    Ferraro, Geraldo A; Monteiro-Cunha, Joana P; Fernandes, Flora M C; Mota-Miranda, Aline C A; Brites, Carlos; Alcantara, Luiz C J; Galvão-Castro, Bernardo; Morgado, Mariza G

    2013-05-01

    HIV-1 provirus activation is under control of the long terminal repeat (LTR)-5' viral promoter region, which presents remarkable genetic variation among HIV-1 subtypes. It is possible that molecular features of the LTR contribute to the unusual profile of the subtype C epidemic in the Brazilian Southern region. To characterize the LTR of Brazilian HIV isolates, we analyzed sequences from 21 infected individuals from Porto Alegre and Salvador cities. Sequences were compared with subtype B and C reference strains from different countries. Phylogenetic analysis showed that 17 (81%) samples were subtype B and four (19%) were subtype C. Common patterns of transcription factor binding sites (TFBS) in subtypes B and C sequences were confirmed and other potential TFBS specific for subtype C were found. Brazilian subtype C sequences contained an additional NF-κB biding site, as previously described for the majority of subtype C isolates. The high level of LTR polymorphisms identified in this study might be important for viral fitness.

  13. Detection of sequence variability of the collagen type IIalpha 1 3' variable number of tandem repeat.

    Science.gov (United States)

    van Meurs, J B; Arp, P P; Fang, Y; Slagboom, P E; Meulenbelt, I; van Leeuwen, J P; Pols, H A; Uitterlinden, A G

    2000-11-01

    The variable number of tandem repeat (VNTR) 3' of the collagen type II (COL2A1) gene has been shown to be highly variable with a complex molecular structure. In a previous pilot experiment we observed discordance between methods to genotype this informative marker. To further investigate the extent and molecular nature of this discordance, we genotyped a random sample of 207 Caucasian individuals with two genotyping methods and sequenced new alleles. We compared single-strand (SS) analysis, which is based on detection of size differences between the different alleles, and heteroduplex analysis (HA), which is sensitive to both size and sequence differences. Overall, 26% of discordance between the two methods was detected. Approximately two thirds of this discordance was caused by subdivision of SS-alleles 13R1 and 14R2 into HA-alleles 4A + 4B and 3B + 3C, respectively. Sequence analysis of the COL2A1 VNTR alleles 4B and 3C showed that these alleles differed in sequence, but not in size, from already described SS-alleles, which explains why they escape detection by SS. The 4B allele is a frequent allele in the population (14%) and is, therefore, important to distinguish in association studies. We conclude that HA is a reliable method when the described optimized electrophoretic conditions are used. HA is a sensitive genotyping method to document allelic diversity at this locus, which can distinguish more alleles compared to the SS method.

  14. Comparative sequence analysis of leucine-rich repeats (LRRs within vertebrate toll-like receptors

    Directory of Open Access Journals (Sweden)

    Taga Masae

    2007-05-01

    Full Text Available Abstract Background Toll-like receptors (TLRs play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T" and "bacterial" ("S". All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here. Results The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T" and sometimes short motifs including LxxLxLxxNxLxxLPx(xLPxx ("S". The TLR7 family (TLR7, TLR8, and TLR9 contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue. Conclusion Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These

  15. Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins

    Directory of Open Access Journals (Sweden)

    Povelones Michael

    2010-09-01

    Full Text Available Abstract Background The discovery and characterisation of factors governing innate immune responses in insects has driven the elucidation of many immune system components in mammals and other organisms. Focusing on the immune system responses of the malaria mosquito, Anopheles gambiae, has uncovered an array of components and mechanisms involved in defence against pathogen infections. Two of these immune factors are LRIM1 and APL1C, which are leucine-rich repeat (LRR containing proteins that activate complement-like defence responses against malaria parasites. In addition to their LRR domains, these leucine-rich repeat immune (LRIM proteins share several structural features including signal peptides, patterns of cysteine residues, and coiled-coil domains. Results The identification and characterisation of genes related to LRIM1 and APL1C revealed putatively novel innate immune factors and furthered the understanding of their likely molecular functions. Genomic scans using the shared features of LRIM1 and APL1C identified more than 20 LRIM-like genes exhibiting all or most of their sequence features in each of three disease-vector mosquitoes with sequenced genomes: An. gambiae, Aedes aegypti, and Culex quinquefasciatus. Comparative sequence analyses revealed that this family of mosquito LRIM-like genes is characterised by a variable number of 6 to 14 LRRs of different lengths. The "Long" LRIM subfamily, with 10 or more LRRs, and the "Short" LRIMs, with 6 or 7 LRRs, also share the signal peptide, cysteine residue patterning, and coiled-coil sequence features of LRIM1 and APL1C. The "TM" LRIMs have a predicted C-terminal transmembrane region, and the "Coil-less" LRIMs exhibit the characteristic LRIM sequence signatures but lack the C-terminal coiled-coil domains. Conclusions The evolutionary plasticity of the LRIM LRR domains may provide templates for diverse recognition properties, while their coiled-coil domains could be involved in the formation

  16. Survey and analysis of simple sequence repeats (SSRs) in three genomes of Candida species.

    Science.gov (United States)

    Jia, Dongmei

    2016-06-15

    Simple sequence repeats (SSRs) or microsatellites, which composed of tandem repeated short units of 1-6 bp, have been paying attention continuously. Here, the distribution, composition and polymorphism of microsatellites and compound microsatellites were analyzed in three available genomes of Candida species (Candida dubliniensis, Candida glabrata and Candida orthopsilosis). The results show that there were 118,047, 66,259 and 61,119 microsatellites in genomes of C. dubliniensis, C. glabrata and C. orthopsilosis, respectively. The SSRs covered more than 1/3 length of genomes in the three species. The microsatellites, which just consist of bases A and (or) T, such as (A)n, (T)n, (AT)n, (TA)n, (AAT)n, (TAA)n, (TTA)n, (ATA)n, (ATT)n and (TAT)n, were predominant in the three genomes. The length of microsatellites was focused on 6 bp and 9 bp either in the three genomes or in its coding sequences. What's more, the relative abundance (19.89/kbp) and relative density (167.87 bp/kbp) of SSRs in sequence of mitochondrion of C. glabrata were significantly great than that in any one of genomes or chromosomes of the three species. In addition, the distance between any two adjacent microsatellites was an important factor to influence the formation of compound microsatellites. The analysis may be helpful for further studying the roles of microsatellites in genomes' origination, organization and evolution of Candida species. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing

    Science.gov (United States)

    Castoe, Todd A.; Hall, Kathryn T.; Guibotsy Mboulas, Marcel L.; Gu, Wanjun; de Koning, A.P. Jason; Fox, Samuel E.; Poole, Alexander W.; Vemulapalli, Vijetha; Daza, Juan M.; Mockler, Todd; Smith, Eric N.; Feschotte, Cédric; Pollock, David D.

    2011-01-01

    We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus). These two genomes are both relatively small (∼1.4 Gb) but have surprisingly extensive differences in the abundance and expansion histories of their repeat elements. In the python, the readily identifiable repeat element content is low (21%), similar to bird genomes, whereas that of the copperhead is higher (45%), similar to mammalian genomes. The copperhead's greater repeat content arises from the recent expansion of many different microsatellites and transposable element (TE) families, and the copperhead had 23-fold greater levels of TE-related transcripts than the python. This suggests the possibility that greater TE activity in the copperhead is ongoing. Expansion of CR1 LINEs in the copperhead genome has resulted in TE-mediated microsatellite expansion (“microsatellite seeding”) at a scale several orders of magnitude greater than previously observed in vertebrates. Snakes also appear to be prone to horizontal transfer of TEs, particularly in the copperhead lineage. The reason that the copperhead has such a small genome in the face of so much recent expansion of repeat elements remains an open question, although selective pressure related to extreme metabolic performance is an obvious candidate. TE activity can affect gene regulation as well as rates of recombination and gene duplication, and it is therefore possible that TE activity played a role in the evolution of major adaptations in snakes; some evidence suggests this may include the evolution of venom repertoires. PMID:21572095

  18. Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats.

    Science.gov (United States)

    Ling, Alison; Cordaux, Richard

    2010-12-20

    Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.

  19. Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

    Directory of Open Access Journals (Sweden)

    Junjie Cui

    2017-06-01

    Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

  20. Nucleotide sequence, DNA damage location and protein stoichiometry influence base excision repair outcome at CAG/CTG repeats

    Science.gov (United States)

    Goula, Agathi-Vasiliki; Pearson, Christopher E.; Della Maria, Julie; Trottier, Yvon; Tomkinson, Alan E.; Wilson, David M.; Merienne, Karine

    2012-01-01

    Expansion of CAG/CTG repeats is the underlying cause of >fourteen genetic disorders, including Huntington’s disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. We provide molecular insights as to how base excision repair (BER) protein stoichiometry may contribute to the tissue-selective instability of CAG/CTG repeats by using specific repair assays. Oligonucleotide substrates with an abasic site were mixed with either reconstituted BER protein stoichiometries mimicking the levels present in HD mouse striatum or cerebellum, or with protein extracts prepared from HD mouse striatum or cerebellum. In both cases, repair efficiency at CAG/CTG repeats and at control DNA sequences was markedly reduced under the striatal conditions, likely due to the lower level of APE1, FEN1 and LIG1. Damage located towards the 5’ end of the repeat tract was poorly repaired accumulating incompletely processed intermediates as compared to an AP lesion in the centre or at the 3’ end of the repeats or within a control sequences. Moreover, repair of lesions at the 5’ end of CAG or CTG repeats involved multinucleotide synthesis, particularly under the cerebellar stoichiometry, suggesting that long-patch BER processes lesions at sequences susceptible to hairpin formation. Our results show that BER stoichiometry, nucleotide sequence and DNA damage position modulate repair outcome, and suggest that a suboptimal LP-BER activity promotes CAG/CTG repeat instability. PMID:22497302

  1. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution

    Directory of Open Access Journals (Sweden)

    Purves Joanne

    2012-09-01

    Full Text Available Abstract Background Staphylococcus aureus Repeat (STAR elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.

  2. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution.

    Science.gov (United States)

    Purves, Joanne; Blades, Matthew; Arafat, Yasrab; Malik, Salman A; Bayliss, Christopher D; Morrissey, Julie A

    2012-09-28

    Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.

  3. Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; SukHa Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7%of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2%were involved in cellular components, 24.2%were involved molecular functions, and 64.6%were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in

  4. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-02-01

    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  5. Complete genome sequence of a recombinant Marek's disease virus field strain with one reticuloendotheliosis virus long terminal repeat insert.

    Science.gov (United States)

    Su, Shuai; Cui, Ning; Cui, Zhizhong; Zhao, Peng; Li, Yanpeng; Ding, Jiabo; Dong, Xuan

    2012-12-01

    Marek's disease virus (MDV) Chinese strain GX0101, isolated in 2001 from a vaccinated flock of layer chickens with severe tumors, was the first reported recombinant MDV field strain with one reticuloendotheliosis virus (REV) long terminal repeat (LTR) insert. GX0101 belongs to very virulent MDV (vvMDV) but has higher horizontal transmission ability than the vvMDV strain Md5. The complete genome sequence of GX0101 is 178,101 nucleotides (nt) and contains only one REV-LTR insert at a site 267 nt upstream of the sorf2 gene. Moreover, GX0101 has 5 repeats of a 217-nt fragment in its terminal repeat short (TRS) region and 3 repeats in internal repeat short (IRS) region, compared to the other 10 strains with only 1 or 2 repeats in both TRS and IRS.

  6. Individual and population variation in invertebrates revealed by Inter-simple Sequence Repeats (ISSRs

    Directory of Open Access Journals (Sweden)

    Patrick Abbot

    2001-08-01

    Full Text Available PCR-based molecular markers are well suited for questions requiring large scale surveys of plant and animal populations. Inter-simple Sequence Repeats or ISSRs are analyzed by a recently developed technique based on the amplification of the regions between inverse-oriented microsatellite loci with oligonucleotides anchored in microsatellites themselves. ISSRs have shown much promise for the study of the population biology of plants, but have not yet been explored for similar studies of animals. The value of ISSRs is demonstrated for the study of animal species with low levels of within-population variation. Sets of primers are identified which reveal variation in two aphid species, Acyrthosiphon pisum and Pemphigus obesinymphae, in the yellow fever mosquito Aedes aegypti, and in a rotifer in the genus Philodina.

  7. Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis.

    Science.gov (United States)

    Li, Shufen; Zhang, Guojun; Li, Xu; Wang, Lianjun; Yuan, Jinhong; Deng, Chuanliang; Gao, Wujun

    2016-06-01

    Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species.

  8. Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.

    Science.gov (United States)

    Qian, Jun; Xu, Haibin; Song, Jingyuan; Xu, Jiang; Zhu, Yingjie; Chen, Shilin

    2013-01-10

    Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.

  9. Evidence for integration of retroviral vectors in a novel human repeat sequence

    Energy Technology Data Exchange (ETDEWEB)

    Kurdi-Haidar, B.; Friedmann, T. [USCD School of Medicine, La Jolla, CA (United States)

    1994-09-01

    Retroviruses have become attractive vehicles for the introduction of foreign genes into mammalian cells not only for gene therapy but also to serve as anchor points for long-range mapping purposes. The information relating to retroviral integration in mammalian cells is derived mostly from studies of rodent genomes. The absence of information regarding integration sites of murine-based retroviral vectors in human cells has prompted us to investigate the characteristics of integration sites in the human genome. We have constructed a Moloney murine leukemia virus-based retroviral vector that carries the pUC8 origin of replication and the chloramphenicol resistance gene to allow the rescue of the flanking genomic sequences in plasmid form. We have infected human primary fibroblasts and myoblasts with this retroviral vector and isolated independently transduced clones. Genomic DNA was obtained from independent clones and the genomic fragment carrying the provirus-host sequence boundary was isolated after digestion of the genomic DNA, circularization, and transformation by electroporation of E. coli C cells to chloramphenicol resistance. Restriction map and nucleotide sequence analysis of the rescued plasmids showed that a number of the clones shared the same integration site within the human genome. We have used the nucleotide sequence information about the human DNA adjacent to the 3{prime}LTR to design a PCR-based assay diagnostic for this common integration site. Analysis revealed the presence of the same integration site in four out of twelve human primary fibroblast clones infected with this specific retroviral vector, and in one out of twelve human primary myoblast clones infected with a second retroviral vector. Further analysis revealed the common integration site to be a previously unreported primate repeat present in monkey and human genomes and absent from rodent, bovine and avian genomes.

  10. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals.

    Science.gov (United States)

    Vukosavljev, M; Esselink, G D; van 't Westende, W P C; Cox, P; Visser, R G F; Arens, P; Smulders, M J M

    2015-01-01

    The first hurdle in developing microsatellite markers, cloning, has been overcome by next-generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6-20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.

  11. Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.

    Directory of Open Access Journals (Sweden)

    Daria A Beshnova

    2014-07-01

    Full Text Available The nucleosome repeat length (NRL is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.

  12. Repeated acquisition and performance chamber for mice: a paradigm for assessment of spatial learning and memory.

    Science.gov (United States)

    Brooks, A I; Cory-Slechta, D A; Murg, S L; Federoff, H J

    2000-11-01

    Molecular genetic manipulation of the mouse offers the possibility of elucidating the function of individual gene products in neural systems underlying learning and memory. Many extant learning paradigms for mice rely on negative reinforcement, involve simple problems that are relatively rapidly acquired and thus preclude time-course assessment, and may impose the need to undertake additional experiments to determine the extent to which noncognitive behaviors influence the measures of learning. To overcome such limitations, a multiple schedule of repeated acquisition and performance was behaviorally engineered to assess learning vs rote performance within-behavioral test session and within-subject utilizing an apparatus modified from the rat (the repeated acquisition and performance chamber; RAPC). The multiple schedule required mice to learn a new sequence of door openings leading to saccharin availability in the learning component during each session, while the sequence of door openings for the performance component remained constant across sessions. The learning and performance components alternated over the course of each test session, with different auditory stimuli signaling which component was currently in effect. To validate this paradigm, learning vs performance was evaluated in two inbred strains of mice: C57BL/6J and 129/SvJ. The hippocampal dependence of this measure was examined in lesioned C57BL/6J mice. Both strains exhibited longer latencies and higher errors in the learning compared to the performance component and evidenced declines in both measures across the trials of each session, consistent with an acquisition phenomenon. These same measures showed little or no evidence of change in the performance component. Whereas three trials per session were utilized with C57BL/65 mice in each component, behavior of 129/SvJ mice could only be sustained for two trials per component per session, demonstrating differences in testing capabilities between

  13. Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

    Directory of Open Access Journals (Sweden)

    Gabriel Dequigiovanni

    2012-01-01

    Full Text Available Simple Sequence Repeats (SSR are molecular markers suitable to assess the genetic variation of germplasm resources; however, large-scale SSR use requires protocol optimization. The present work aimed to identify SSR markers, developed for pear and other fruit species that are effective in characterizing pear germplasm collections and in demonstrating their use in providing support for genetic breeding programs. From a total of 62 SSR markers investigated, 23 yielding reproducible and polymorphic patterns were used to genotype a sample of 42 pear accessions of the Brazilian Pear Germplasm Bank (PGB. When compared to these 23 SSR markers, a subset of eleven markers, selected based on He, PIC and PId, was used to distinguish individual accessions and perform cluster analysis with similar efficacy. Genetic diversity analysis clustered the European, Japanese and Chinese accessions in distinct groups. This markers subset constitutes a valuable tool for several applications related to pear genetic resources management and breeding.

  14. Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi and related species

    Directory of Open Access Journals (Sweden)

    Odvody Gary N

    2008-11-01

    Full Text Available Abstract Background A recent outbreak of sorghum downy mildew in Texas has led to the discovery of both metalaxyl resistance and a new pathotype in the causal organism, Peronosclerospora sorghi. These observations and the difficulty in resolving among phylogenetically related downy mildew pathogens dramatically point out the need for simply scored markers in order to differentiate among isolates and species, and to study the population structure within these obligate oomycetes. Here we present the initial results from the use of a biotin capture method to discover, clone and develop PCR primers that permit the use of simple sequence repeats (microsatellites to detect differences at the DNA level. Results Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55% with dinucleotide repeats and 6 (11% with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abundant (40% and GA/AG or CT/TC types contribute 15% in our collection. When used to amplify DNA from 19 isolates from P. sorghi, as well as from 5 related species that cause downy mildew on other hosts, the number of different bands detected for each SSR primer pair using a LI-COR- DNA Analyzer ranged from two to eight. Successful cross-amplification for 12 primer pairs studied in detail using DNA from downy mildews that attack maize (P. maydis & P. philippinensis, sugar cane (P. sacchari, pearl millet (Sclerospora graminicola and rose (Peronospora sparsa indicate that the flanking regions are conserved in all these species. A total of 15 SSR amplicons unique to P. philippinensis (one of the potential threats to US maize production were detected, and these have potential for development of diagnostic tests. A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34

  15. Long terminal repeat sequences from virulent and attenuated equine infectious anemia virus demonstrate distinct promoter activities.

    Science.gov (United States)

    Zhou, Tao; Yuan, Xiu-Fang; Hou, Shao-Hua; Tu, Ya-Bin; Peng, Jin-Mei; Wen, Jian-Xin; Qiu, Hua-Ji; Wu, Dong-Lai; Chen, Huan-Chun; Wang, Xiao-Jun; Tong, Guang-Zhi

    2007-09-01

    In the early 1970s, the Chinese Equine Infectious Anemia Virus (EIAV) vaccine, EIAV(DLA), was developed through successive passages of a wild-type virulent virus (EIAV(L)) in donkeys in vivo and then in donkey macrophages in vitro. EIAV attenuation and cell tropism adaptation are associated with changes in both envelope and long terminal repeat (LTR). However, specific LTR changes during Chinese EIAV attenuation have not been demonstrated. In this study, we compared LTR sequences from both virulent and attenuated EIAV strains and documented the diversities of LTR sequence from in vivo and in vitro infections. We found that EIAV LTRs of virulent strains were homologous, while EIAV vaccine have variable LTRs. Interestingly, experimental inoculation of EIAV(DLA) into a horse resulted in a restriction of the LTR variation. Furthermore, LTRs from EIAV(DLA) showed higher Tat transactivated activity than LTRs from virulent strains. By using chimeric clones of wild-type LTR and vaccine LTR, the main difference of activity was mapped to the changes of R region, rather than U3 region.

  16. Transcriptome characterisation and simple sequence repeat marker discovery in the seagrass Posidonia oceanica

    Science.gov (United States)

    D’Esposito, D.; Orrù, L.; Dattolo, E.; Bernardo, L.; Lamontara, A.; Orsini, L.; Serra, I.A; Mazzuca, S.; Procaccini, G.

    2016-01-01

    Posidonia oceanica is an endemic seagrass in the Mediterranean Sea, where it provides important ecosystem services and sustains a rich and diverse ecosystem. P. oceanica meadows extend from the surface to 40 meters depth. With the aim of boosting research in this iconic species, we generated a comprehensive RNA-Seq data set for P. oceanica by sequencing specimens collected at two depths and two times during the day. With this approach we attempted to capture the transcriptional diversity associated with change in light and other depth-related environmental factors. Using this extensive data set we generated gene predictions and identified an extensive catalogue of potential Simple Sequence Repeats (SSR) markers. The data generated here will open new avenues for the analysis of population genetic features and functional variation in P. oceanica. In total, 79,235 contigs were obtained by the assembly of 70,453,120 paired end reads. 43,711 contigs were successfully annotated. A total of 17,436 SSR were identified within 13,912 contigs. PMID:27996971

  17. Creation and structure determination of an artificial protein with three complete sequence repeats

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Motoyasu, E-mail: adachi.motoyasu@jaea.go.jp; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)

    2013-11-01

    An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine–glycine sequences of Symfoil-4P are replaced with glutamine–glycine (Symfoil-QG) or serine–glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of

  18. Characterization of comparative genome-derived simple sequence repeats for acanthopterygian fishes.

    Science.gov (United States)

    Gotoh, Ryo O; Tamate, Satoshi; Yokoyama, Jun; Tamate, Hidetoshi B; Hanzawa, Naoto

    2013-05-01

    Simple sequence repeats (SSRs) have become one of the most popular molecular markers for population genetic studies. The application of SSR markers has often been limited to source species because SSR loci are too labile to be maintained in even closely related species. However, a few extremely conserved SSR loci have been reported. Here, we tested for the presence of conserved SSR loci in acanthopterygian fishes, which include over 14 000 species, by comparing the genome sequences of four acanthopterygian fishes. We also examined the comparative genome-derived SSRs (CG-SSRs) for their transferability across acanthopterygian fishes and their applicability to population genetic analysis. Forty-six SSR loci with conserved flanking regions were detected and examined for their transferability among seven nonacanthopterygian and 27 acanthopterygian fishes. The PCR amplification success rate in nonacanthopterygian fishes was low, ranging from 2.2% to 21.7%, except for Lophius litulon (Lophiiformes; 80.4%). Conversely, the rate in most acanthopterygian fishes exceeded 70.0%. Sequencing of these 46 loci revealed the presence of SSRs suitable for scoring while fragment analysis of 20 loci revealed polymorphisms in most of the acanthopterygian fishes. Population genetic analysis of Cottus pollux (Scorpaeniformes) and Sphaeramia orbicularis (Perciformes) using CG-SSRs showed that these populations did not deviate from linkage equilibrium or Hardy-Weinberg equilibrium. Furthermore, almost no loci showed evidence of null alleles, suggesting that CG-SSRs have strong resolving power for population genetic analysis. Our findings will facilitate the use of these markers in species in which markers remain to be identified.

  19. Next generation sequencing (NGS database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Directory of Open Access Journals (Sweden)

    Chinta Someswara Rao

    2016-03-01

    Full Text Available Next generation sequencing (NGS technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  20. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S. Viswanadha

    2016-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  1. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching.

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  2. Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

    Science.gov (United States)

    Hamblin, Martha T.; Warburton, Marilyn L.; Buckler, Edward S.

    2007-01-01

    While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system. PMID:18159250

  3. Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome.

    Science.gov (United States)

    Tang, Xiaomin; Datema, Erwin; Guzman, Myriam Olortegui; de Boer, Jan M; van Eck, Herman J; Bachem, Christian W B; Visser, Richard G F; de Jong, Hans

    2014-12-01

    One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.

  4. Performances of regenerative and non-regenerative satellite repeaters with MPSK signalling

    Science.gov (United States)

    Woo, K. T.

    1978-01-01

    Linear (translation), hard-limited, and demod/remod types of satellite repeaters are considered in this paper. Both uncoded and coded multiple phase shift keyed (MPSK) signals are assumed to be transmitted through these repeaters. Relative performances of these repeaters in the presence of uplink and downlink noises are then compared quantitatively. Probabilities of bit errors and the computational cutoff rates are computed for 2, 4, and 8 phases PSK signals, with uplink and downlink SNRs as parameters.

  5. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.

    Science.gov (United States)

    Gao, Song; Bertrand, Denis; Chia, Burton K H; Nagarajan, Niranjan

    2016-05-11

    The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.

  6. Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici.

    Science.gov (United States)

    Orquera-Tornakian, Gabriela K; Garrido, Patricia; Kronmiller, Brent; Hunger, Robert; Tyler, Brett M; Garzon, Carla D; Marek, Stephen M

    2017-08-01

    Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Identification and Analysis of Novel Amino-Acid Sequence Repeats in Bacillus anthracis str. Ames Proteome Using Computational Tools

    Directory of Open Access Journals (Sweden)

    D. Satyanarayana Rao

    2007-02-01

    Full Text Available We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1 57-amino-acid-residue PxV domain, (2 122-amino-acid-residue FxF domain, (3 111-amino-acid-residue YEFF domain, (4 109-amino-acid-residue IMxxH domain, (5 103-amino-acid-residue VxxT domain, (6 84-amino-acid-residue ExW domain, (7 104-amino-acid-residue NTGFIG domain, (8 36-amino-acid-residue NxGK repeat, (9 95-amino-acid-residue VYV domain, (10 75-amino-acid-residue KEWE domain, (11 59-amino-acid-residue AFL domain, (12 53-amino-acid-residue RIDVK repeat, (13 (a 41-amino-acid-residue AGQF repeat and (b 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

  8. Genetic Diversity Assessment and Identification of New Sour Cherry Genotypes Using Intersimple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Roghayeh Najafzadeh

    2014-01-01

    Full Text Available Iran is one of the chief origins of subgenus Cerasus germplasm. In this study, the genetic variation of new Iranian sour cherries (which had such superior growth characteristics and fruit quality as to be considered for the introduction of new cultivars was investigated and identified using 23 intersimple sequence repeat (ISSR markers. Results indicated a high level of polymorphism of the genotypes based on these markers. According to these results, primers tested in this study specially ISSR-4, ISSR-6, ISSR-13, ISSR-14, ISSR-16, and ISSR-19 produced good and various levels of amplifications which can be effectively used in genetic studies of the sour cherry. The genetic similarity among genotypes showed a high diversity among the genotypes. Cluster analysis separated improved cultivars from promising Iranian genotypes, and the PCoA supported the cluster analysis results. Since the Iranian genotypes were superior to the improved cultivars and were separated from them in most groups, these genotypes can be considered as distinct genotypes for further evaluations in the framework of breeding programs and new cultivar identification in cherries. Results also confirmed that ISSR is a reliable DNA marker that can be used for exact genetic studies and in sour cherry breeding programs.

  9. The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

    Science.gov (United States)

    Zou, Geng; Bello-Orti, Bernardo; Aragon, Virginia; Tucker, Alexander W.; Luo, Rui; Ren, Pinxing; Bi, Dingren; Zhou, Rui; Jin, Hui

    2015-01-01

    Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales, and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3, and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation. PMID:26215592

  10. Molecular identification of Aquilaria spp. by using inter-simple sequence repeat (ISSR)

    Science.gov (United States)

    Azhari, Hanif; Mohamad, Azhar; Othman, Roohaida

    2015-09-01

    Aquilaria species are very important economic plant for production of resin locally known as gaharu in Malaysia. There are five species that can be found in Malaysia and the most important Aquilaria species for gaharu production is A. malaccensis. Molecular markers for Aquilaria species are still insufficient and require more efficient, robust and reproducible molecular marker. Inter-simple sequence repeat (ISSR) markers are highly polymorphic and have high reproducibility which will be useful in areas of genetic diversity, phylogenetic studies, gene tagging, genome mapping and evolutionary biology in a wide range of crop species. Five selected ISSR primers were used to identify four Aquilaria species commonly found in Malaysia namely A. malaccensis, A. sub-integra, A. crassna and A. hirta. All the primers showed sufficient polymorphism to distinguish between the four species. Hence, the markers derived from ISSR can be used for molecular identification of Aquilaria spp. in ensuring homogenous species for plantation which may improve the quality of resin derived from known and certified materials.

  11. Agarose gel electrophoresis and polyacrylamide gel electrophoresis for visualization of simple sequence repeats.

    Science.gov (United States)

    Anderson, James; Wright, Drew; Meksem, Khalid

    2013-01-01

    In the modern age of genetic research there is a constant search for ways to improve the efficiency of plant selection. The most recent technology that can result in a highly efficient means of selection and still be done at a low cost is through plant selection directed by simple sequence repeats (SSRs or microsatellites). The molecular markers are used to select for certain desirable plant traits without relying on ambiguous phenotypic data. The best way to detect these is the use of gel electrophoresis. Gel electrophoresis is a common technique in laboratory settings which is used to separate deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) by size. Loading DNA and RNA onto gels allows for visualization of the size of fragments through the separation of DNA and RNA fragments. This is achieved through the use of the charge in the particles. As the fragments separate, they form into distinct bands at set sizes. We describe the ability to visualize SSRs on slab gels of agarose and polyacrylamide gel electrophoresis.

  12. Genetic characterization of the gypsy moth from China (Lepidoptera, Lymantriidae using inter simple sequence repeats markers.

    Directory of Open Access Journals (Sweden)

    Fang Chen

    Full Text Available This study provides the first genetic characterization of the gypsy moth from China (Lymantriadispar, one of the most recognized pests of forests and ornamental trees in the world. We assessed genetic diversity and structure in eight geographic populations of gypsy moths from China using five polymorphic Inter simple sequence repeat markers, which produced reproducible banding patterns. We observed 102 polymorphic loci across the 176 individuals sampled. Overall genetic diversity (Nei's, H was 0.2357, while the mean genetic diversity within geographic populations was 0.1845 ± 0.0150. The observed genetic distance among the eight populations ranged from 0.0432 to 0.1034. Clustering analysis (using an unweighted pair-group method with arithmetic mean and multidimensional scaling, revealed strong concordance between the strength of genetic relationships among populations and their geographic proximity. Analysis of molecular variance demonstrated that 25.43% of the total variability (F ST = 0.2543, P < 0.001 was attributable to variation among geographic populations. The results of our analyses investigating the degree of polymorphism, genetic diversity (Nei's and Shannon and genetic structure, suggest that individuals from Hebei may be better able to adapt to different environments and to disperse to new habitats. This study provides crucial genetic information needed to assess the distribution and population dynamics of this important pest species of global concern.

  13. Genetic diversity analysis of Lepidium sativum (Chandrasur) using inter simple sequence repeat (ISSR) markers

    Institute of Scientific and Technical Information of China (English)

    Amandeep Kaur; Rakesh Kumar; Suman Rani; Anita Grewal

    2015-01-01

    Lepidium sativum (commonly known as garden cress) belongs to the family Brassicaceae. It is a fast-growing erect, annual herbaceous plant. Its seeds possess significant fracture healing, anti-asthmatic, anti-diabetic, hypoglycemic, nephrocurative and nephroprotective activ-ities. In the present study, we assessed the genetic diversity of various genotypes of L. sativum using inter-simple sequence repeat (ISSR) markers. Out of 41 ISSR primers screened, 32 primers showed significant, clear and repro-ducible bands. A total of 510 amplified bands were obtained using 32 ISSR primers, out of which 422 bands were poly-morphic and 88 bands were monomorphic. The percentage of polymorphism was found to be 82. A total of 35 unique alleles ranging insize from 200 to 2,900 bp were observed. Cluster analysis based on unweighted pair-group method, arithmetic mean divided the 18 genotypes into two main clusters, with the first having only HCS-08 genotype of L. sativum and other having all of the other 17 genotypes. The Jaccard similarity coefficient revealed a broad range 32–72%genetic relatedness among the 18 genotypes.

  14. Simple Sequence Repeat Genetic Linkage Maps of A-genome Diploid Cotton (Gossypium arboreum)

    Institute of Scientific and Technical Information of China (English)

    Xue-Xia Ma; Bao-Liang Zhou; Yan-Hui Lü; Wang-Zhen Guo; Tian-Zhen Zhang

    2008-01-01

    This study introduces the construction of the first intraspacific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F2 plants derived from the cross of two Asiatic parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR pdmers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, Including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) ≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.

  15. Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs

    Directory of Open Access Journals (Sweden)

    Sadiye Peral Eyduran

    2016-01-01

    Full Text Available In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively, whereas the lowest number was recorded in VrZAG83 (three alleles per locus. Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

  16. Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome

    Directory of Open Access Journals (Sweden)

    Vandamme Peter

    2003-03-01

    Full Text Available Abstract Background Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and compositon of simple sequence repeats (SSRs between both replicons and also compared the respective compositional biases. Results Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed. Conclusions The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome.

  17. Simple Sequence Repeat Analysis of Selected NSIC-registered Coffee Varieties in the Philippines

    Directory of Open Access Journals (Sweden)

    Daisy May C. Santos

    2016-06-01

    Full Text Available Coffee (Coffea sp. is an important commercial crop worldwide. Three species of coffee are used as beverage, namely Coffea arabica, C. canephora, and C. liberica. Coffea arabica L. is the most cultivated among the three coffee species due to its taste quality, rich aroma, and low caffeine content. Despite its inferior taste and aroma, C. canephora Pierre ex A. Froehner, which has the highest caffeine content, is the second most widely cultivated because of its resistance to coffee diseases. On the other hand, C. liberica W.Bull ex Hierncomes is characterized by its very strong taste and flavor. The Philippines used to be a leading exporter of coffee until coffee rust destroyed the farms in Batangas, home of the famous Kapeng Barako. The country has been attempting to revive the coffee industry by focusing on the production of specialty coffee with registered varieties on the National Seed Industry Council (NSIC. Correct identification and isolation of pure coffee beans are the main factors that determine coffee’s market value. Local farms usually misidentify and mix coffee beans of different varieties, leading to the depreciation of their value. This study used simple sequence repeat (SSR markers to evaluate and distinguish Philippine NSIC-registered coffee species and varieties. The neighbor-joining tree generated using PAUP showed high bootstrap support, separating C. arabica, C. canephora, and C. liberica from each other. Among the twenty primer pairs used, seven were able to distinguish C. arabica, nine for C. liberica, and one for C. canephora.

  18. Frequency of Repeated Courses Its Relation to Persistence and Performance in Lebanon's Higher Education

    Science.gov (United States)

    Nasser, Ramzi; Nauffal, Diane

    2012-01-01

    This study assesses the relationship between the frequency of repeating courses and students' performance in college. The study uses cohort data from academic years 2000/2001, 2001/2002, 2002/2003 and 2003/2004. We compared those who had repeated one, two and three courses on GPA and whether a relation exists of those who graduated/did not…

  19. [Homologous simple sequence repeats (SSRs) analysis in tetraploid (AD1) and diploid (A₂, D₅) genomes of Gossypium].

    Science.gov (United States)

    Gaofei, Sun; Shoupu, He; Zhaoe, Pan; Xiongming, Du

    2015-02-01

    Simple sequence repeats (SSRs)are a class of repetitive DNA sequences, which are commonly used for genome analysis. Comparison of the homologous SSRs among different genomes is helpful to understand the evolutionary process in relative species. In this study, SSR scanning was performed to investigate their distribution and length variation among the genomes of G. raimondii (D₅), G. arboretum (A₂) and G. hirsutum (AD₁). The results demonstrated that the distribution of SSRs in A genome was very similar with that in D genome, while the length variation of homologous SSRs between A and AD genome was more conserved than that between D and AD genome. Compared with SSRs in AD genome, the number of SSRs with longer motif length in A genome was about five times of those with shorter motif length, while it was about three times in D genome. This implied that the length variation rates of homologous SSRs between diploid cotton and tetraploid cotton were different during the parallel evolution due to the subgenome fusion, and the motif length of most SSRs in tetraoploid genome tended to become shorter than homologous SSRs in diploid genome during the process of evolution. This study comprehensively compared the SSRs in three cotton genomes and revealed the significant difference among them, providing a foundation for further evolutionary study of Gossypium genome.

  20. Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers.

    Science.gov (United States)

    Yu, Mina; Yu, Junjie; Li, Huanhuan; Wang, Yahui; Yin, Xiaole; Bo, Huiwen; Ding, Hui; Zhou, Yuxin; Liu, Yongfeng

    2016-07-01

    Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens.

  1. De novo characterization of the Dialeurodes citri transcriptome: mining genes involved in stress resistance and simple sequence repeats (SSRs) discovery.

    Science.gov (United States)

    Chen, E-H; Wei, D-D; Shen, G-M; Yuan, G-R; Bai, P-P; Wang, J-J

    2014-02-01

    The citrus whitefly, Dialeurodes citri (Ashmead), is one of the three economically important whitefly species that infest citrus plants around the world; however, limited genetic research has been focused on D. citri, partly because of lack of genomic resources. In this study, we performed de novo assembly of a transcriptome using Illumina paired-end sequencing technology (Illumina Inc., San Diego, CA, USA). In total, 36,766 unigenes with a mean length of 497 bp were identified. Of these unigenes, we identified 17,788 matched known proteins in the National Center for Biotechnology Information database, as determined by Blast search, with 5731, 4850 and 14,441 unigenes assigned to clusters of orthologous groups (COG), gene ontology (GO), and SwissProt, respectively. In total, 7507 unigenes were assigned to 308 known pathways. In-depth analysis of the data showed that 117 unigenes were identified as potentially involved in the detoxification of xenobiotics and 67 heat shock protein (Hsp) genes were associated with environmental stress. In addition, these enzymes were searched against the GO and COG database, and the results showed that the three major detoxification enzymes and Hsps were classified into 18 and 3, 6, and 8 annotations, respectively. In addition, 149 simple sequence repeats were detected. The results facilitate the investigation of molecular resistance mechanisms to insecticides and environmental stress, and contribute to molecular marker development. The findings greatly improve our genetic understanding of D. citri, and lay the foundation for future functional genomics studies on this species.

  2. Triplet repeat sequences in human DNA can be detected by hybridization to a synthetic (5'-CGG-3')17 oligodeoxyribonucleotide

    DEFF Research Database (Denmark)

    Behn-Krappa, A; Mollenhauer, J; Doerfler, W

    1993-01-01

    The seemingly autonomous amplification of naturally occurring triplet repeat sequences in the human genome has been implicated in the causation of human genetic disease, such as the fragile X (Martin-Bell) syndrome, myotonic dystrophy (Curshmann-Steinert), spinal and bulbar muscular atrophy...

  3. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related Botryosphaeraceae

    Science.gov (United States)

    Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (U.S.). Genetic diversity was assessed using Nei’s minimum genetic distance and th...

  4. Effects of GABA[subscript A] Modulators on the Repeated Acquisition of Response Sequences in Squirrel Monkeys

    Science.gov (United States)

    Campbell, Una C.; Winsauer, Peter J.; Stevenson, Michael W.; Moerschbaecher, Joseph M.

    2004-01-01

    The present study investigated the effects of positive and negative GABA[subscript A] modulators under three different baselines of repeated acquisition in squirrel monkeys in which the monkeys acquired a three-response sequence on three keys under a second-order fixed-ratio (FR) schedule of food reinforcement. In two of these baselines, the…

  5. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    Science.gov (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  6. Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers

    Directory of Open Access Journals (Sweden)

    Hongwei Cai

    2017-04-01

    Full Text Available To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3, with a few lines that instead grouped with L. multiflorum (C4 or Lolium rigidum (C6. Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.

  7. Genetic Diversity of Landraces in Gossypium arboreum L. Race sinense Assessed with Simple Sequence Repeat Markers

    Institute of Scientific and Technical Information of China (English)

    Wang-Zhen Guo; Bao-Liang Zhou; Lu-Ming Yang; Wei Wang; Tian-Zhen Zhang

    2006-01-01

    Asiatic cotton (Gossypium arboreum L.) is an "Old World" cultivated cotton species, the sinense race of which is planted extensively in China. This species is still used in the current tetraploid cotton breeding program as an elite germplasm line, and is also used as a model for genomic research in Gossypium. In the present study, 60 cotton microsatellite markers, averaging 4.6 markers for each A-genome chromosome,were chosen to assess the genetic diversity of 109 accessions. These included 106 G. arboreum landraces,collected from 18 provinces throughout four Asiatic cotton-growing regions in China. A total of 128 alleles were detected, with an average of 2.13 alleles per locus. The largest number of alleles, as well as the maximum number of polymorphic loci, was detected in the A03 linkage group. No polymorphic alleles were detected on chromosome 10. The polymorphism information content for the 22 polymorphic microsatellite loci varied from 0.52 to 0.98, with an average of 0.89. Genetic diversity analysis revealed that the landraces in the Southern region had more genetic variability than those from the other two regions, and no significant difference was detected between landraces in the Yangtze and the Yellow River Valley regions. These findings are consistent with the history of sinense introduction, with the Southern region being the presumed center of origin for Chinese Asiatic cotton, and with subsequent northeastward extension to the Yangtze and Yellow River Valleys. Cluster analysis, based on simple sequence repeat data for 60 microsatellite loci, clearly differentiated Vietnamese and G. herbaceum landraces from the sinense landrace. No relationship between inter-variety similarity and geographical ecological region was observed. The present findings indicate that the Southern region landraces may have been directly introduced into the provinces in the middle and lower Yangtze River Valley, where Asiatic cotton was most extensively grown, and further race

  8. Simple sequence repeat marker associated with a natural leaf defoliation trait in tetraploid cotton.

    Science.gov (United States)

    Abdurakhmonov, I Y; Abdullaev, A A; Saha, S; Buriev, Z T; Arslanov, D; Kuryazov, Z; Mavlonov, G T; Rizaeva, S M; Reddy, U K; Jenkins, J N; Abdullaev, A; Abdukarimov, A

    2005-01-01

    Cotton (Gossypium hirsutum L.) leaf defoliation has a significant ecological and economical impact on cotton production. Thus the utilization of a natural leaf defoliation trait, which exists in wild diploid cotton species, in the development of tetraploid cultivated cotton will not only be cost effective, but will also facilitate production of very high-grade fiber. The primary goal of our research was to tag loci associated with natural leaf defoliation using microsatellite markers in Upland cotton. The F2 populations developed from reciprocal crosses between the two parental cotton lines--AN-Boyovut-2 (2n = 52), a late leaf defoliating type, and Listopad Beliy (2n = 52), a naturally early leaf defoliating type--demonstrated that the naturally early leaf defoliation trait has heritability values of 0.74 and 0.84 in the reciprocal F2 population. The observed phenotypic segregation difference in reciprocal crosses suggested a minor cytoplasmic effect in the phenotypic expression of the naturally early leaf defoliation trait. Results from the Kruskal-Wallis (KW) nonparametric test revealed that JESPR-13 (KW = 6.17), JESPR-153 (KW = 9.97), and JESPR-178 (KW = 13.45) Simple sequence repeat (SSR) markers are significantly associated with natural leaf defoliation in the mapping population having stable estimates at empirically obtained critical thresholds (P < .05-.0001). JESPR-178 revealed the highest estimates (P < .0001) for association with the natural leaf defoliation trait, exceeding maximum empirical threshold values. JESPR-178 was assigned to the short arm of chromosome 18, suggesting indirectly that genes associated with natural leaf defoliation might be located on this chromosome. This microsatellite marker may have the potential for use to introgress the naturally early leaf defoliation quantitative trait loci (QTL) from the donor line Listopad Beliy to commercial varieties of cotton through marker-assisted selection programs.

  9. Extended Logistic Chaotic Sequence and Its Performance Analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xuefeng; FAN Jiulun

    2007-01-01

    In order to improve performance and security of image encryption algorithm effectively based on chaotic sequences, an extended chaotic sequence generating method is presented based on logistic chaotic system using Bernstein form Bezier curve generating algorithm. In order to test the pseudorandom performance of the extended chaotic sequence, we also analyze random performance, autocorrelation performance, and balance performance of the extended chaotic sequence. Simulation results show that the extended chaotic sequence generated using our method is pseudorandom and its correlation performance and balance performance are good. As an application, we apply the extended chaotic sequence in image encryption algorithm, the simulation results show that the performance of the encrypted image using our method is better than that using logistic chaotic sequence.

  10. Identification of the porcine homologous of human disease causing trinucleotide repeat sequences

    DEFF Research Database (Denmark)

    Madsen, Lone Bruhn; Thomsen, Bo; Sølvsten, Christina Ane Elisabeth

    2007-01-01

    expansion in the repeat number of intragenic trinucleotide repeats (TNRs) is associated with a variety of inherited human neurodegenerative diseases. To study the compositionof TNRs in a mammalian species representing an evolutionary intermediate between humans and arodents, we describe in this p...

  11. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish.

    Science.gov (United States)

    Terencio, Maria Leandra; Schneider, Carlos Henrique; Gross, Maria Claudia; Feldberg, Eliana; Porto, Jorge Ivan Rebelo

    2013-02-01

    Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.

  12. Performance and physiological responses to repeated-sprint exercise: a novel multiple-set approach.

    Science.gov (United States)

    Serpiello, Fabio R; McKenna, Michael J; Stepto, Nigel K; Bishop, David J; Aughey, Robert J

    2011-04-01

    We investigated the acute and chronic responses to multiple sets of repeated-sprint exercise (RSE), focusing on changes in acceleration, intermittent running capacity and physiological responses. Ten healthy young adults (7 males, 3 females) performed an incremental test, a Yo-Yo intermittent recovery test level1 (Yo-Yo IR1), and one session of RSE. RSE comprised three sets of 5 × 4-s maximal sprints on a non-motorised treadmill, with 20 s of passive recovery between repetitions and 4.5 min of passive recovery between sets. After ten repeated-sprint training sessions, participants repeated all tests. During RSE, performance was determined by measuring acceleration, mean and peak power/velocity. Recovery heart rate (HR), HR variability, and finger-tip capillary lactate concentration ([Lac(-)]) were measured. Performance progressively decreased across the three sets of RSE, with the indices of repeated-sprint ability being impaired to a different extent before and after training. Training induced a significant increase (p RSE. There were strong correlations between Yo-Yo IR1 performance and indices of RSE performance, especially acceleration post-training (r = 0.88, p = 0.004). Repeated-sprint training, comprising only 10 min of exercise overall, effectively improved performance during multiple-set RSE. This exercise model better reflects team-sport activities than single-set RSE. The rapid training-induced improvement in acceleration, quantified here for the first time, has wide applications for professional and recreational sport activities.

  13. Multilocus variable-number tandem-repeat analysis scheme for chlamydia felis genotyping: comparison with multilocus sequence typing.

    Science.gov (United States)

    Laroucau, Karine; Di Francesco, Antonietta; Vorimore, Fabien; Thierry, Simon; Pingret, Jean Luc; Bertin, Claire; Willems, Hermann; Bölske, Goran; Harley, Ross

    2012-06-01

    Chlamydia felis is an important ocular pathogen in cats worldwide. A multilocus variable-number tandem-repeat analysis (MLVA) system for the detection of tandem repeats across the whole genome of C. felis strain Fe/C-56 was developed. Nine selected genetic loci were tested by MLVA in 17 C. felis isolates, including the C. felis Baker vaccine strain, and 122 clinical samples from different geographic origins. Analysis of the results identified 25 distinct C. felis MLVA patterns. In parallel, a recently described multilocus sequence typing scheme for the typing of Chlamydia was applied to 13 clinical samples with 12 different C. felis MLVA patterns. Rare sequence differences were observed. Thus, the newly developed MLVA system provides a highly sensitive high-resolution test for the differentiation of C. felis isolates from different origins that is suitable for molecular epidemiological studies.

  14. A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins.

    Science.gov (United States)

    Marold, Jacob D; Kavran, Jennifer M; Bowman, Gregory D; Barrick, Doug

    2015-11-01

    Linear repeat proteins often have high structural similarity and low (∼25%) pairwise sequence identities (PSI) among modules. We identified a unique P. anserina (Pa) sequence with tetratricopeptide repeat (TPR) homology, which contains longer (42 residue) repeats (42PRs) with an average PSI >91%. We determined the crystal structure of five tandem Pa 42PRs to 1.6 Å, and examined the stability and solution properties of constructs containing three to six Pa 42PRs. Compared with 34-residue TPRs (34PRs), Pa 42PRs have a one-turn extension of each helix, and bury more surface area. Unfolding transitions shift to higher denaturant concentration and become sharper as repeats are added. Fitted Ising models show Pa 42PRs to be more cooperative than consensus 34PRs, with increased magnitudes of intrinsic and interfacial free energies. These results demonstrate the tolerance of the TPR motif to length variation, and provide a basis to understand the effects of helix length on intrinsic/interfacial stability.

  15. Minimum length of direct repeat sequences required for efficient homologous recombination induced by zinc finger nuclease in yeast.

    Science.gov (United States)

    Ren, ChongHua; Yan, Qiang; Zhang, ZhiYing

    2014-10-01

    Zinc finger nuclease (ZFN) technology is a powerful molecular tool for targeted genome modifications and genetic engineering. However, screening for specific ZFs and validation of ZFN activity are labor intensive and time consuming. We previously designed a yeast-based ZFN screening and validation system by inserting a ZFN binding site flanked by a 164 bp direct repeat sequence into the middle of a Gal4 transcription factor, disrupting the open reading frame of the yeast Gal4 gene. Expression of the ZFN causes a double stranded break at its binding site, which promotes the cellular DNA repair system to restore expression of a functional Gal transcriptional factor via homologous recombination. Expression of Gal4 transcription factor leads to activation of three reporter genes in an AH109 yeast two-hybrid strain. However, the 164 bp direct repeat appears to generate spontaneous homologous recombination frequently, resulting in many false positive ZFNs. To overcome this, a series of DNA fragments of various lengths from 10 to 150 bp with 10 bp increase each and 164 bp direct repeats flanking the ZFN binding site were designed and constructed. The results demonstrated that the minimum length required for ZFN-induced homologous recombination was 30 bp, which almost eliminated spontaneous recombination. Using the 30 bp direct repeat sequence, ZFN could efficiently induce homologous recombination, while false positive ZFNs resulting from spontaneous homologous recombination were minimized. Thus, this study provided a simple, fast and sensitive ZFN screening and activity validation system in yeast.

  16. Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci.

    Science.gov (United States)

    Buonaccorsi, Vincent P; Kimbrell, Carol A; Lynn, Eric A; Hyde, John R

    2012-01-01

    Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates. No F(ST)-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between F(ST) and variation or marker class was observed. General linear model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates but did not affect the observed pattern of population structure.

  17. Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae).

    Science.gov (United States)

    Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

    2013-07-01

    The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.

  18. Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India.

    Directory of Open Access Journals (Sweden)

    Saroj K Young

    2008-04-01

    Full Text Available Inadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological studies and contribute to our understanding of the disease.Genotyping assays based on variation in the copy number of short tandem repeat sequences were applied to biopsies collected in population-based epidemiological studies of leprosy in northern Malawi, and from members of multi-case households in Hyderabad, India. In the Malawi series, considerable genotypic variability was observed between patients, and also within patients, when isolates were collected at different times or from different tissues. Less within-patient variability was observed when isolates were collected from similar tissues at the same time. Less genotypic variability was noted amongst the closely related Indian patients than in the Malawi series.Lineages of M. leprae undergo changes in their pattern of short tandem repeat sequences over time. Genetic divergence is particularly likely between bacilli inhabiting different (e.g., skin and nerve tissues. Such variability makes short tandem repeat sequences unsuitable as a general tool for population-based strain typing of M. leprae, or for distinguishing relapse from reinfection. Careful use of these markers may provide insights into the development of disease within individuals and for tracking of short transmission chains.

  19. Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation.

    Science.gov (United States)

    Visca, Paolo; D'Arezzo, Silvia; Ramisse, Françoise; Gelfand, Yevgeniy; Benson, Gary; Vergnaud, Gilles; Fry, Norman K; Pourcel, Christine

    2011-09-01

    The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.

  20. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.

    Directory of Open Access Journals (Sweden)

    Nisha Joy

    Full Text Available Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L., an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs. We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.

  1. 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.

  2. The SIDER2 elements, interspersed repeated sequences that populate the Leishmania genomes, constitute subfamilies showing chromosomal proximity relationship

    Directory of Open Access Journals (Sweden)

    Thomas M Carmen

    2008-06-01

    Full Text Available Abstract Background Protozoan parasites of the genus Leishmania are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryotic lineage possess a number of unusual genomic, molecular and biochemical features. The completion of the genome projects for three Leishmania species has generated invaluable information enabling a direct analysis of genome structure and organization. Results By using DNA macroarrays, made with Leishmania infantum genomic clones and hybridized with total DNA from the parasite, we identified a clone containing a repeated sequence. An analysis of the recently completed genome sequence of L. infantum, using this repeated sequence as bait, led to the identification of a new class of repeated elements that are interspersed along the different L. infantum chromosomes. These elements turned out to be homologues of SIDER2 sequences, which were recently identified in the Leishmania major genome; thus, we adopted this nomenclature for the Leishmania elements described herein. Since SIDER2 elements are very heterogeneous in sequence, their precise identification is rather laborious. We have characterized 54 LiSIDER2 elements in chromosome 32 and 27 ones in chromosome 20. The mean size for these elements is 550 bp and their sequence is G+C rich (mean value of 66.5%. On the basis of sequence similarity, these elements can be grouped in subfamilies that show a remarkable relationship of proximity, i.e. SIDER2s of a given subfamily locate close in a chromosomal region without intercalating elements. For comparative purposes, we have identified the SIDER2 elements existing in L. major and Leishmania braziliensis chromosomes 32. While SIDER2 elements are highly conserved both in number and location between L. infantum and L. major, no such conservation exists when comparing with SIDER2s in L. braziliensis chromosome 32. Conclusion

  3. COMPARATIVE ANALYSIS OF INTER SIMPLE SEQUENCE REPEATS AND SIMPLE SEQUENCE REPEATS MARKERS: GENETIC ANALYSIS OF DESCHAMPSIA CESPITOSA POPULATIONS GROWING IN METAL CONTAMINATED REGIONS IN CANADA

    Directory of Open Access Journals (Sweden)

    K.K. Nkongolo

    2014-01-01

    Full Text Available Comparative studies conducted on the genetic variation of metal-tolerant populations and their non-metal-tolerant counterparts have been performed on numerous species using isozyme markers. Analysis of genetic differences among plant populations growing in heavy metal-contaminated and uncontaminated regions are limited. The main objectives of the present study were to compare ISSR and microsatellite markers in assessing genetic variation in D. cespitosa populations that colonized metal-contaminated and uncontaminated regions in Northern Ontario, Canada. Total genomic DNA from D. cespitosa samples were amplified with ISSR and SSR primers using optimized PCR conditions. The level of polymorphic loci varies from 46 to 74% for ISSR analysis. The level of observed heterozygosity was moderate to high ranging from 0.44 to 0.68 for the SSR primers used. But no significant difference in genetic variation levels was detected between metal contaminated and uncontaminated sites with SSR markers. There was a significant reduction of polymorphic loci in samples from highly metal-contaminated areas of the Cobalt region compared to the reference sites based on ISSR analysis. Use of a combination of different marker systems is recommended to analyse genetic variation in plant populations.

  4. Repeatability of phasic muscle activity: performance of surface and intramuscular wire electrodes in gait analysis.

    Science.gov (United States)

    Kadaba, M P; Wootten, M E; Gainey, J; Cochran, G V

    1985-01-01

    Repeatability is an important consideration for gait analysis data that are being used as an adjunct to clinical decision making. An index of repeatability may be based on a statistical criterion (variance ratio) that reflects similarity of wave forms over a number of identical cycles. The purpose of this study was to use the variance ratio to assess the repeatability of phasic muscle activity recorded with surface and bipolar intramuscular wire electrodes during gait on 10 normal subjects. Variance ratios were calculated using rectified and smoothed electromyographic data recorded simultaneously from the two types of electrodes. Three measures of repeatability (reproducibility, reliability, and constancy--defined as the cycle-to-cycle, run-to-run, and day-to-day repeatability of phasic muscle activity) were used to compare the performance of the two electrode techniques. Results show that the reproducibility and reliability were better for surface electrodes than for intramuscular wire electrodes, and constancy was good for surface electrodes and poor for intramuscular wire electrodes. Repeatability improved with increasing smoothing window lengths but was better for surface electrodes than wire electrodes, irrespective of the smoothing window. This study indicates that surface electrode data represent a more consistent measure of activity of superficial muscles, if comparisons are to be made between gait data from different test days.

  5. Isolation and Characterization of Simple Sequence Repeats (SSR) Markers from the Moss Genus Orthotrichum Using a Small Throughput Pyrosequencing Machine

    Science.gov (United States)

    Sawicki, Jakub; Kwaśniewski, Mirosław; Szczecińska, Monika; Chwiałkowska, Karolina; Milewicz, Monika; Plášek, Vítězslav

    2012-01-01

    Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment) genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats) motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing. PMID:22837714

  6. The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination

    Science.gov (United States)

    Moumen, Abdeladim; Polomack, Lucette; Roques, Bernard; Buc, Henri; Negroni, Matteo

    2001-01-01

    Template switching during reverse transcription is crucial for retroviral replication. While strand transfer on the terminal repeated sequence R is essential to achieve reverse transcription, template switching from internal regions of the genome (copy choice) leads to genetic recombination. We have developed an experimental system to study copy-choice recombination in vitro along the HIV-1 genome. We identify here several genomic regions, including the R sequence, where copy choice occurred at high rates. The frequency of copy choice occurring in a given region of template was strongly influenced by the surrounding sequences, an observation that suggests a pivotal role of the folding of template RNA in the process. The sequence R, instead, constituted an exception to this rule since it was a strong hot-spot for copy choice in the different sequence contexts tested. We suggest therefore that the structure of this region has been optimised during viral evolution to ensure efficient template switching independently from the sequences that might surround it. PMID:11557813

  7. Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers

    Energy Technology Data Exchange (ETDEWEB)

    Kandpal, R.P.; Kandpal, G.; Weissman, S.M. (Yale Univ. School of Medicine, New Haven, CT (United States))

    1994-01-04

    The authors describe a simple and rapid method for constructing small-insert genomic libraries highly enriched for dimeric, trimeric, and tetrameric nucleotide repeat motifs. The approach involves use of DNA inserts recovered by PCR amplification of a small-insert sonicated genomic phage library or by a single-primer PCR amplification of Mbo I-digested and adaptor-ligated genomic DNA. The genomic DNA inserts are heat denatured and hybridized to a biotinylated oligonucleotde. The biotinylated hybrids are retained on a Vectrex-avidin matrix and eluted specifically. The eluate is PCR amplified and cloned. More than 90% of the clones in a library enriched for (CA)[sub n] microsatellites with this approach contained clones with inserts containing CA repeats. They have also used this protocol for enrichment of (CAG)[sub n] and (AGAT)[sub n] sequence repeats and for Not I jumping clones. They have used the enriched libraries with an adaptation of the cDNA selection method to enrich for repeat motifs encoded in yeast artificial chromosomes.

  8. Longitudinal study of repeated sprint performance in youth soccer players of contrasting skeletal maturity status

    NARCIS (Netherlands)

    Valente-dos-Santos, Joao; Coelho-e-Silva, Manuel J.; Severino, Vitor; Duarte, Joao; Martins, Raul S.; Figueiredo, Antonio J.; Seabra, Andre T.; Philippaerts, Renaat M.; Cumming, Sean P.; Elferink-Gemser, Marije; Malina, Robert M.

    The purpose of the study was to evaluate the developmental changes in performance in a repeated-sprint ability (RSA) test in young soccer players of contrasting maturity status. A total of 83 regional level Portuguese youth soccer players, aged 11-13 years at baseline was assessed annually. Stature,

  9. Longitudinal study of repeated sprint performance in youth soccer players of contrasting maturity status

    NARCIS (Netherlands)

    V. Duarte; A. Seabra; A. Figueiredo; S. Cumming; R. Martins; R. Philippaerts; M. Coelho e Silva; J. Valente dos Santos; V. Severino; Marije Elferink-Gemser

    2012-01-01

    The purpose of the study was to evaluate the developmental changes in performance in a repeated-sprint ability (RSA) test in young soccer players of contrasting maturity status. A total of 83 regional level Portuguese youth soccer players, aged 11- 13 years at baseline was assessed annually.

  10. Does Repeating a Year Improve Performance? The Case of Teaching English

    Science.gov (United States)

    Morrison, Keith; No, Anna Ieong On

    2007-01-01

    This paper examines whether having school students repeat a year improves their performance, focusing on learning English as a foreign language. It takes students' English examination results from five years from a Chinese-medium school, together with data on their learning styles and learning strategies. Drawing on local cultural and pedagogic…

  11. Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

    Directory of Open Access Journals (Sweden)

    Juana M. Córdoba

    2010-11-01

    Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

  12. Development of simple sequence repeats (SSR) markers of ramie and comparison of SSR and inter-SSR marker systems

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jianlin; JIE Yucheng; JIANG Yanbo; ZHONG Yingli; LIU Yunhai; ZHANG Jian

    2005-01-01

    Ramie (Boehmeria nivea L. ) is an important bast fiber crop. To study genetic background of this species, we isolated and characterized microsatellite markers of ramie. A genomic library containing inserts of rapid amplification of polymorphic DNA (RAPD)fragments was constructed, and screened by PCR amplification using anchored simple sequence repeats as primers. A total of 26 clones were identified as positives, and 13 microsatellite loci were found after sequencing. The polymorphism of these 13 microsatellite loci was examined and the utility of simple sequence repeats (SSR) and inter-SSR (ISSR) marker systems for genetic characterization compared using 19 selected ramie cultivars. Both approaches successfully discriminated the 19 cultivars which differed in the amount of polymorphism detected. The level of polymorphism detected by SSR was 95.0 %, higher than that by ISSR (72.3 % ), but the average polymorphism information content (PIC) of ISSR (0. 651) was higher than that of SSR (0. 441). The higher PIC value of ISSR suggests that ISSR is more efficient for fingerprinting ramie cultivars than SSR markers. However, because the SSR loci are codominant, they are more suitable for determining the homozygosity levels of ramie, constructing linkage map, quantitative trait loci study of complex traits and marker-as-sisted selection.

  13. Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system

    Directory of Open Access Journals (Sweden)

    Lillis Rebecca

    2008-07-01

    Full Text Available Abstract Background Several methods have been reported for strain typing of Mycoplasma genitalium. The value of these methods has never been comparatively assessed. The aims of this study were: 1 to identify new potential genetic markers based on an analysis of short tandem repeat (STR sequences in the published M. genitalium genome sequence; 2 to apply previously and newly identified markers to a panel of clinical strains in order to determine the optimal combination for an efficient multi-locus genotyping system; 3 to further confirm sexual transmission of M. genitalium using the newly developed system. Results We performed a comprehensive analysis of STRs in the genome of the M. genitalium type strain G37 and identified 18 loci containing STRs. In addition to one previously studied locus, MG309, we chose two others, MG307 and MG338, for further study. Based on an analysis of 74 unrelated patient specimens from New Orleans and Scandinavia, the discriminatory indices (DIs for these three markers were 0.9153, 0.7381 and 0.8730, respectively. Two other previously described markers, including single nucleotide polymorphisms (SNPs in the rRNA genes (rRNA-SNPs and SNPs in the MG191 gene (MG191-SNPs were found to have DIs of 0.5820 and 0.9392, respectively. A combination of MG309-STRs and MG191-SNPs yielded almost perfect discrimination (DI = 0.9894. An additional finding was that the rRNA-SNPs distribution pattern differed significantly between Scandinavia and New Orleans. Finally we applied multi-locus typing to further confirm sexual transmission using specimens from 74 unrelated patients and 31 concurrently infected couples. Analysis of multi-locus genotype profiles using the five variable loci described above revealed 27 of the couples had concordant genotype profiles compared to only four examples of concordance among the 74 unrelated randomly selected patients. Conclusion We propose that a combination of the MG309-STRs and MG191-SNPs is

  14. Importance of muscle power variables in repeated and single sprint performance in soccer players.

    Science.gov (United States)

    López-Segovia, Manuel; Dellal, Alexandre; Chamari, Karim; González-Badillo, Juan José

    2014-03-27

    This study examined the relationship between lower body power and repeated as well as single sprint performance in soccer players. The performance of nineteen male soccer players was examined. The first testing session included the countermovement jump (CMJL) and the progressive full squat (FSL), both with external loads. Power in the CMJL and FSL was measured with each load that was lifted. The second session included a protocol of 40-m repeated sprints with a long recovery period (2 min). The number of sprints executed until there was a 3% decrease in performance for the best 40-m sprint time was recorded as a repeated sprint index (RSI). The RSI was moderately associated with power output relative to body mass in the CMJL and FSL (r = 0.53/0.54, p ≤ 0.05). The most and least powerful players (determined by FSL) showed significant differences in the RSI (9.1 ± 4.2 vs. 6.5 ± 1.6) and 10 m sprint time (p ± 0.01). Repeated and single sprints are associated with relatively lower body power in soccer players.

  15. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  16. Germline mutations of STR-alleles include multi-step mutations as defined by sequencing of repeat and flanking regions.

    Science.gov (United States)

    Dauber, Eva-Maria; Kratzer, Adelgunde; Neuhuber, Franz; Parson, Walther; Klintschar, Michael; Bär, Walter; Mayr, Wolfgang R

    2012-05-01

    Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.

  17. Effect of training in hypoxia on repeated sprint performance in female athletes.

    Science.gov (United States)

    Kasai, Nobukazu; Mizuno, Sahiro; Ishimoto, Sayuri; Sakamoto, Etsuko; Maruta, Misato; Goto, Kazushige

    2015-01-01

    This study determined the effect of repeated sprint training in hypoxia (RSH) in female athletes. Thirty-two college female athletes performed repeated cycling sprints of two sets of 10 × 7-s sprints with a 30-s rest between sprints twice per week for 4 weeks under either normoxic conditions (RSN group; FiO2, 20.9%; n = 16) or hypoxic conditions (RSH group; FiO2, 14.5%; n = 16). The repeated sprint ability (10 × 7-s sprints) and maximal oxygen uptake ([Formula: see text]) were determined before and after the training period. After training, when compared to pre-values, the mean power output was higher in all sprints during the repeated sprint test in the RSH group but only for the second half of the sprints in the RSN group (P ≤ 0.05). The percentage increases in peak and mean power output between before and after the training period were significantly greater in the RSH group than in the RSN group (peak power output, 5.0 ± 0.7% vs. 1.5 ± 0.9%, respectively; mean power output, 9.7 ± 0.9% vs. 6.0 ± 0.8%, respectively; P repeated sprint test compared with RSN.

  18. DNA polymorphism among Fusarium oxysporum f.sp. elaeidis populations from oil palm, using a repeated and dispersed sequence "Palm".

    Science.gov (United States)

    Mouyna, I; Renard, J L; Brygoo, Y

    1996-07-31

    A worldwide collection, of 76 F. oxysporum f.sp. elaeidis isolates (Foe), and of 21 F. oxysporum isolates from the soil of several palm grove was analysed by RFLP. As a probe, we used a random DNA fragment (probe 46) from a genomic library of a Foe isolate. This probe contains two different types of sequence, one being repeated and dispersed in the genome "Palm", the other being a single-copy sequence. All F. oxysporum isolates from the palm-grove soils were non-pathogenic to oil palm. They all had a simple restriction pattern with one band homologous to the single-copy sequence of probe 46. All Foe isolates were pathogenic to oil palm and they all had complex patterns due to hybridization with "Palm". This repetitive sequence reveals that Foe isolates are distinct from the other F. oxysporum palm-grove soils isolates. The sequence can reliably discriminate pathogenic from non-pathogenic oil palm isolates. Based on DNA fingerprint similarities, Foe populations were divided into ten groups consisting of isolates with the same geographic origin. Isolates from Brazil and Ecuador were an exception to that rule as they had the same restriction pattern as a few isolates from the Ivory Coast, suggesting they may originated from Africa.

  19. ProtRepeatsDB: a database of amino acid repeats in genomes

    Directory of Open Access Journals (Sweden)

    Chauhan Virander S

    2006-07-01

    Full Text Available Abstract Background Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. Description ProtRepeatsDB (v1.2 consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO annotation IDs and regular expressions (REGEXP describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. Conclusion ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific

  20. Comparison of creatine monohydrate and carbohydrate supplementation on repeated jump height performance.

    Science.gov (United States)

    Koenig, Chad A; Benardot, Dan; Cody, Mildred; Thompson, Walter R

    2008-07-01

    Creatine monohydrate (CrMH) supplementation aids the ability to maintain performance during repeated bouts of high-intensity exercise, including jump performance. However, carbohydrate supplementation may also provide similar benefits and is less expensive. This study compared the effects of an energy-free placebo, 2 different caloric concentrations of carbohydrate drinks, and a CrMH supplement on repeated jump heights. Sixty active males (mean age, 22 +/- 3.2 years) performed 2 sets of countermovement static jump height tests (10 jumps over 60 seconds) separated by 5 days to determine the differential effects of the placebo, carbohydrate, and CrMH on jump height sustainability over 10 jumps. Subjects were randomly assigned to groups (15 subjects per group) to receive daily doses (x5 days) of carbohydrate drinks containing 100 or 250 kilocalories (kcal), a 25-g CrMH supplement, or an energy-free placebo. After 5 days, the CrMH group experienced a significant weight gain (+1.52; +/-0.89 kg, p energy-free placebo over the final 3-4 jumps. The 250-kcal carbohydrate-supplemented group experienced a level of benefit (p < 0.01) that was at least equal to that of the CrMH group (p < 0.05), suggesting that the higher dose of carbohydrate was as effective as CrMH in maintaining repeated bouts of high-intensity activity as measured by repeated static jumps. Given the equivalent performance improvement and the absence of weight gain, the carbohydrate supplementation could be considered the preferred option for weight-conscious power athletes involved in activities that require repeated- motion high-intensity activities.

  1. Rapid functional and sequence differentiation of a tandemly repeated species-specific multigene family in Drosophila

    DEFF Research Database (Denmark)

    Clifton, Bryan D.; Sanz, Pablo Librado; Yeh, Shu-Dan

    2017-01-01

    Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typical...

  2. In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

    Directory of Open Access Journals (Sweden)

    Andrea Vásquez

    2014-01-01

    Full Text Available We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp. It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.

  3. Race: A scalable and elastic parallel system for discovering repeats in very long sequences

    KAUST Repository

    Mansour, Essam

    2013-08-26

    A wide range of applications, including bioinformatics, time series, and log analysis, depend on the identification of repetitions in very long sequences. The problem of finding maximal pairs subsumes most important types of repetition-finding tasks. Existing solutions require both the input sequence and its index (typically an order of magnitude larger than the input) to fit in memory. Moreover, they are serial algorithms with long execution time. Therefore, they are limited to small datasets, despite the fact that modern applications demand orders of magnitude longer sequences. In this paper we present RACE, a parallel system for finding maximal pairs in very long sequences. RACE supports parallel execution on stand-alone multicore systems, in addition to scaling to thousands of nodes on clusters or supercomputers. RACE does not require the input or the index to fit in memory; therefore, it supports very long sequences with limited memory. Moreover, it uses a novel array representation that allows for cache-efficient implementation. RACE is particularly suitable for the cloud (e.g., Amazon EC2) because, based on availability, it can scale elastically to more or fewer machines during its execution. Since scaling out introduces overheads, mainly due to load imbalance, we propose a cost model to estimate the expected speedup, based on statistics gathered through sampling. The model allows the user to select the appropriate combination of cloud resources based on the provider\\'s prices and the required deadline. We conducted extensive experimental evaluation with large real datasets and large computing infrastructures. In contrast to existing methods, RACE can handle the entire human genome on a typical desktop computer with 16GB RAM. Moreover, for a problem that takes 10 hours of serial execution, RACE finishes in 28 seconds using 2,048 nodes on an IBM BlueGene/P supercomputer.

  4. Assessment of Genetic Diversities of Selected Laminaria (Laminariales,Phaeophyta) Gametophytes by Inter-Simple Sequence Repeat Analysis

    Institute of Scientific and Technical Information of China (English)

    Xiu-Liang WANG; Chen-Lin LIU; Xiao-Jie LI; Yi-Zhou CONG; De-Lin DUAN

    2005-01-01

    Inter-simple sequence repeat (ISSR) analysis was used to assess genetic diversity among 10pairs of male and female Laminaria gametophytes. A total of 58 amplification loci was obtained from 10selected ISSR primers, of which 34 revealed polymorphism among the gametophytes. Genetic distances were calculated with the Dice coefficient ranging from 0.006 to 0.223. A dendrogram based on the unweighted pair-group method arithmetic (UPGMA) average showed that most male and female gametophytes of the same species were clustered together and that 10 pairs of gametophytes were divided into four groups. This was generally consistent with the taxonomic categories. The main group consisted of six pairs of gametophytes, which were selected from Laminaria japonica Aresch. by intensive inbreeding through artificial hybridization. One specific marker was cloned, but was not converted successfully into a sequence characterized amplified region (SCAR) marker. Our results demonstrate the feasibility of applying ISSR markers to evaluate Laminaria germplasm diversities.

  5. Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats

    Directory of Open Access Journals (Sweden)

    Osenberg Sivan

    2010-10-01

    Full Text Available Abstract Background Adenosine to inosine (A-to-I RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several human pathologies. However, the variability across human individuals of editing levels in other tissues has not been studied so far. Results Here, we analyzed 32 skin samples, looking at A-to-I editing level in three genes within coding sequences and in the Alu repeats of six different genes. We observed highly consistent editing levels across different individuals as well as across tissues, not only in coding targets but, surprisingly, also in the non evolutionary conserved Alu repeats. Conclusions Our findings suggest that A-to-I RNA-editing of Alu elements is a tightly regulated process and, as such, might have been recruited in the course of primate evolution for post-transcriptional regulatory mechanisms.

  6. Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

    Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

  7. Individual variation and repeatability in aerobic and anaerobic swimming performance of European sea bass, Dicentrarchus labrax.

    Science.gov (United States)

    Marras, S; Claireaux, G; McKenzie, D J; Nelson, J A

    2010-01-01

    Studies of inter-individual variation in fish swimming performance may provide insight into how selection has influenced diversity in phenotypic traits. We investigated individual variation and short-term repeatability of individual swimming performance by wild European sea bass in a constant acceleration test (CAT). Fish were challenged with four consecutive CATs with 5 min rest between trials. We measured maximum anaerobic speed at exhaustion (U(CAT)), gait transition speed from steady aerobic to unsteady anaerobic swimming (U(gt)), routine metabolic rate (RMR), post-CAT maximum metabolic rate (MMR), aerobic scope and recovery time from the CATs. Fish achieved significantly higher speeds during the first CAT (U(CAT)=170 cm s(-1)), and had much more inter-individual variation in performance (coefficient of variation, CV=18.43%) than in the subsequent three tests (U(CAT)=134 cm s(-1); CV=7.3%), which were very repeatable among individuals. The individual variation in U(CAT) in the first trial could be accounted for almost exclusively by variation in anaerobic burst-and-coast performance beyond U(gt). The U(gt) itself varied substantially between individuals (CV=11.4%), but was significantly repeatable across all four trials. Individual RMR and MMR varied considerably, but the rank order of post-CAT MMR was highly repeatable. Recovery rate from the four CATs was highly variable and correlated positively with the first U(CAT) (longer recovery for higher speeds) but negatively with RMR and aerobic scope (shorter recovery for higher RMR and aerobic scope). This large variation in individual performance coupled with the strong correlations between some of the studied variables may reflect divergent selection favouring alternative strategies for foraging and avoiding predation.

  8. Analysis of genetic relationship in mutant silkworm strains of Bombyx mori using inter simple sequence repeat (ISSR) markers

    Institute of Scientific and Technical Information of China (English)

    Dhanikachalam Velu; Kangayam M. Ponnuvel; Murugiah Muthulakshmi; Randhir K. Sinha; Syed M.H. Qadri

    2008-01-01

    Amplified inter simple sequence repeats (ISSR) markers were used to determine genetic relationships among mutant silkworm strains of Bombyx mori. Fifteen ISSR primers containing simple sequence repeat (SSR) motifs were used in this study. A total of 113 markers were produced among 20 mutant swains, of which 73.45% were found to be polymorphic. In selected mutant genetic stocks, the average number of observed allele was (1.7080±0.4567), effective alleles (1.5194±0.3950) and genetic diversity (Ht) (0.2901±0.0415). The dendrogram produced using the unweighted pair group method with arithmetic means (UPGMA) and cluster analysis made using Nei's genetic distance resulted in the formation of one major group containing 6 groups separated 20 mutant silkworm strains. Therefore, ISSR amplification is a valuable method for determining the genetic variability among mutant silkworm swains. This efficient molecular marker would be useful for characterizing a considerable number of silkworm swains maintained at the germplasm center.

  9. Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis.

    Science.gov (United States)

    Li, Yi; Hsiang, Tom; Yang, Rui-Heng; Hu, Xiao-Di; Wang, Ke; Wang, Wen-Jing; Wang, Xiao-Liang; Jiao, Lei; Yao, Yi-Jian

    2016-09-01

    Ophiocordyceps sinensis is one of the most expensive medicinal fungi world-wide, and has been used as a traditional Chinese medicine for centuries. In a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of Roche 454 (223Mb) and Illumina HiSeq (10.6Gb) sequencing data, producing a genome of 87.7Mb with an N50 scaffold length of 12kb and 6972 predicted genes. To test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic DNA extractions of a single ascospore isolate (strain 1229) on an Illumina HiSeq platform (25Gb total data). Assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (ABySS, SOAP and Velvet). In nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher N50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher N50 values. Depending on the assembly program and data type, the maximal N50 was reached with between 50% to 90% of the total read data, equivalent to 100× to 200× coverage. The draft genome assembly was improved over the previously published version resulting in a 114Mb assembly, scaffold N50 of 70kb and 9610 predicted genes. Among the predicted genes, 9213 were validated by RNA-Seq analysis in this study, of which 8896 were found to be singletons. Evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100× and 200×.

  10. Sequence Selection and Performance in DS/CDMA Systems

    Directory of Open Access Journals (Sweden)

    Jefferson Santos Ambrosio

    2016-03-01

    Full Text Available In this work key concepts on coding division multiple access (CDMA communication systems have been discussed. The sequence selection impact on the performance and capacity of direct sequence CDMA (DS/CDMA systems under AWGN and increasing system loading, as well as under multiple antennas channels was investigated.

  11. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer

    Science.gov (United States)

    2013-01-01

    Background Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. Results Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. Conclusions This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel

  12. A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK.

    Science.gov (United States)

    Lennon, E; Gutman, P D; Yao, H L; Minton, K W

    1991-03-01

    A DNA fragment containing a portion of a DNA damage-inducible gene from Deinococcus radiodurans SARK hybridized to numerous fragments of SARK genomic DNA because of a highly conserved repetitive chromosomal element. The element is of variable length, ranging from 150 to 192 bp, depending on the absence or presence of one or two 21-bp sequences located internally. A putative translational start site of the damage-inducible gene is within the reiterated element. The element contains dyad symmetries that suggest modes of transcriptional and/or translational control.

  13. A Nonpolynomial Optimal Algorithm for Sequencing Inspectors in a Repeat Inspection System with Rework

    Directory of Open Access Journals (Sweden)

    Moon Hee Yang

    2015-01-01

    Full Text Available Assuming that two types of inspection errors are nonidentical and that only the items rejected by an inspector are reworked and sent to the next inspection cycle, we formulate a combinatorial optimization problem for simultaneously determining both the minimum frequency of inspection-rework cycles and the optimal sequence of inspectors selected from a set of available inspectors, in order to meet the constraints of the outgoing quality level. Based on the inherent properties from our mathematical model, we provide a nonpolynomial optimal algorithm with a time complexity of O(2m.

  14. The effect of heavy resistance exercise on repeated sprint performance in youth athletes.

    Science.gov (United States)

    Low, Daniel; Harsley, Paul; Shaw, Matthew; Peart, Daniel

    2015-01-01

    This investigation assessed whether prior heavy resistance exercise would improve the repeated sprint performance of 16 trained youth soccer players (Age 17.05 ± 0.65 years; height 182.6 ± 8.9 cm; body mass 77.8 ± 8.2 kg). In session 1, individual 1 repetition max was measured utilising a squat movement. In sessions 2 and 3, participants performed a running-based repeated anaerobic sprint test with and without prior heavy resistance exercise of 91% of their 1 repetition max. Times were recorded for each of the 6 sprints performed in the repeated sprint test and summed to provide total time. T-tests compared the two exercise conditions via differences in corresponding sprint times and total time. Analysis revealed significantly reduced total time with use of heavy resistance exercise (33.48 (±1.27) vs. 33.59 (±1.27); P = 0.01). Sprints 1 (P = 0.05) and 2 (P = 0.02) were also faster in the heavy resistance exercise condition (5.09 (±0.16) vs. 5.11 (±0.16) and 5.36 (±0.24) vs. 5.45 (±0.26) seconds respectively) although no other differences were shown. Findings demonstrate improved sprint times of trained adolescent soccer players after heavy resistance exercise although benefits appear not as sustained as in adult participants.

  15. Genetic diversity of Pinus nigra Arn. populations in Southern Spain and Northern Morocco revealed by inter-simple sequence repeat profiles.

    Science.gov (United States)

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E; Tiscar, Pedro A; Viñegla, Benjamin; Linares, Juan C; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei's genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei's genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups-Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco-while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  16. Tandem repeat sequence variation and length heteroplasmy in the mitochondrial DNA D-loop of the threatened Gulf of Mexico sturgeon, Acipenser oxyrhynchus desotoi.

    Science.gov (United States)

    Miracle, A L; Campton, D E

    1995-01-01

    Genetic variability within the Suwannee River, Florida, population of Gulf of Mexico sturgeon, Acipenser oxyrhynchus desotoi, was assessed by examining sequence and length variation within the control region, or D-loop, of the mitochondrial genome. Although once abundant throughout the Gulf of Mexico, Gulf sturgeon are now listed as a threatened species by the U.S. Fish and Wildlife Service. Mitochondrial DNA was analyzed for length variation from 168 individual Gulf sturgeon by PCR amplification and visualization of PCR products using ethidium bromide-stained agarose gels. Of the 168 individual Gulf sturgeon, 31 (18.5%) were heteroplasmic for one to four copies of an 81-base pair, tandemly repeated sequence in the D-loop region. However, no individuals homoplasmic for multiple copies of the repeat sequence were observed. The existence and nature of these tandem repeats in heteroplasmic individuals was confirmed by direct sequencing of the PCR products for a subset of 22 individuals. The results are consistent with the apparent nature and mechanism of heteroplasmy observed in a congeneric species, A. transmontanus. In addition, sequences for 187 base pairs outside of the tandem repeats were identical among all 16 individuals assayed for this region. Lack of variable sequences is concordant with earlier studies involving mtDNA restriction fragment length profiles of Gulf sturgeon found in the Suwannee River. The absence of sequence variation exclusive of the tandem repeats is consistent with the hypothesis that the subspecies has undergone a population or evolutionary bottleneck.

  17. The TIS11 primary response gene is a member of a gene family that encodes proteins with a highly conserved sequence containing an unusual Cys-His repeat.

    OpenAIRE

    Varnum, B C; Ma, Q F; T. H. Chi; Fletcher, B.; Herschman, H.R.

    1991-01-01

    The TIS11 primary response gene is rapidly and transiently induced by both 12-O-tetradecanoylphorbol-13-acetate and growth factors. The predicted TIS11 protein contains a 6-amino-acid repeat, YKTELC. We cloned two additional cDNAs, TIS11b and TIS11d, that contain the YKTELC sequence. TIS11, TIS11b, and TIS11d proteins share a 67-amino-acid region of sequence similarity that includes the YKTELC repeat and two cysteine-histidine containing repeats. TIS11 gene family members are not coordinately...

  18. The effect of a short practical warm-up protocol on repeated sprint performance.

    Science.gov (United States)

    Taylor, Jonathan M; Weston, Matthew; Portas, Matthew D

    2013-07-01

    The aim of our study was to investigate the effect of a short, practical, 2-phase warm-up on repeated sprint performance when compared with more traditional warm-up protocols that contain stretching activities. Eleven subelite male soccer players completed a warm-up protocol that commenced with 5 minutes jogging at approximately 65% of maximal heart rate, followed by no stretching, static stretching, or dynamic stretching and finishing with a task-specific high-intensity activity. Using a crossover design, the 3 warm-up protocols were performed in a counterbalanced order with at least 48 hours between sessions. Repeated sprint performance was measured using a repeated sprint test that consisted of 6 × 40-m maximal sprints interspersed with a 20-second recovery. There were trivial differences in mean sprint time (0.2%) and posttest blood lactate (3.1%) between the 2-phase warm-up and the 3-phase warm-up that included dynamic stretching, whereas the short warm-up had a possibly detrimental effect on fastest sprint time (0.7%). Fastest (-1.1%) and mean (-1.2%) sprint times were quicker and posttest blood lactates were higher (13.2%) after the 2-phase warm-up when compared with the 3-phase warm-up that included static stretching. Although it is not harmful to complete a traditional 3-phase warm-up that includes dynamic stretching, it appears practical for athletes preparing for activities dependent on repeated sprint ability to complete a 2-phase warm-up consisting of a cardiovascular and specific high-intensity activity.

  19. C-terminal sequences of hsp70 and hsp90 as non-specific anchors for tetratricopeptide repeat (TPR) proteins.

    Science.gov (United States)

    Ramsey, Andrew J; Russell, Lance C; Chinkers, Michael

    2009-10-12

    Steroid-hormone-receptor maturation is a multi-step process that involves several TPR (tetratricopeptide repeat) proteins that bind to the maturation complex via the C-termini of hsp70 (heat-shock protein 70) and hsp90 (heat-shock protein 90). We produced a random T7 peptide library to investigate the roles played by the C-termini of the two heat-shock proteins in the TPR-hsp interactions. Surprisingly, phages with the MEEVD sequence, found at the C-terminus of hsp90, were not recovered from our biopanning experiments. However, two groups of phages were isolated that bound relatively tightly to HsPP5 (Homo sapiens protein phosphatase 5) TPR. Multiple copies of phages with a C-terminal sequence of LFG were isolated. These phages bound specifically to the TPR domain of HsPP5, although mutation studies produced no evidence that they bound to the domain's hsp90-binding groove. However, the most abundant family obtained in the initial screen had an aspartate residue at the C-terminus. Two members of this family with a C-terminal sequence of VD appeared to bind with approximately the same affinity as the hsp90 C-12 control. A second generation pseudo-random phage library produced a large number of phages with an LD C-terminus. These sequences acted as hsp70 analogues and had relatively low affinities for hsp90-specific TPR domains. Unfortunately, we failed to identify residues near hsp90's C-terminus that impart binding specificity to individual hsp90-TPR interactions. The results suggest that the C-terminal sequences of hsp70 and hsp90 act primarily as non-specific anchors for TPR proteins.

  20. Repeat Finding Techniques, Data Structures and Algorithms in DNA sequences: A Survey

    Directory of Open Access Journals (Sweden)

    Freeson Kaniwa

    2015-09-01

    Full Text Available DNA sequencing technologies keep getting faster and cheaper leading to massive availability of entire human genomes. This massive availability calls for better analysis tools with a potential to realize a shift from reactive to predictive medicine. The challenge remains, since the entire human genomes need more space and processing power than that can be offered by a standard Desktop PC for their analysis. A background of key concepts surrounding the area of DNA analysis is given and a review of selected prominent algorithms used in this area. The significance of this paper would be to survey the concepts surrounding DNA analysis so as to provide a deep rooted understanding and knowledge transfer regarding existing approaches for DNA analysis using Burrows-Wheeler transform, Wavelet tree and their respective strengths and weaknesses. Consequent to this survey, the paper attempts to provide some directions for future research.

  1. Expression of a new chimeric protein with a highly repeated sequence in tobacco cells.

    Science.gov (United States)

    Saumonneau, Amélie; Rottier, Karine; Conrad, Udo; Popineau, Yves; Guéguen, Jacques; Francin-Allami, Mathilde

    2011-07-01

    In wheat, the high-molecular weight (HMW) glutenin subunits are known to contribute to gluten viscoelasticity, and show some similarities to elastomeric animal proteins as elastin. When combining the sequence of a glutenin with that of elastin is a way to create new chimeric functional proteins, which could be expressed in plants. The sequence of a glutenin subunit was modified by the insertion of several hydrophobic and elastic motifs derived from elastin (elastin-like peptide, ELP) into the hydrophilic repetitive domain of the glutenin subunit to create a triblock protein, the objective being to improve the mechanical (elastomeric) properties of this wheat storage protein. In this study, we investigated an expression model system to analyze the expression and trafficking of the wild-type HMW glutenin subunit (GS(W)) and an HMW glutenin subunit mutated by the insertion of elastin motifs (GS(M)-ELP). For this purpose, a series of constructs was made to express wild-type subunits and subunits mutated by insertion of elastin motifs in fusion with green fluorescent protein (GFP) in tobacco BY-2 cells. Our results showed for the first time the expression of HMW glutenin fused with GFP in tobacco protoplasts. We also expressed and localized the chimeric protein composed of plant glutenin and animal elastin-like peptides (ELP) in BY-2 protoplasts, and demonstrated its presence in protein body-like structures in the endoplasmic reticulum. This work, therefore, provides a basis for heterologous production of the glutenin-ELP triblock protein to characterize its mechanical properties.

  2. Complete gene sequence of spider attachment silk protein (PySp1) reveals novel linker regions and extreme repeat homogenization.

    Science.gov (United States)

    Chaw, Ro Crystal; Saski, Christopher A; Hayashi, Cheryl Y

    2017-02-01

    Spiders use a myriad of silk types for daily survival, and each silk type has a unique suite of task-specific mechanical properties. Of all spider silk types, pyriform silk is distinct because it is a combination of a dry protein fiber and wet glue. Pyriform silk fibers are coated with wet cement and extruded into "attachment discs" that adhere silks to each other and to substrates. The mechanical properties of spider silk types are linked to the primary and higher-level structures of spider silk proteins (spidroins). Spidroins are often enormous molecules (>250 kDa) and have a lengthy repetitive region that is flanked by relatively short (∼100 amino acids), non-repetitive amino- and carboxyl-terminal regions. The amino acid sequence motifs in the repetitive region vary greatly between spidroin type, while motif length and number underlie the remarkable mechanical properties of spider silk fibers. Existing knowledge of pyriform spidroins is fragmented, making it difficult to define links between the structure and function of pyriform spidroins. Here, we present the full-length sequence of the gene encoding pyriform spidroin 1 (PySp1) from the silver garden spider Argiope argentata. The predicted protein is similar to previously reported PySp1 sequences but the A. argentata PySp1 has a uniquely long and repetitive "linker", which bridges the amino-terminal and repetitive regions. Predictions of the hydrophobicity and secondary structure of A. argentata PySp1 identify regions important to protein self-assembly. Analysis of the full complement of A. argentata PySp1 repeats reveals extreme intragenic homogenization, and comparison of A. argentata PySp1 repeats with other PySp1 sequences identifies variability in two sub-repetitive expansion regions. Overall, the full-length A. argentata PySp1 sequence provides new evidence for understanding how pyriform spidroins contribute to the properties of pyriform silk fibers. Copyright © 2017 The Authors. Published by

  3. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.

    Science.gov (United States)

    Isobe, Sachiko N; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

    2013-02-01

    The cultivated strawberry (Fragaria × ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

  4. Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif.

    Science.gov (United States)

    Martin, Bryan T; Serrano, Pedro; Geralt, Michael; Wüthrich, Kurt

    2016-01-01

    The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.

  5. Effects of Carbohydrate Ingestion and Carbohydrate Mouth Rinse on Repeat Sprint Performance.

    Science.gov (United States)

    Krings, Ben M; Peterson, Timothy J; Shepherd, Brandon D; McAllister, Matthew J; Smith, JohnEric W

    2017-06-01

    The purpose of this investigation was to examine to the influence of carbohydrate ingestion (CHOI) and carbohydrate mouth rinse (CHOR) on acute repeat maximal sprint performance. Fourteen healthy males (age: 21.7 ± 1.8 years, mass: 82.3 ± 12.3 kg) completed a total of five 15-s maximal repeat sprints on a cycle ergometer against 0.075 kg ・ kg(-1) body mass each separated by 4 min of active recovery. Subjects completed four experimental trials and were randomly assigned one of four treatments: (1) CHOI, (2) CHOR, (3) placebo mouth rinse (PLAR), (4) placebo ingestion (PLAI). Subjects rinsed or ingested six 50 mL 10% CHO solutions throughout each trial. Performance variables measured included rating of perceived exertion, peak heart rate, peak and mean power output, fatigue index, and total work. Significant treatment main effects were observed for mean power output (p = 0.026), total work (p = 0.020), fatigue index (p = 0.004), and heart rate (p = 0.013). Overall mean power output and total work were significantly greater with CHOI (659.3 ± 103.0 watts, 9849.8 ± 1598.8 joules) compared with CHOR (645.8 ± 99.7 watts, 9447.5 ± 1684.9 joules, p PLAI, and PLAR. Athletes required to complete repeat bouts of high intensity exercise may benefit from CHOI.

  6. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

    Science.gov (United States)

    Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

    2015-10-01

    Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

  7. Effects of red bull energy drink on repeated sprint performance in women athletes.

    Science.gov (United States)

    Astorino, Todd A; Matera, Angela J; Basinger, Jency; Evans, Mindy; Schurman, Taylor; Marquez, Rodney

    2012-05-01

    Energy drinks are frequently consumed by athletes prior to competition to improve performance. This study examined the effect of Red Bull™ on repeated sprint performance in women athletes. Fifteen collegiate soccer players participated, with mean age, height, and body mass equal to 19.5±1.1 year, 168.4±5.8 cm, and 63.4±6.1 kg, respectively. After performing a familiarization trial, subjects performed three sets of eight bouts of the modified t test after ingestion of 255 mL of placebo or Red Bull 1 h pre-exercise in a randomized, placebo-controlled crossover design. Throughout testing, sprint time, heart rate (HR), and rating of perceived exertion (RPE) were continuously obtained. Repeated measures analysis of variance was used to examine differences in variables between drink conditions. Across athletes, t test time ranged from 10.4 to 12.7 s. Mean sprint time was similar (p>0.05) between Red Bull (11.31±0.61 s) and placebo (11.35±0.61 s). HR and RPE increased (p0.05) of Red Bull on either variable versus placebo. Findings indicate that 255 mL of Red Bull containing 1.3 mg/kg of caffeine and 1 g of taurine does not alter repeated sprint performance, RPE, or HR in women athletes versus placebo. One serving of this energy drink provides no ergogenic benefit for women athletes engaging in sprint-based exercise.

  8. Effects of sodium bicarbonate, caffeine, and their combination on repeated 200-m freestyle performance.

    Science.gov (United States)

    Pruscino, Cathryn L; Ross, Megan L R; Gregory, John R; Savage, Bernard; Flanagan, Troy R

    2008-04-01

    The purpose of this study was to investigate the effects of sodium bicarbonate (NaHCO(3)), caffeine, and their combination on repeated 200-m freestyle performance. Six elite male freestyle swimmers ingested NaHCO(3) (0.3 g/kg; B), caffeine (6.2 +/- 0.3 mg/kg; C), a combination of both (B+C), and placebo (P) on 4 separate occasions before completing 2 maximal 200-m freestyle time trials (TT1 and TT2) separated by 30 min. No significant differences (p = .06) were observed for performance in TT1 (B 2:03.01 +/- 0:03.68 min, C 2:02.42 +/- 0:03.17 min, B+C 2:01.69 +/- 0:03.19 min, P 2:03.77 +/- 0:03.21 min) or TT2 (B 2:02.62 +/- 0:04.16 min, C 2:03.90 +/- 0:03.58 min, B+C 2:01.70 +/- 0:02.84 min, P 2:04.22 +/- 0:03.75 min). The drop-off in performance time from TT1 to TT2, however, was significantly greater when C was ingested than with B (-1.5%, p = .002) or B+C (-1.2%, p = .024). This is likely because of the lower blood pH and slower recovery of blood HCO(3) post-TT1 after C ingestion. These findings suggest that the ergogenic benefit of taking C alone for repeated 200-m swimming performance appears limited. When combined with NaHCO(3), however, its negative impact on repeated maximal exercise performance is reversed.

  9. Relationship Between Repeated Sprint Performance and both Aerobic and Anaerobic Fitness.

    Science.gov (United States)

    Dardouri, Wajdi; Selmi, Mohamed Amin; Sassi, Radhouane Haj; Gharbi, Zied; Rebhi, Ahmed; Yahmed, Mohamed Haj; Moalla, Wassim

    2014-03-27

    The aims of this study were firstly, to examine the relationship between repeated sprint performance indices and anaerobic speed reserve (AnSR), aerobic fitness and anaerobic power and secondly, to identify the best predictors of sprinting ability among these parameters. Twenty nine subjects (age: 22.5 ± 1.6 years, body height: 1.8 ± 0.1 m, body mass: 68.8 ± 8.5 kg, body mass index (BMI): 22.2 ± 2.1 kg•m-2, fat mass: 11.3 ± 2.9 %) participated in this study. All participants performed a 30 m sprint test (T30) from which we calculated the maximal anaerobic speed (MAnS), vertical and horizontal jumps, 20m multi-stage shuttle run test (MSRT) and repeated sprint test (10 × 15 m shuttle run). AnSR was calculated as the difference between MAnS and the maximal speed reached in the MSRT. Blood lactate sampling was performed 3 min after the RSA protocol. There was no significant correlation between repeated sprint indices (total time (TT); peak time (PT), fatigue index (FI)) and both estimated VO2max and vertical jump performance). TT and PT were significantly correlated with T30 (r=0.63, p=0.001 and r=0.62, p=0.001; respectively), horizontal jump performance (r = -0.47, p = 0.001 and r = -0.49, p = 0.006; respectively) and AnSR (r=-0.68, p= 0.001 and r=-0.70, p=0.001, respectively). Significant correlations were found between blood lactate concentration and TT, PT, and AnSR (r=-0.44, p=0.017; r=-0.43, p=0.018 and r=0.44, p=0.016; respectively). Stepwise multiple regression analyses demonstrated that AnSR was the only significant predictor of the TT and PT, explaining 47% and 50% of the shared variance, respectively. Our findings are of particular interest for coaches and fitness trainers in order to predict repeated sprint performance by using AnSR that can easily identify the respective upper performance limits supported by aerobic and anaerobic power of a player involved in multi-sprint team sports.

  10. Relationship Between Repeated Sprint Performance and both Aerobic and Anaerobic Fitness

    Science.gov (United States)

    Dardouri, Wajdi; Selmi, Mohamed Amin; Sassi, Radhouane Haj; Gharbi, Zied; Rebhi, Ahmed; Yahmed, Mohamed Haj; Moalla, Wassim

    2014-01-01

    The aims of this study were firstly, to examine the relationship between repeated sprint performance indices and anaerobic speed reserve (AnSR), aerobic fitness and anaerobic power and secondly, to identify the best predictors of sprinting ability among these parameters. Twenty nine subjects (age: 22.5 ± 1.6 years, body height: 1.8 ± 0.1 m, body mass: 68.8 ± 8.5 kg, body mass index (BMI): 22.2 ± 2.1 kg•m-2, fat mass: 11.3 ± 2.9 %) participated in this study. All participants performed a 30 m sprint test (T30) from which we calculated the maximal anaerobic speed (MAnS), vertical and horizontal jumps, 20m multi-stage shuttle run test (MSRT) and repeated sprint test (10 × 15 m shuttle run). AnSR was calculated as the difference between MAnS and the maximal speed reached in the MSRT. Blood lactate sampling was performed 3 min after the RSA protocol. There was no significant correlation between repeated sprint indices (total time (TT); peak time (PT), fatigue index (FI)) and both estimated VO2max and vertical jump performance). TT and PT were significantly correlated with T30 (r=0.63, p=0.001 and r=0.62, p=0.001; respectively), horizontal jump performance (r = −0.47, p = 0.001 and r = −0.49, p = 0.006; respectively) and AnSR (r=−0.68, p= 0.001 and r=−0.70, p=0.001, respectively). Significant correlations were found between blood lactate concentration and TT, PT, and AnSR (r=−0.44, p=0.017; r=−0.43, p=0.018 and r=0.44, p=0.016; respectively). Stepwise multiple regression analyses demonstrated that AnSR was the only significant predictor of the TT and PT, explaining 47% and 50% of the shared variance, respectively. Our findings are of particular interest for coaches and fitness trainers in order to predict repeated sprint performance by using AnSR that can easily identify the respective upper performance limits supported by aerobic and anaerobic power of a player involved in multi-sprint team sports. PMID:25031682

  11. Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; Suk Ha Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop.Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers.In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice

  12. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

    Science.gov (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

    2014-11-01

    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  13. Selection and development of representative simple sequence repeat primers and multiplex SSR sets for high throughput automated genotyping in maize

    Institute of Scientific and Technical Information of China (English)

    WANG FengGe; ZHAO JiuRan; DAI JingRui; YI HongMei; KUANG Meng; SUN YanMei; YU XinYan; GUO JingLun; WANG Lu

    2007-01-01

    In the current study, 1900 maize simple sequence repeat (SSR) primers published in MaizeGDB were screened utilizing reference literature, 15 representative Chinese maize inbred lines and 15 Chinese maize hybrids from national regional testing. In total, 500 highly polymorphic primers were identified and used to construct a genetic map. 100 evenly distributed primers, 10 primers per chromosome, were further selected as a set of universal SSR core primers, recommended as preferred primers for general studies. These core primers were then redesigned and used to construct a high throughput multiplex PCR system based on a five-color fluorescence capillary detection system. We report here that two sets of ten-plex PCR combinations have been constructed, each consisting of 10 primers, with one primer per chromosome.

  14. Common interruptions in the repeating tripeptide sequence of non-fibrillar collagens: sequence analysis and structural studies on triple-helix peptide models.

    Science.gov (United States)

    Thiagarajan, Geetha; Li, Yingjie; Mohs, Angela; Strafaci, Christopher; Popiel, Magdalena; Baum, Jean; Brodsky, Barbara

    2008-02-22

    Interruptions in the repeating (Gly-X1-X2)(n) amino acid sequence pattern are found in the triple-helix domains of all non-fibrillar collagens, and perturbations to the triple-helix at such sites are likely to play a role in collagen higher-order structure and function. This study defines the sequence features and structural consequences of the most common interruption, where one residue is missing from the tripeptide pattern, Gly-X1-X2-Gly-AA(1)-Gly-X1-X2, designated G1G interruptions. Residues found within G1G interruptions are predominantly hydrophobic (70%), followed by a significant amount of charged residues (16%), and the Gly-X1-X2 triplets flanking the interruption are atypical. Studies on peptide models indicate the degree of destabilization is much greater when Pro is in the interruption, GP, than when hydrophobic residues (GF, GY) are present, and a rigid Gly-Pro-Hyp tripeptide adjacent to the interruption leads to greater destabilization than a flexible Gly-Ala-Ala sequence. Modeling based on NMR data indicates the Phe residue within a GF interruption is located on the outside of the triple helix. The G1G interruptions resemble a previously studied collagen interruption GPOGAAVMGPO, designated G4G-type, in that both are destabilizing, but allow continuation of rod-like triple helices and maintenance of the single residue stagger throughout the imperfection, with a loss of axial register of the superhelix on both sides. Both kinds of interruptions result in a highly localized perturbation in hydrogen bonding and dihedral angles, but the hydrophobic residue of a G4G interruption packs near the central axis of the superhelix, while the hydrophobic residue of a G1G interruption is located on the triple-helix surface. The different structural consequences of G1G and G4G interruptions in the repeating tripeptide sequence pattern suggest a physical basis for their differential susceptibility to matrix metalloproteinases in type X collagen.

  15. Development and characterization of 1,827 expressed sequence tag-derived simple sequence repeat markers for ramie (Boehmeria nivea L. Gaud.

    Directory of Open Access Journals (Sweden)

    Touming Liu

    Full Text Available Ramie (Boehmeria nivea L. Gaud is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strategies have been hampered by the shortage of simple sequence repeat (SSR markers. In our previous study, we had assembled de novo 43,990 expressed sequence tags (ESTs. In the present study, we searched these previously assembled ESTs for SSRs and identified 1,685 ESTs (3.83% containing 1,878 SSRs. Next, we designed 1,827 primer pairs complementary to regions flanking these SSRs, and these regions were designated as SSR markers. Among these markers, dinucleotide and trinucleotide repeat motifs were the most abundant types (36.4% and 36.3%, respectively, whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented <10% of the markers. The motif AG/CT was the most abundant, accounting for 28.74% of the markers. One hundred EST-SSR markers (97 SSRs located in genes encoding transcription factors and 3 SSRs in genes encoding cellulose synthases were amplified using polymerase chain reaction for detecting 24 ramie varieties. Of these 100 markers, 98 markers were successfully amplified and 81 markers were polymorphic, with 2-6 alleles among the 24 varieties. Analysis of the genetic diversity of all 24 varieties revealed similarity coefficients that ranged from 0.51 to 0.80. The EST-SSRs developed in this study represent the first large-scale development of SSR markers for ramie. These SSR markers could be used for development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping, and cultivar fingerprinting.

  16. Molecular cloning and long terminal repeat sequences of human endogenous retrovirus genes related to types A and B retrovirus genes

    Energy Technology Data Exchange (ETDEWEB)

    Ono, M.

    1986-06-01

    By using a DNA fragment primarily encoding the reverse transcriptase (pol) region of the Syrian hamster intracisternal A particle (IAP; type A retrovirus) gene as a probe, human endogenous retrovirus genes, tentatively termed HERV-K genes, were cloned from a fetal human liver gene library. Typical HERV-K genes were 9.1 or 9.4 kilobases in length, having long terminal repeats (LTRs) of ca. 970 base pairs. Many structural features commonly observed on the retrovirus LTRs, such as the TATAA box, polyadenylation signal, and terminal inverted repeats, were present on each LTR, and a lysine (K) tRNA having a CUU anticodon was identified as a presumed primer tRNA. The HERV-K LTR, however, had little sequence homology to either the IAP LTR or other typical oncovirus LTRs. By filter hybridization, the number of HERV-K genes was estimated to be ca. 50 copies per haploid human genome. The cloned mouse mammary tumor virus (type B) gene was found to hybridize with both the HERV-K and IAP genes to essentially the same extent.

  17. Repeated-sprint performance and vastus lateralis oxygenation: effect of limited O₂ availability.

    Science.gov (United States)

    Billaut, F; Buchheit, M

    2013-06-01

    This study examined the influence of muscle deoxygenation and reoxygenation on repeated-sprint performance via manipulation of O2 delivery. Fourteen team-sport players performed 10 10-s sprints (30-s recovery) under normoxic (NM: FI O2 0.21) and acute hypoxic (HY: FI O2 0.13) conditions in a randomized, single-blind fashion and crossover design. Mechanical work was calculated and arterial O2 saturation (Sp O2 ) was estimated via pulse oximetry for every sprint. Muscle deoxyhemoglobin concentration ([HHb]) was monitored continuously by near-infrared spectroscopy. Differences between NM and HY data were analyzed for practical significance using magnitude-based inferences. HY reduced Sp O2 (-10.7 ± 1.9%, with chances to observe a higher/similar/lower value in HY of 0/0/100%) and mechanical work (-8.2 ± 2.1%; 0/0/100%). Muscle deoxygenation increased during sprints in both environments, but was almost certainly higher in HY (12.5 ± 3.1%, 100/0/0%). Between-sprint muscle reoxygenation was likely more attenuated in HY (-11.1 ± 11.9%; 2/7/91%). The impairment in mechanical work in HY was very largely correlated with HY-induced attenuation in muscle reoxygenation (r = 0.78, 90% confidence limits: 0.49; 0.91). Repeated-sprint performance is related, in part, to muscle reoxygenation capacity during recovery periods. These results extend previous findings that muscle O2 availability is important for prolonged repeated-sprint performance, in particular when the exercise is taken in hypoxia.

  18. Repeated-sprint performance, locomotor profile and muscle oxygen uptake recovery: effect of training background.

    Science.gov (United States)

    Ufland, P; Ahmaidi, S; Buchheit, M

    2013-10-01

    The aim of the present study was to examine the respective importance of locomotor profile and muscle oxygen uptake (mV(˙)O₂) recovery on repeated-sprint ability (RSA) and overall repeated-sprint performance. 11 sprint- (STR) and 10 middle-distance-trained (MDTR) athletes (20.8±4.0 yr) performed an incremental test and a 40-to-50-m sprint to estimate their maximal aerobic (MAS) and sprinting (MSS) speeds. They also performed 6×30-m sprints, departing every 30 s, where mean (RS(mean)) sprint time was calculated. Muscle oxygenation (Near-infrared spectroscopy, NIRS, [Hb(diff)]) was measured for ~ 4 min post test. The mean response time of [Hb(diff)]-mV(˙)O₂ recovery (monoexponential curve fitting, MRT[Hb(diff)]-mV(˙)O₂) was calculated. Compared with MDTR, STR presented faster MSS (+11.4±6.7%, with 99% chances to observe a substantially greater value) and RS(mean) (-3.7±5.4%, 78%), but slower MAS (-15.8±8.0%, 100%) and MRT[Hb(diff)]-mV(˙)O₂ (+46.2±31.7%, 96%). RS(mean) was largely correlated with MSS [r=-0.83 (90%CL, -0.92;-0.67)], but neither with MAS [r=-0.12 (-0.47;0.25)] nor MRT[Hb(diff)]-mV(˙)O₂ [r=-0.27(-0.58;0.11)]. RS(mean) adjusted for MSS (which indirectly reflects RSA) was largely correlated with both MAS [r=0.51(0.18;0.74)] and MRT[Hb(diff)]-mV(˙)O₂ [r=0.53(0.20;0.75)]. While a fast mV(˙)O₂ recovery is associated with an improved RSA, MSS remains of primary importance for overall repeated-sprint performance (i.e., RS(mean)).

  19. Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer.

    Directory of Open Access Journals (Sweden)

    Huping Xue

    Full Text Available BACKGROUND: Horizontal gene transfer (HGT is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr family has been compared among different sources of Staphylococcus aureus (S. aureus to discover sequence diversities within their genomes. METHODOLOGY/PRINCIPAL FINDINGS: Four sdr genes were analyzed for 21 different S. aureus strains and 218 mastitis-associated S. aureus isolates from Canada. Comparative genomic analyses revealed that S. aureus strains from bovine mastitis (RF122 and mastitis isolates in this study, ovine mastitis (ED133, pig (ST398, chicken (ED98, and human methicillin-resistant S. aureus (MRSA (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9 were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in sdr genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of sdrC gene among different strains. Moreover, the sdr genes could be used to type S. aureus. Regional difference of sdr genes distribution was also indicated among the tested S. aureus isolates. Finally, certain associations were found between sdr genes and subclinical or clinical mastitis isolates. CONCLUSIONS: Certain sdr gene sequences were shared in S. aureus strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may

  20. The relationship between short- and long-distance swimming performance and repeated sprint ability.

    Science.gov (United States)

    Meckel, Yoav; Bishop, David J; Rabinovich, Moran; Kaufman, Leonid; Nemet, Dan; Eliakim, Alon

    2012-12-01

    The purpose of this study was to determine indices of repeated sprint ability (RSA) during a repeated sprint swimming test (RST), to compare these with previous similar running and cycling RST, and to correlate these indices with the best short (100 m, as an index of anaerobic performance) and long (2,000 m, as an index of aerobic performance) distance swimming times in 20 elite, national team level, male swimmers. Indices of RSA included the ideal sprint time (IS), the total sprint time (TS), and the performance decrement (PD) recorded during an 8 × 15-m swimming RST. The PD during the present swimming RST (4.7 ± 2.3%) was similar to that in previous running or cycling RSTs. However, the physiological responses after the swimming RST (heart rate 168 ± 7 b·min(-1) and blood lactate concentration 5.5 ± 2.0 mmol·L(-1)) were lower than typical responses after running or cycling RSTs. There was no significant relationship between any of the RST performance indices and either the 100-m or 2,000-m swimming results. Multiple regression analysis indicated that the 3 RST indices (IS, TS, and PD), contributed 36% of the variance of the 2,000-m, but not the 100-m, swimming time. A strong correlation was found between the 100- and 2,000-m swim times (r = 0.74, p 100- and 2,000-m swim times is unique for swimming.

  1. Improvement of Repeated-Sprint Ability and Horizontal-Jumping Performance in Elite Young Basketball Players With Low-Volume Repeated-Maximal-Power Training.

    Science.gov (United States)

    Gonzalo-Skok, Oliver; Tous-Fajardo, Julio; Arjol-Serrano, José Luis; Suarez-Arrones, Luis; Casajús, José Antonio; Mendez-Villanueva, Alberto

    2016-05-01

    To examine the effects of a low-volume repeated-power-ability (RPA) training program on repeated-sprint and change-of- direction (COD) ability and functional jumping performance. Twenty-two male elite young basketball players (age 16.2 ± 1.2 y, height 190.0 ± 10.0 cm, body mass 82.9 ± 10.1 kg) were randomly assigned either to an RPA-training group (n = 11) or a control group (n = 11). RPA training consisted of leg-press exercise, twice a week for 6 wk, of 1 or 2 blocks of 5 sets × 5 repetitions with 20 s of passive recovery between sets and 3 min between blocks with the load that maximized power output. Before and after training, performance was assessed by a repeated-sprint-ability (RSA) test, a repeated-COD-ability test, a hop for distance, and a drop jump followed by tests of a double unilateral hop with the right and left legs. Within-group and between-groups differences showed substantial improvements in slowest (RSAs) and mean time (RSAm) on RSA; best, slowest and mean time on repeated-COD ability; and unilateral right and left hop in the RPA group in comparison with control. While best time on RSA showed no improvement in any group, there was a large relationship (r = .68, 90% CI .43;.84) between the relative decrement in RSAm and RSAs, suggesting better sprint maintenance with RPA training. The relative improvements in best and mean repeated-COD ability were very largely correlated (r = .89, 90% CI .77;.94). Six weeks of lowvolume (4-14 min/wk) RPA training improved several physical-fitness tests in basketball players.

  2. Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers.

    Science.gov (United States)

    Wu, Zhi-Gang; Jiang, Wu; Mantri, Nitin; Bao, Xiao-Qing; Chen, Song-Lin; Tao, Zheng-Ming

    2015-04-30

    Yam (Dioscorea alata L.) is an important tuber crop and purple pigmented elite cultivar has recently become popular because of associated health benefits. Identifying candidate genes responsible for flavonoid biosynthesis pathway (FBP) will facilitate understanding the molecular mechanism of controlling pigment formation in yam tubers. Here, we used Illumina sequencing to characterize the transcriptome of tubers from elite purple-flesh cultivar (DP) and conventional white-flesh cultivar (DW) of yam. In this process, we also designed high quality molecular markers to assist molecular breeding for tuber trait improvement. A total of 125,123 unigenes were identified from the DP and DW cDNA libraries, of which about 49.5% (60,020 unigenes) were annotated by BLASTX analysis using the publicly available protein database. These unigenes were further annotated functionally and subject to biochemical pathway analysis. 511 genes were identified to be more than 2-fold (FDR yam cultivars, of which 288 genes were up-regulated and 223 genes were down-regulated in the DP tubers. Transcriptome analysis detected 61 unigenes encoding multiple well-known enzymes in the FBP. Furthermore, the unigenes encoding chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3'-monooxygenase (F3'H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were found to be significantly up-regulated in the DP, implying that these genes were potentially associated with tuber color formation in this elite cultivar. The expression of these genes was further confirmed by qRT-PCR. Finally, 11,793 SSRs were successfully identified with these unigenes and 6,082 SSR markers were developed using Primer 3. This study provides the first comprehensive transcriptomic dataset for yam tubers, which will significantly contribute to genomic research of this and other related species. Some key genes associated with purple-flesh trait were

  3. 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.

  4. The effects of oral creatine supplementation on performance in single and repeated sprint swimming.

    Science.gov (United States)

    Peyrebrune, M C; Nevill, M E; Donaldson, F J; Cosford, D J

    1998-04-01

    We studied the effects of oral creatine supplementation on sprint swimming performance in 14 elite competitive male swimmers. The subjects performed a single sprint (1 x 50 yards [45.72 m]) and repeated sprint set (8 x 50 yards at intervals of 1 min 30 s) before and after a 5 day period of either creatine (9 g creatine + 4.5 g maltodextrin + 4.5 g glucose day(-1)) or placebo (18 g glucose day(-1); double-blind protocol) supplementation. Venous and capillary blood samples were taken for the determination of plasma ammonia, blood pH and lactate. Mean times recorded for the single 50 yard sprint were unchanged as a result of supplementation (creatine vs control, N.S.). During the repeated sprint test, mean times increased (Pcreatine supplementation (sprints 1-8: control pre-, 23.35+/-0.68 to 26.32+/-1.34 s; control post-, 23.59+/-0.66 to 26.19+/-1.48 s; creatine pre-, 23.20+/-0.67 to 26.85+/-0.42 s; creatine post-, 23.39+/-0.54 to 25.73+/-0.26 s; P creatine supplementation (control, 12.7+/-5.7% vs 11.0+/-5.5%; creatine, 15.7+/-4.3% vs 10.0+/-2.5%; Pcreatine in this group of swimmers after an identical supplementation regimen. In summary, our results suggest that ingesting 9 g creatine per day for 5 days can improve swimming performance in elite competitors during repeated sprints, but appears to have no effect on a single 50 yard sprint.

  5. Effect of Beta alanine and sodium bicarbonate supplementation on repeated-sprint performance.

    Science.gov (United States)

    Ducker, Kagan J; Dawson, Brian; Wallman, Karen E

    2013-12-01

    This study aimed to investigate if combining beta alanine (BA) and sodium bicarbonate (NaHCO3) supplementation could lead to enhanced repeated-sprint performance in team-sport athletes, beyond what is possible with either supplement alone. Participants (n = 24) completed duplicate trials of a repeated-sprint test (3 sets; 6 × 20 m departing every 25 seconds, 4 minutes active recovery between sets) and were then allocated into 4 groups as follows: BA only (n = 6; 28 days BA, acute sodium chloride placebo); NaHCO3 only (n = 6; 28 days glucose placebo, acute NaHCO3); BA/NaHCO3 (n = 6; 28 days BA, acute NaHCO3); placebo only (n = 6; 28 days glucose placebo, acute sodium chloride placebo), then completed duplicate trials postsupplementation. Sodium bicarbonate alone resulted in moderate effect size (d = 0.40-0.71) and "likely" and "very likely" benefit for overall total sprint times (TST) and for each individual set and for first sprint (sets 2 and 3) and best sprint time (sets 2 and 3). Combining BA and NaHCO3 resulted in "possible" to "likely" benefits for overall TST and for sets 2 and 3. First sprint (set 3) and best sprint time (sets 2 and 3) also showed "likely" benefit after this trial. The BA and placebo groups showed no differences in performance after supplementation. In conclusion, these results indicate that supplementation with acute NaHCO3 improved repeated-sprint performance more than either a combination of NaHCO3 and BA or BA alone.

  6. Influence of repeated bouts of eccentric exercise on high-intensity aerobic performance.

    Science.gov (United States)

    Higino, Wonder Passoni; Aparecido de Souza, Renato; Cavalcanti, Fabio de Sousa; Cardoso, Anderlei Dos Santos; Vasconcelos, Murilo Victor; Fernandes da Silva, Fabiano; Leme, José Alexandre C A

    2016-08-01

    [Purpose] It is believed that eccentric high-intensity exercise can decrease performance in subsequent exercise. However, with repetition, the deleterious effects can be minimized. Thus, this study evaluated the influence of repeated bouts of eccentric exercise on subsequent high-intensity aerobic performance. [Subjects and Methods] Seven healthy and sedentary male volunteers were recruited. a) Visit 1: determination of maximum oxygen uptake (VO2max) and speed associated with maximum oxygen uptake (vVO2max) in incremental treadmill testing; b) Visit 2: run to exhaustion at vVO2max (Tlim control); c) Visit 3: 10 sets of 10 depth jumps, followed by a run to exhaustion at vVO2max (Tlim 1); d) Visit 4: after 6 weeks without any physical training, the volunteers carried out the same procedures as on the third visit (Tlim 2). Data were analyzed using one-way analysis of variance (ANOVA) with the post-hoc Tukey test. [Results] Significant differences were found between Tlim control and Tlim 1 (283.4 ± 47.7 s vs. 125.2 ± 64.1 s, respectively), these were not different from Tlim 2. [Conclusion] Eccentric exercise showed deleterious effects on subsequent high-intensity aerobic performance. These effects were minimized after the exercise protocol was repeated 6 weeks after the first event.

  7. Phylogenetic placement of Cynomorium in Rosales inferred from sequences of the inverted repeat region of the chloroplast genome

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong ZHANG; Chun-Qi LI; Jian-hua LI

    2009-01-01

    Cynomorium is a herbaceous holoparasite that has been placed in Santalales, Saxifragales, Myrtales, or Sapindales. The inverted repeat (IR) region of the chloroplast genome region is slow evolving and, unlike mitochondrial genes, the chloroplast genome experiences few horizontal gene transfers between the host and parasite. Thus, in the present study, we used sequences of the IR region to test the phylogenetic placements of Cynomorium. Phylogenetic analyses of the chloroplast IR sequences generated largely congruent ordinal relationships with those from previous studies of angiosperm phylogeny based on single or multiple genes. Santalales was closely related to Caryophyllales and asterids. Saxifragales formed a clade where Peridiscus was sister to the remainder of the order, whereas Paeonia was sister to the woody clade of Saxifragales. Cynomorium is not closely related to Santalales, Saxifragales, Myrtales, or Sapindales; instead, it is included in Rosales and sister to Rosaceae. The various placements of the holoparasite on the basis of different regions of the mitochondrial genome may indicate the heterogeneous nature of the genome in the parasite. However, it is unlikely that the placement of Cynomorium in Rosales is the result of chloroplast gene transfer because Cynomorium does not parasitize on rosaceous plants and there is no chloroplast gene transfer between Cynomorium and Nitraria, a confirmed host of Cynomorium and a member of Sapindales.

  8. Development and Characterization of Simple Sequence Repeat Markers Providing Genome-Wide Coverage and High Resolution in Maize

    Science.gov (United States)

    Xu, Jie; Liu, Ling; Xu, Yunbi; Chen, Churun; Rong, Tingzhao; Ali, Farhan; Zhou, Shufeng; Wu, Fengkai; Liu, Yaxi; Wang, Jing; Cao, Moju; Lu, Yanli

    2013-01-01

    Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study. PMID:23804557

  9. Effect of endurance training on performance and muscle reoxygenation rate during repeated-sprint running.

    Science.gov (United States)

    Buchheit, Martin; Ufland, Pierre

    2011-02-01

    The aim of the present study was to examine the effect of an 8-week endurance training program on repeated-sprint (RS) performance and post-sprints muscle reoxygenation rate in 18 moderately trained males (34 ± 5 years). Maximal aerobic speed (MAS), 10 km running and RS (2 × 15-s shuttle-sprints, interspersed with 15 s of passive recovery) performance were assessed before and after the training intervention. Total distance covered (TD) and the percentage of distance decrement (%Dec) were calculated for RS. Between-sprints muscle reoxygenation rate (Reoxy rate) was assessed with near-infrared spectroscopy during RS before and after training. After training, MAS (+9.8 ± 5.8%, with 100% chances to observe a substantial improvement), 10 km time (-6.2 ± 5.3%, 99%), TD (+9.6 ± 7.7%, 98%), %Dec (-25.6 ± 73.6%, 93%) and Reoxy rate (+152.4 ± 308.1%, 95%) were improved. The improvement of Reoxy rate was largely correlated with improvements in MAS [r = 0.63 (90% CL, 0.31;-0.82)] and %Dec [r = -0.52 (-0.15;-0.76)]. Present findings confirm the beneficial effect of endurance training on post-sprint muscle reoxygenation rate, which is likely to participate in the improvement of repeated-sprint ability after training. These data also confirm the importance of aerobic conditioning in sports, where repeating high-intensity/maximal efforts within a short time-period are required.

  10. Effect of cold water immersion on repeated cycling performance and limb blood flow.

    Science.gov (United States)

    Vaile, J; O'Hagan, C; Stefanovic, B; Walker, M; Gill, N; Askew, C D

    2011-08-01

    The purpose of the present study was to compare the effects of cold water immersion (CWI) and active recovery (ACT) on resting limb blood flow, rectal temperature and repeated cycling performance in the heat. Ten subjects completed two testing sessions separated by 1 week; each trial consisted of an initial all-out 35-min exercise bout, one of two 15-min recovery interventions (randomised: CWI or ACT), followed by a 40-min passive recovery period before repeating the 35-min exercise bout. Performance was measured as the change in total work completed during the exercise bouts. Resting limb blood flow, heart rate, rectal temperature and blood lactate were recorded throughout the testing sessions. There was a significant decline in performance after ACT (mean (SD) -1.81% (1.05%)) compared with CWI where performance remained unchanged (0.10% (0.71%)). Rectal temperature was reduced after CWI (36.8°C (1.0°C)) compared with ACT (38.3°C (0.4°C)), as was blood flow to the arms (CWI 3.64 (1.47) ml/100 ml/min; ACT 16.85 (3.57) ml/100 ml/min) and legs (CW 4.83 (2.49) ml/100 ml/min; ACT 4.83 (2.49) ml/100 ml/min). Leg blood flow at the end of the second exercise bout was not different between the active (15.25 (4.33) ml/100 ml/min) and cold trials (14.99 (4.96) ml/100 ml/min), whereas rectal temperature (CWI 38.1°C (0.3°C); ACT 38.8°C (0.2°C)) and arm blood flow (CWI 20.55 (3.78) ml/100 ml/min; ACT 23.83 (5.32) ml/100 ml/min) remained depressed until the end of the cold trial. These findings indicate that CWI is an effective intervention for maintaining repeat cycling performance in the heat and this performance benefit is associated with alterations in core temperature and limb blood flow.

  11. Association Analysis of Simple Sequence Repeat (SSR Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb..

    Directory of Open Access Journals (Sweden)

    Yanhong Lou

    Full Text Available Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia, were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR markers. The panel displayed significant variation in spike count per plant (SCP and spike weight (SW. However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single

  12. Sequence analysis of the fragile X trinucleotide repeat: Correlations with stability and haplotype and implications for the origin of fragile X alleles

    Energy Technology Data Exchange (ETDEWEB)

    Snow, K.; Tester, D.J.; Kruckeberg, K.E.; Thibodeau, S.N. [Mayo Clinic, Rochester, MN (United States)

    1994-09-01

    Fragile X (FX) syndrome is associated with amplification of a CGG trinucleotide repeat in the 5{prime} untranslated region of the gene FMR-1. To address mechanism of instability and concern related to overlap between sizes of normal stable alleles and FX unstable alleles, we have sequenced 165 alleles to analyze patterns of AGG interruptions within the CGG repeat, and have typed the (CA)n at DXS548 for 204 chromosomes. Overall, our data is consistent with the idea that the length of uninterrupted CGG repeats determines instability. For 17 stably transmitted alleles with total repeat lengths between 33 and 51, the longest stretch of uninterrupted CGGs was 41. In contrast, for 13 premutation alleles, the shortest stretch of uninterrupted CGGs was 48, suggesting a threshold for expansion between 41 and 48 pure CGGs. For expansion from a premutation to a full mutation, the threshold appears to be {ge}70 uninterrupted repeats. Interestingly, an AGG was detected in some carriers of a full mutation. Comparison of the number of {open_quote}shadow bands{close_quote} in PCR products from similar size alleles with different AGG interruption patterns supports replication slippage as a potential mechanism, i.e. replication slippage occurs more readily as the length of pure repeat increases. Alleles with high total repeat lengths but up to 3 AGGs may be relatively protected against expansion, whereas smaller alleles with pure CGG sequence could be at higher risk for instability. Comparison of sequence data and DXS548 (CA)n data revealed specific sequence trends for each of the DXS548 alleles, explaining the previously reported haplotype association with FX. Incorporating these observations into models for the origin of FX alleles, we consider replication slippage, unequal crossover within the CGG repeat region, recombination between FMR-1 and DXS548, and loss of AGGs by A to C transversion.

  13. Data driven models of the performance and repeatability of NIF high foot implosions

    Science.gov (United States)

    Gaffney, Jim; Casey, Dan; Callahan, Debbie; Hartouni, Ed; Ma, Tammy; Spears, Brian

    2015-11-01

    Recent high foot (HF) inertial confinement fusion (ICF) experiments performed at the national ignition facility (NIF) have consisted of enough laser shots that a data-driven analysis of capsule performance is feasible. In this work we use 20-30 individual implosions of similar design, spanning laser drive energies from 1.2 to 1.8 MJ, to quantify our current understanding of the behavior of HF ICF implosions. We develop a probabilistic model for the projected performance of a given implosion and use it to quantify uncertainties in predicted performance including shot-shot variations and observation uncertainties. We investigate the statistical significance of the observed performance differences between different laser pulse shapes, ablator materials, and capsule designs. Finally, using a cross-validation technique, we demonstrate that 5-10 repeated shots of a similar design are required before real trends in the data can be distinguished from shot-shot variations. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-674957.

  14. Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy.

    Directory of Open Access Journals (Sweden)

    Shengpei Chen

    Full Text Available Ultra-low coverage sequencing (ULCS is one of the most promising strategies for sequencing based clinical application. These clinical applications, especially prenatal diagnosis, have a strict requirement of turn-around-time; therefore, the application of ULCS is restricted by current high throughput sequencing platforms. Recently, the emergence of rapid sequencing platforms, such as MiSeq and Ion Proton, brings ULCS strategy into a new era. The comparison of their performance could shed lights on their potential application in large-scale clinic trials. In this study, we performed ULCS (<0.1X coverage on both MiSeq and Ion Proton platforms for 18 spontaneous abortion fetuses carrying aneuploidy and compared their performance on different levels. Overall basic data and GC bias showed no significant difference between these two platforms. We also found the sex and aneuploidy detection indicated 100% sensitivity and 100% specificity on both platforms. Our study generated essential data from these two rapid sequencing platforms, which provides useful reference for later research and potentially accelerates the clinical applications of ULCS.

  15. Assessing the performance of quantum repeaters for all phase-insensitive Gaussian bosonic channels

    Science.gov (United States)

    Goodenough, K.; Elkouss, D.; Wehner, S.

    2016-06-01

    One of the most sought-after goals in experimental quantum communication is the implementation of a quantum repeater. The performance of quantum repeaters can be assessed by comparing the attained rate with the quantum and private capacity of direct transmission, assisted by unlimited classical two-way communication. However, these quantities are hard to compute, motivating the search for upper bounds. Takeoka, Guha and Wilde found the squashed entanglement of a quantum channel to be an upper bound on both these capacities. In general it is still hard to find the exact value of the squashed entanglement of a quantum channel, but clever sub-optimal squashing channels allow one to upper bound this quantity, and thus also the corresponding capacities. Here, we exploit this idea to obtain bounds for any phase-insensitive Gaussian bosonic channel. This bound allows one to benchmark the implementation of quantum repeaters for a large class of channels used to model communication across fibers. In particular, our bound is applicable to the realistic scenario when there is a restriction on the mean photon number on the input. Furthermore, we show that the squashed entanglement of a channel is convex in the set of channels, and we use a connection between the squashed entanglement of a quantum channel and its entanglement assisted classical capacity. Building on this connection, we obtain the exact squashed entanglement and two-way assisted capacities of the d-dimensional erasure channel and bounds on the amplitude-damping channel and all qubit Pauli channels. In particular, our bound improves on the previous best known squashed entanglement upper bound of the depolarizing channel.

  16. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    Directory of Open Access Journals (Sweden)

    Oussama Ahrazem

    2012-05-01

    Full Text Available Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  17. Procedural Memory Consolidation in the Performance of Brief Keyboard Sequences

    Science.gov (United States)

    Duke, Robert A.; Davis, Carla M.

    2006-01-01

    Using two sequential key press sequences, we tested the extent to which subjects' performance on a digital piano keyboard changed between the end of training and retest on subsequent days. We found consistent, significant improvements attributable to sleep-based consolidation effects, indicating that learning continued after the cessation of…

  18. Retroviral sequence located in border region of short unique region and short terminal repeat of Md5 strain of Marek's disease virus type 1.

    Science.gov (United States)

    Endoh, D; Ito, M; Cho, K O; Kon, Y; Morimura, T; Hayashi, M; Kuwabara, M

    1998-02-01

    A 246-base pair (bp) retroviral sequence, which was homologous to a long terminal repeat of avian erythroblastosis virus (AEV), was detected and cloned from Md5 strain (Md5) of Marek's disease virus type 1 (MDV1) by representational difference analysis (RDA). The retroviral sequence was thought to be located in the border region of short unique region (U(s) and short terminal repeat (TRs), but did not exist in the border region of U(s) and the inverted short repeat (IRs) of the Md5 genome. A cloned fragment of the US/TRs border region of the Md5 genome showed a construction of U-E'-R-U'-E-TRs with the regions designated as follows: E, expanded TRs reported by Jones et al. [Proc. Natl. Acad. Sci. U.S.A. 90, 3855, 1993]; E', a partial copy of the expanded TRs; R, the retroviral sequence detected in Md5 genome; U, TRs-end sequence of U(s); U', a partial copy of TRs-end sequence of U(s). The sequence unit indicated as E'-R-U' was thought to be heterogeneously repeated in the Md5 genome. Since this retroviral sequence reportedly did not exist in the original stock of Md5, the retroviral sequence is thought to be inserted in the Md5 genome without experimental co-infection of avian cells with retrovirus and MDV1. These results suggest that RDA could be useful for the detection of retroviral sequences in the herpesvirus genome.

  19. Effects of Learning on Performance When Computerized Dynamic Posturography Assessments Are Repeated

    Science.gov (United States)

    Taylor, Laura C.; Paloski, William H.; Wood, Scott J.

    2008-01-01

    Background: Computerized dynamic posturography is widely used to measure balance control performance. Clinically, performance is assessed by comparing individual data against standards obtained from a normative population. When performing repeated assessments to track performance changes, one must be concerned with the influence of learning effects. Subjects do not have the opportunity to practice before the first session, and often a second session is not performed prior to an experiment. Thus, the objective of this activity was to examine learning effects on balance control performance. We hypothesize that subjects will perform better on the second session when compared to the first, and that the difference will be greater for more difficult conditions. Methods: Data were collected from 204 subjects using the NeuroCom Equitest system during quiet stance with arms crossed at the chest on up to two sessions. All subjects performed standard sensory organization tests (SOTs) including 1) normal vision, fixed support; 2) absent vision, fixed support; 3) sway-referenced vision, fixed support; 4) normal vision, swayreferenced support; 5) absent vision, sway-referenced support; and 6) sway-referenced vision, sway-referenced support. 120 of these subjects performed modified sensory organization tests (mSOTs 2 and 5) which included static (20 back) and dynamic (20, 0.33Hz) head tilts. Median equilibrium scores (mEQ) were calculated from peak-to-peak anterior-posterior sway across trials. Data collected on the first session were then compared with the second to examine learning effect. Results: There were no differences in mEQ scores between the first and second sessions for SOTs 1, 2, and 4, while mEQ scores were higher for the second session when compared to the first for SOTs 3, 5, and 6 and for all mSOTs. Discussion: An additional familiarization session or practice trials prior to the first session may be necessary for more challenging SOT and mSOT conditions to

  20. Effects of combined creatine and sodium bicarbonate supplementation on repeated sprint performance in trained men.

    Science.gov (United States)

    Barber, James J; McDermott, Ann Y; McGaughey, Karen J; Olmstead, Jennifer D; Hagobian, Todd A

    2013-01-01

    Creatine and sodium bicarbonate supplementation independently increase exercise performance, but it remains unclear whether combining these 2 supplements is more beneficial on exercise performance. The purpose of this study was to evaluate the impact of combining creatine monohydrate and sodium bicarbonate supplementation on exercise performance. Thirteen healthy, trained men (21.1 ± 0.6 years, 23.5 ± 0.5 kg·m(-2), 66.7 ± 5.7 ml·(kg·m)(-1) completed 3 conditions in a double-blinded, crossover fashion: (a) Placebo (Pl; 20 g maltodextrin + 0.5 g·kg(-1) maltodextrin), (b) Creatine (Cr; 20 g + 0.5 g·kg(-1) maltodextrin), and (c) Creatine plus sodium bicarbonate (Cr + Sb; 20 g + 0.5 g·kg(-1) sodium bicarbonate). Each condition consisted of supplementation for 2 days followed by a 3-week washout. Peak power, mean power, relative peak power, and bicarbonate concentrations were assessed during six 10-second repeated Wingate sprint tests on a cycle ergometer with a 60-second rest period between each sprint. Compared with Pl, relative peak power was significantly higher in Cr (4%) and Cr + Sb (7%). Relative peak power was significantly lower in sprints 4-6, compared with that in sprint 1, in both Pl and Cr. However, in Cr + Sb, sprint 6 was the only sprint significantly lower compared with sprint 1. Pre-Wingate bicarbonate concentrations were significantly higher in Cr + Sb (10%), compared with in Pl and Cr, and mean concentrations remained higher after sprint 6, although not significantly. Combining creatine and sodium bicarbonate supplementation increased peak and mean power and had the greatest attenuation of decline in relative peak power over the 6 repeated sprints. These data suggest that combining these 2 supplements may be advantageous for athletes participating in high-intensity, intermittent exercise.

  1. Frequent mutations of the CA simple sequence repeat in intron 1 of EGFR in mismatch repair-deficient colorectal cancers

    Institute of Scientific and Technical Information of China (English)

    Marie-Pierre Buisine; Thècla Lesuffleur; Agnès Wacrenier; Christophe Mariette; Emmanuelle Leteurtre; Fabienne Escande; Sana Aissi; Amandine Ketele; Annette Leclercq; Nicole Porchet

    2008-01-01

    AIM:To investigate the polymorphic simple sequence repeat in intron 1 of the epidermal growth factor receptor gene(EGFR)(CA-SSR I),which is known to affect the efficiency of gene transcription as a putative target of the mismatch repair (MMR) machinery in colorectal tumors.METHODS:The CA-SSR I genotype was analyzed in a total of 86 primary colorectal tumors,selected upon their microsatellite instability (MSI) status [42 with high frequency MSI (MSI-H) and 44 microsatellite stable (MSS)]and their respective normal tissue.The effect of the CASSR I genotype on the expression of the EGFR gene was evaluated in 18 specimens using quantitative real-time reverse transcription PCR and immunohistochemistry.RESULTS:Mutations in CA-SSR I were detected in 86%(36 of 42) of MSI-H colorectal tumors and 0% (0 of 44) of MSS tumors,indicating the EGFR gene as a novel putative specific target of the defective MMR system (P<0.001).Impaired expression of EGFR was detected in most of the colorectal tumors analyzed [6/12 (50%) at the mRNA level and 15/18 (83%) at the peptide level].However,no association was apparent between EGFR expression and CA-SSR I status in tumors or normal tissues.CONCLUSION:Our results suggest that CA-SSR I sequence does not contribute to the regulation of EGFR transcription in colon,and should thus not be considered as a promising predictive marker for response to EGFR inhibitors in patients with colorectal cancer.

  2. Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers.

    Science.gov (United States)

    Silva, A V C; Nascimento, A L S; Vitória, M F; Rabbani, A R C; Soares, A N R; Lédo, A S

    2017-02-23

    Banana (Musa spp) is a fruit species frequently cultivated and consumed worldwide. Molecular markers are important for estimating genetic diversity in germplasm and between genotypes in breeding programs. The objective of this study was to analyze the genetic diversity of 21 banana genotypes (FHIA 23, PA42-44, Maçã, Pacovan Ken, Bucaneiro, YB42-47, Grand Naine, Tropical, FHIA 18, PA94-01, YB42-17, Enxerto, Japira, Pacovã, Prata-Anã, Maravilha, PV79-34, Caipira, Princesa, Garantida, and Thap Maeo), by using inter-simple sequence repeat (ISSR) markers. Material was generated from the banana breeding program of Embrapa Cassava & Fruits and evaluated at Embrapa Coastal Tablelands. The 12 primers used in this study generated 97.5% polymorphism. Four clusters were identified among the different genotypes studied, and the sum of the first two principal components was 48.91%. From the Unweighted Pair Group Method using Arithmetic averages (UPGMA) dendrogram, it was possible to identify two main clusters and subclusters. Two genotypes (Garantida and Thap Maeo) remained isolated from the others, both in the UPGMA clustering and in the principal cordinate analysis (PCoA). Using ISSR markers, we could analyze the genetic diversity of the studied material and state that these markers were efficient at detecting sufficient polymorphism to estimate the genetic variability in banana genotypes.

  3. Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Wang, Hui-Zhong; Wu, Zhen-Xing; Lu, Jiang-Jie; Shi, Nong-Nong; Zhao, Yan; Zhang, Zhi-Tao; Liu, Jun-Jun

    2009-07-01

    Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii.

  4. Inter-Simple Sequence Repeat (ISSR Markers to Study Genetic Diversity Among Cotton Cultivars in Associated with Salt Tolerance

    Directory of Open Access Journals (Sweden)

    Ali Akbar ABDI

    2012-11-01

    Full Text Available Developing salt-tolerant crops is very important as a significant proportion of cultivated land is salt-affected. Screening and selection of salt tolerant genotypes of cotton using DNA molecular markers not only introduce tolerant cultivars useful for hybridization and breeding programs but also detect DNA regions involved in mechanism of salinity tolerance. To study this, 28 cotton cultivars, including 8 Iranian cotton varieties were grown in pots under greenhouse condition and three salt treatments were imposed with salt solutions (0, 70 and 140 mM NaCl. Eight agronomic traits including root length, root fresh weight, root dry weight, chlorophyll and fluorescence index, K+ and Na+ contents in shoot (above ground biomass, and K+/Na+ ratio were measured. Cluster analysis of cultivars based on measured agronomic traits, showed �Cindose� and �Ciacra� as the most tolerant cultivars, and �B-557� and �43347� as the most sensitive cultivars of salt damage. A total of 65 polymorphic DNA fragments were generated at 14 inter-simple sequence repeat (ISSR loci. Plants of 28 cultivars of cotton grouped into three clusters based on ISSR markers. Regression analysis of markers in relation with traits data showed that 23, 33 and 30 markers associated with the measured traits in three salt treatments respectively. These markers might help breeders in any marker assisted selection program in order to improving cotton cultivars against salt stress.

  5. Regeneration and assessment of genetic fidelity of the endangered tree Moringa peregrina (Forsk.) Fiori using Inter Simple Sequence Repeat (ISSR).

    Science.gov (United States)

    Al Khateeb, Wesam; Bahar, Eman; Lahham, Jamil; Schroeder, Dana; Hussein, Emad

    2013-01-01

    Moringa peregrinais an endangered species of Moringaceae.M. peregrinais a multipurpose tree with a wide variety of potential uses including its medicinal activity. In our study, a rapid and efficient micropropagation protocol for M. peregrina has been established. In vitro germinated seedlings were cultured on Murashige and Skoog (MS) medium supplemented with different levels of either 6-benzyladenine (BA) or kinetin (Kin). The maximum shoot proliferation of 6.5 shoots per explant with 100 % shoot proliferation rate was observed on MS medium supplemented with 1.0 mg/l BA. On the other hand, MS medium supplemented with 1 mg/l indole-3-butyric acid (IBA) resulted in the maximum number of roots. Micropropagated plants were successfully acclimatized. Genetic stability of micropropagated plants was assessed using Inter-Simple Sequence Repeat (ISSR). The amplification products were monomorphic in all in vitro grown plants. No polymorphism was detected indicating the genetic integrity of in vitro propagated plants. This micropropagation protocol could be useful for raising genetically uniform plants for plant propagation and commercial cultivation.

  6. Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species.

    Science.gov (United States)

    Rai, Manoj K; Phulwaria, Mahendra; Shekhawat, N S

    2013-08-01

    Present study demonstrated the cross-genera transferability of 23 simple sequence repeat (SSR) primer pairs developed for guava (Psidium guajava L.) to four new targets, two species of eucalypts (Eucalyptus citriodora, Eucalyptus camaldulensis), bottlebrush (Callistemon lanceolatus) and clove (Syzygium aromaticum), belonging to the family Myrtaceae and subfamily Myrtoideae. Off the 23 SSR loci assayed, 18 (78.2%) gave cross-amplification in E. citriodora, 14 (60.8%) in E. camaldulensis and 17-17 (73.9%) in C. lanceolatus and S. aromaticum. Eight primer pairs were found to be transferable to all four species. The number of alleles detected at each locus ranged from one to nine, with an average of 4.8, 2.6, 4.5 and 4.6 alleles in E. citriodora, E. camaldulensis, C. lanceolatus and S. aromaticum, respectively. The high levels of cross-genera transferability of guava SSRs may be applicable for the analysis of intra- and inter specific genetic diversity of target species, especially in E. citriodora, C. lanceolatus and S. aromaticum, for which till date no information about EST-derived as well as genomic SSR is available.

  7. Genetic Diversity among Parents of Hybrid Rice Based on Cluster Analysis of Morphological Traits and Simple Sequence Repeat Markers

    Institute of Scientific and Technical Information of China (English)

    WANG Sheng-jun; LU Zuo-mei; WAN Jian-min

    2006-01-01

    The genetic diversity of 41 parental lines popularized in commercial hybrid rice production in China was studied by using cluster analysis of morphological traits and simple sequence repeat (SSR) markers. Forty-one entries were assigned into two clusters (I.e. Early or medium-maturing cluster; medium or late-maturing cluster) and further assigned into six sub-clusters based on morphological trait cluster analysis. The early or medium-maturing cluster was composed of 15 maintainer lines, four early-maturing restorer lines and two thermo-sensitive genic male sterile lines, and the medium or late-maturing cluster included 16 restorer lines and 4 medium or late-maturing maintainer lines. Moreover, the SSR cluster analysis classified 41 entries into two clusters (I.e. Maintainer line cluster and restorer line cluster) and seven sub-clusters. The maintainer line cluster consisted of all 19 maintainer lines, two thermo-sensitive genic male sterile lines, while the restorer line cluster was composed of all 20 restorer lines. The SSR analysis fitted better with the pedigree information. From the views on hybrid rice breeding, the results suggested that SSR analysis might be a better method to study the diversity of parental lines in indica hybrid rice.

  8. Genetic diversity of wild Cymbidium goeringii (Orchidaceae)populations from Hubei based on Inter-simple sequence repeats analysis

    Institute of Scientific and Technical Information of China (English)

    YAO Xiaohong; GAO Li; YANG Bo

    2007-01-01

    Cymbidium goeringii is a diploid and nonrewarding,bumblebee-pollinated species,which is distributed in China,Japan and Korea Peninsula.This species is now highly endangered due to the mass collection and forest clearance in China.In the present study,we investigated the distribution of genetic variation within and between eleven populations of Cymbidium goeringii in central China by using Inter-simple sequence repeats (ISSR) markers.Eleven primers produced a total of 127 clear and reproducible bands of which 112 were polymorphic.High genetic diversity was detected in Cymbidium goeringii for both population level (P = 63.1%;He = 0.194 5) and species level (P = 88.2%;He = 0.262 8).A higher level of genetic differentiation was detected among populations (GST = 0.244 0,FST = 0.220 7)with Nei's Gsr analysis and analysis of molecular variance (AMOVA),and no correlation was found between geographical and genetic distance.Genetic drift rather than gene flow played an important role in forming the present population structure of Cymbidium goeringii.Limited gene flow among populations and gene drift increase the extinction risk of local populations.Some conservation concerns are therefore discussed together with possible strategies for implementing in situ and ex situ conservation.

  9. Genetic Diversity of Chinese and Swedish Rapeseed (Brassica napus L. ) Analyzed by Inter-Simple Sequence Repeats (ISSRs)

    Institute of Scientific and Technical Information of China (English)

    MA Chao-zhi; FU Ting-dong; Stine Tuevesson; Bo Gertsson

    2003-01-01

    We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B.napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in the group Ⅰ and the group Ⅱ were two Chinese weakwinter lines Xiangyou15 and Bao81. The third group contained eight Swedish spring lines. Principal co-ordinates analysis (PCO) showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than Swedish spring or winter accessions did. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.

  10. Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Li Mao-bai

    2015-07-01

    Full Text Available Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon's diversity index (I of 0.748 and the heterozygosity (He of 0.434. In each regional population, I value varied widely. The widest range of I (0.228–0.489 was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea (0.168–0.270. The F-statistics of regional populations (Fis, Fit and Fst also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

  11. Repeated sprint swimming performance after low- or high-intensity active and passive recoveries.

    Science.gov (United States)

    Toubekis, Argyris G; Adam, Georgios V; Douda, Helen T; Antoniou, Panagiotis D; Douroundos, Ioannis I; Tokmakidis, Savvas P

    2011-01-01

    The purpose of this study was to examine the effects on sprint swimming performance after low- and high-intensity active recovery (AR) as compared to passive recovery. Ten male competitive swimmers (age: 17.9 ± 2.3 years; body mass: 73.2 ± 4.0 kg; height: 1.81 ± 0.04 m, 100-m best time: 54.90 ± 1.96 seconds) performed 8 × 25-m sprints with 120-second rest intervals followed by a 50-m sprint 6 minutes later. During the 120-second and the 6-minute interval periods swimmers rested passively (PAS) or swam at an intensity of 40% (ACT40; 36 ± 8% of the V(O2)max) and 60% (ACT60; 59 ± 7% of the V(O2)max) of their individual 100-m velocity. Performance time of the 8 × 25-m after ACT60 was slower compared with PAS and ACT40, but no difference was observed between ACT40 and PAS conditions (PAS: 12.15 ± 0.48, ACT40: 12.23 ± 0.54, ACT60: 12.35 ± 0.57 seconds, p sprint was no different between conditions (PAS: 26.45 ± 0.91; ACT40: 26.30 ± 1.18; ACT60: 26.21 ± 1.19 seconds; p > 0.05). Blood lactate concentration was not different between PAS, ACT40, and ACT60 after the 8 × 25-m and the 50-m sprints (p > 0.05). Passive recovery, or low intensity of AR (40% of the 100-m velocity), is advised to maintain repeated 25-m sprint swimming performance when a 2-minute interval period is provided. Active recovery at an intensity corresponding to 60% of the 100-m velocity decreases performance during the 25-m repeated sprints without affecting the performance time on a subsequent longer duration sprint (i.e., 50 m).

  12. The effect of temperature on repeat swimming performance in juvenile qingbo (Spinibarbus sinensis).

    Science.gov (United States)

    Pang, Xu; Yuan, Xing-Zhong; Cao, Zhen-Dong; Zhang, Yao-Guang; Fu, Shi-Jian

    2015-02-01

    To investigate the effect of temperature on the repeat constant acceleration swimming performance and on the metabolic recovery capacity in juvenile qingbo (Spinibarbus sinensis), their constant acceleration test speed (U(CAT)) and excess post-exercise oxygen consumption (EPOC) recovery process were measured twice with 1-h intervals at different acclimation temperatures (10, 15, 20, 25 and 30 °C). Temperature significantly affected U(CAT), the pre-exercise metabolic rate (MO(2)), metabolic peak values (MO(2peak)), the metabolic scope (MS, MO(2peak)--pre-exercise MO(2)) and the magnitude of the EPOC (P EPOC magnitude) or did not change (MO(2peak) and MS) when the temperature increased from 25 to 30 °C in the first test (P EPOC magnitude) in the first test were as follows: U(CAT) = 62.14/{1 + [(T - 25.1)/21.1](2)} (r = 0.847, P EPOC = 195.42/{1 + [(T - 25.6)/8.7](2)} (r = 0.752, P EPOC magnitude in juvenile qingbo were 25.1, 29.2, 27.1 and 28.6 °C, respectively. Repeat exercise had different effect on U(CAT) and EPOC magnitude at different temperature (interaction effect, P EPOC magnitude between the first and second tests at low temperatures (10-20 °C). However, both U(CAT) and EPOC magnitude decreased significantly during the second test compared with the first test at high temperatures (25 and 30 °C) (P < 0.05). The present study showed that the recovery of the constant acceleration swimming performance was poorer at higher temperatures than at low temperatures in juvenile qingbo. These differences may be related to larger anaerobic metabolism, a lower pH value in the blood, larger ionic fluids and/or higher levels of hormones present at high temperatures.

  13. Performance Degradation of the Repeated Recycled Aggregate Concrete with 70% Replacement of Three-generation Recycled Coarse Aggregate

    Institute of Scientific and Technical Information of China (English)

    ZHU Pinghua; ZHANG Xinxin; WU Junyong; WANG Xinjie

    2016-01-01

    The feasibility of using different generations recycled coarse aggregate (RCA) on structural concrete was fully evaluated by studying the performance of the recycled coarse aggregates and their corresponding concretes, the different generations of RCA were recycled by following the repeated mode of ‘concrete-waste concrete-coarse aggregate-concrete’. Moreover, the focus was on ‘three generations’ of repeated RCAs, the RCA was produced by crushing and regenerating the artiifcial accelerated degraded concrete, the process was designed to follow the nature degradation of the concrete with a coupling action of accelerated carbonation and bending load. The properties ofx-generation (x=1, 2 or 3) of repeated RCA were systematically investigated and the compressive and splitting tensile strengths of relating structural concretes(with 70% replacement ofx-generation of RCA) were studied accordingly. The results show a competent compressive and splitting tensile strength of 30 MPa at 28th day of structural concretes with all generations of repeated RAC. And the gradual degraded performance of the repeated RCAs was observed with an increased numbers of repetition (1﹥2﹥3 generations), the overall performances of all repeated RCAs fulifll the ClassⅢaccording to Chinese Standards GB25177-2010. Our gained insight demonstrates a feasibility of using at least 3 generations of repeated RCA for the production of normal structural concrete.

  14. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

    Science.gov (United States)

    Yi, Xuan; Gao, Lei; Wang, Bo; Su, Ying-Juan; Wang, Ting

    2013-01-01

    We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

  15. An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers

    Science.gov (United States)

    Watermelon (Citrullus lanatus var. lanatus) is an important vegetable fruit throughout the world. A high number of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers should provide large coverage of the watermelon genome and high phylogenetic resolution of germplasm acces...

  16. Characterization of clonal relatedness among the natural population of Staphylococcus aureus strains by using spa sequence typing and the BURP (based upon repeat patterns) algorithm

    NARCIS (Netherlands)

    Mellmann, Alexander; Weniger, Thomas; Berssenbrügge, Christoph; Keckevoet, Ursula; Friedrich, Alexander W; Harmsen, Dag; Grundmann, Hajo

    2008-01-01

    We evaluated the BURP (based upon repeat patterns) algorithm, which relies on sequencing of the Staphylococcus aureus protein A gene (spa), for its ability to infer clonal relatedness within a population of 110 wild-type strains. BURP clustering of the resulting 66 spa types was highly concordant wi

  17. Cyclotriveratrylene (CTV) as a new chiral triacid scaffold capable of inducing triple helix formation of collagen peptides containing either a native sequence or Pro-Hyp-Gly repeats

    NARCIS (Netherlands)

    Rump, ET; Rijkers, DTS; Hilbers, HW; de Groot, PG; Liskamp, RMJ

    2002-01-01

    A new triacid scaffold is described based on the cone-shaped cyclotriveratrylene (CTV) molecule that facilitates the triple, helical folding of peptides containing either a unique blood platelet binding collagen sequence or collagen peptides composed of Pro-Hyp-Gly repeats. The latter were synthesiz

  18. Comparison of Multilocus Variable-Number Tandem-Repeat Analysis and Multilocus Sequence Typing for Differentiation of Hemolytic-Uremic Syndrome-Associated Escherichia coli (HUSEC) Collection Strains▿

    OpenAIRE

    2011-01-01

    Multilocus variable-number tandem-repeat analysis (MLVA) was compared to multilocus sequence typing (MLST) to differentiate hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli strains. Although MLVA—like MLST—was highly discriminatory (index of diversity, 0.988 versus 0.984), a low level of concordance demonstrated the limited ability of MLVA to reflect long-term evolutionary events.

  19. Effect of Repeated Stress Treatments During the Follicular Phase and Early Pregnancy on Reproductive Performance of Gilts

    NARCIS (Netherlands)

    Soede, N.M.; Roelofs, J.B.; Verheijen, R.J.E.; Schouten, W.G.P.; Hazeleger, W.; Kemp, B.

    2007-01-01

    In pig husbandry, stress is being considered an important cause of impaired reproductive performance. Therefore, an experiment was performed to quantify effects of repeated stressors during the follicular phase and/or during early pregnancy on reproductive performance of gilts. Eighty-one cyclic

  20. Repeated sprint performance and metabolic recovery curves: effects of aerobic and anaerobic characteristics.

    Science.gov (United States)

    de Aguiar, Rafael Alves; Turnes, Tiago; Santos de Oliveira Cruz, Rogério; Salvador, Amadeo Félix; Caputo, Fabrizio

    2015-05-01

    To examine the influence of aerobic and anaerobic indices on repeated sprint (RS) performance and ability (RSA), 8 sprinters (SPR), 8 endurance runners (END), and 8 active participants (ACT) performed the following tests: (i) incremental test; (ii) 1-min test to determine first decay time constant of pulmonary oxygen uptake off-kinetics and parameters related to anaerobic energy supply, lactate exchange, and removal abilities from blood lactate kinetics; and (iii) RS test (ten 35-m sprints, departing every 20 s) to determine best (RSbest) and mean (RSmean) sprint times and percentage of sprint decrement (%Dec). While SPR had a 98%-100% likelihood of having the fastest RSbest (Cohen's d of 1.8 and 1.4 for ACT and END, respectively) and RSmean (2.1 and 0.9 for ACT and END, respectively), END presented a 97%-100% likelihood of having the lowest %Dec (0.9 and 2.2 for ACT and SPR, respectively). RSmean was very largely correlated with RSbest (r=0.85) and moderately correlated with estimates of anaerobic energy supply (r=-0.40 to -0.49). RSmean adjusted for RSbest (which indirectly reflects RSA) was largely correlated with lactate exchange ability (r=0.55). Our results confirm the importance of locomotor- and anaerobic-related variables to RS performance, and highlight the importance of disposal of selected metabolic by-products to RSA.

  1. Skeletal muscle fiber type composition and performance during repeated bouts of maximal, concentric contractions

    Science.gov (United States)

    Colliander, E. B.; Dudley, G. A.; Tesch, P. A.

    1988-01-01

    Force output and fatigue and recovery patterns were studied during intermittent short-term exercise. 27 men performed three bouts of 30 maximal unilateral knee extensions on 2 different occasions. Blood flow was maintained or occluded during recovery periods (60 s). Blood flow was restricted by inflating a pneumatic cuff placed around the proximal thigh. Muscle biopsies from vastus lateralis were analyzed for identification of fast twitch (FT) and slow twitch (ST) fibers and relative FT area. Peak torque decreased during each bout of exercise and more when blood flow was restricted during recovery. Initial peak torque (IPT) and average peak torque (APT) decreased over the three exercise bouts. This response was 3 fold greater without than with blood flow during recovery. IPT and APT decreased more in individuals with mainly FT fibers than in those with mainly ST fibers. It is suggested that performance during repeated bouts of maximal concentric contractions differs between individuals with different fiber type composition. Specifically, in high intensity, intermittent exercise with emphasis on anaerobic energy release a high FT composition may not necessarily be advantageous for performance.

  2. Repeating Knowledge Application Practice to Improve Student Performance in a Large, Introductory Science Course

    Science.gov (United States)

    Fujinuma, Ryosuke; Wendling, Laura A.

    2015-11-01

    There is a tendency for lecture-based instruction in large introductory science courses to strongly focus on the delivery of discipline-specific technical terminology and fundamental concepts, sometimes to the detriment of opportunities for application of learned knowledge in evidence-based critical-thinking activities. We sought to improve student performance on evidence-based critical-thinking tasks through the implementation of peer learning and problem-based learning tutorial activities. Small-group discussions and associated learning activities were used to facilitate deeper learning through the application of new knowledge. Student performance was assessed using critical-thinking essay assignments and a final course exam, and student satisfaction with tutorial activities was monitored using online surveys. Overall, students expressed satisfaction with the small-group-discussion-based tutorial activities (mean score 7.5/10). Improved critical thinking was evidenced by improved student performance on essay assignments during the semester, as well as a 25% increase in mean student scores on the final course exam compared to previous years. These results demonstrate that repeated knowledge application practice can improve student learning in large introductory-level science courses.

  3. Sequence variations in C9orf72 downstream of the hexanucleotide repeat region and its effect on repeat-primed PCR interpretation

    DEFF Research Database (Denmark)

    Nordin, Angelica; Akimoto, Chizuru; Wuolikainen, Anna

    2017-01-01

    -PCR data. Our objective was to determine the properties of these sequence variations with regard to prevalence, the range of variation, and effect on disease prognosis. We screened a multi-national cohort (n = 6981) for the HREM and samples with deviant RP-PCR curves were identified. The deviant samples...

  4. Effects of caffeine and carbohydrate mouth rinses on repeated sprint performance.

    Science.gov (United States)

    Beaven, C Martyn; Maulder, Peter; Pooley, Adrian; Kilduff, Liam; Cook, Christian

    2013-06-01

    Our purpose was to examine the effectiveness of carbohydrate and caffeine mouth rinses in enhancing repeated sprint ability. Previously, studies have shown that a carbohydrate mouth rinse (without ingestion) has beneficial effects on endurance performance that are related to changes in brain activity. Caffeine ingestion has also demonstrated positive effects on sprint performance. However, the effects of carbohydrate or caffeine mouth rinses on intermittent sprints have not been examined previously. Twelve males performed 5 × 6-s sprints interspersed with 24 s of active recovery on a cycle ergometer. Twenty-five milliliters of either a noncaloric placebo, a 6% glucose, or a 1.2% caffeine solution was rinsed in the mouth for 5 s prior to each sprint in a double-blinded and balanced cross-over design. Postexercise maximal heart rate and perceived exertion were recorded, along with power measures. A second experiment compared a combined caffeine-carbohydrate rinse with carbohydrate only. Compared with the placebo mouth rinse, carbohydrate substantially increased peak power in sprint 1 (22.1 ± 19.5 W; Cohen's effect size (ES), 0.81), and both caffeine (26.9 ± 26.9 W; ES, 0.71) and carbohydrate (39.1 ± 25.8 W; ES, 1.08) improved mean power in sprint 1. Experiment 2 demonstrated that a combination of caffeine and carbohydrate improved sprint 1 power production compared with carbohydrate alone (36.0 ± 37.3 W; ES, 0.81). We conclude that carbohydrate and (or) caffeine mouth rinses may rapidly enhance power production, which could have benefits for specific short sprint exercise performance. The ability of a mouth-rinse intervention to rapidly improve maximal exercise performance in the absence of fatigue suggests a central mechanism.

  5. The repeated bout effect of traditional resistance exercises on running performance across 3 bouts.

    Science.gov (United States)

    Doma, Kenji; Schumann, Moritz; Leicht, Anthony Scott; Heilbronn, Brian Edward; Damas, Felipe; Burt, Dean

    2017-09-01

    This study investigated the repeated bout effect of 3 typical lower body resistance-training sessions on maximal and submaximal effort running performance. Twelve resistance-untrained men (age, 24 ± 4 years; height, 1.81 ± 0.10 m; body mass, 79.3 ± 10.9 kg; peak oxygen uptake, 48.2 ± 6.5 mL·kg(-1)·min(-1); 6-repetition maximum squat, 71.7 ± 12.2 kg) undertook 3 bouts of resistance-training sessions at 6-repetitions maximum. Countermovement jump (CMJ), lower-body range of motion (ROM), muscle soreness, and creatine kinase (CK) were examined prior to and immediately, 24 h (T24), and 48 h (T48) after each resistance-training bout. Submaximal (i.e., below anaerobic threshold (AT)) and maximal (i.e., above AT) running performances were also conducted at T24 and T48. Most indirect muscle damage markers (i.e., CMJ, ROM, and muscle soreness) and submaximal running performance were significantly improved (P resistance-training bout compared with the second bout. Whilst maximal running performance was also improved following the third bout (P 0.05). In conclusion, the initial bout induced the greatest change in CK; however, at least 2 bouts were required to produce protective effects on other indirect muscle damage markers and submaximal running performance measures. This suggests that submaximal running sessions should be avoided for at least 48 h after resistance training until the third bout, although a greater recovery period may be required for maximal running sessions.

  6. Mental fatigue negatively influences manual dexterity and anticipation timing but not repeated high-intensity exercise performance in trained adults.

    Science.gov (United States)

    Duncan, Michael J; Fowler, Nicholas; George, Oliver; Joyce, Samuel; Hankey, Joanne

    2015-01-01

    This study examined the impact of a period of mental fatigue on manual dexterity, anticipation timing and repeated high intensity exercise performance. Using a randomised, repeated measures experimental design, eight physically trained adults (mean age = 24.8 ± 4.1 years) undertook a 40 minute vigilance task to elicit mental fatigue or a control condition followed by four repeated Wingate anaerobic performance tests. Pre, post fatigue/control and post each Wingate test, manual dexterity (Seconds), coincidence anticipation (absolute error) were assessed. A series of two (condition) by six (time) ways repeated measures ANOVAs indicated a significant condition by time interactions for manual dexterity time (p = 0.021) and absolute error (p = 0.028). Manual dexterity and coincidence anticipation were significantly poorer post mental fatigue compared with control. There were no significant differences in mean power between conditions or across trials (all p > 0.05).

  7. Long CAG Repeat Sequence and Protein Expression of Androgen Receptor Considered as Prognostic Indicators in Male Breast Carcinoma

    OpenAIRE

    Yan-Ni Song; Jing-Shu Geng; Tong Liu; Zhen-Bin Zhong; Yang Liu; Bing-Shu Xia; Hong-Fei Ji; Xiao-Mei Li; Guo-Qiang Zhang; Yan-Lv Ren; Zhi-Gao Li; Da Pang

    2012-01-01

    BACKGROUND: The androgen receptor (AR) expression and the CAG repeat length within the AR gene appear to be involved in the carcinogenesis of male breast carcinoma (MBC). Although phenotypic differences have been observed between MBC and normal control group in AR gene, there is lack of correlation analysis between AR expression and CAG repeat length in MBC. The purpose of the study was to investigate the prognostic value of CAG repeat lengths and AR protein expression. METHODS: 81 tumor tiss...

  8. Who Repeats Algebra I, and How Does Initial Performance Relate to Improvement When the Course Is Repeated? REL 2015-059

    Science.gov (United States)

    Fong, Anthony B.; Jaquet, Karina; Finkelstein, Neal

    2014-01-01

    This REL West study explores the prevalence of students repeating Algebra I, who is most likely to repeat the course, and the level of improvement for students who repeat. Using six years of data from a cohort of 3,400 first-time seventh grade students in a California school district, authors found that 44 percent of students repeated algebra I.…

  9. A Clustered Repeated-Sprint Running Protocol for Team-Sport Athletes Performed in Normobaric Hypoxia

    Directory of Open Access Journals (Sweden)

    Jaime Morrison, Chris McLellan, Clare Minahan

    2015-12-01

    Full Text Available The present study compared the performance (peak speed, distance, and acceleration of ten amateur team-sport athletes during a clustered (i.e., multiple sets repeated-sprint protocol, (4 sets of 4, 4-s running sprints; i.e., RSR444 in normobaric normoxia (FiO2 = 0.209; i.e., RSN with normobaric hypoxia (FiO2 = 0.140; i.e., RSH. Subjects completed two separate trials (i. RSN, ii. RSH; randomised order between 48 h and 72 h apart on a non-motorized treadmill. In addition to performance, we examined blood lactate concentration [La-] and arterial oxygen saturation (SpO2 before, during, and after the RSR444. While there were no differences in peak speed or distance during set 1 or set 2, peak speed (p = 0.04 and 0.02, respectively and distance (p = 0.04 and 0.02, respectively were greater during set 3 and set 4 of RSN compared with RSH. There was no difference in the average acceleration achieved in set 1 (p = 0.45, set 2 (p = 0.26, or set 3 (p = 0.23 between RSN and RSH; however, the average acceleration was greater in RSN than RSH in set 4 (p < 0.01. Measurements of [La-] were higher during RSH than RSN immediately after Sprint 16 (10.2 ± 2.5 vs 8.6 ± 2.6 mM; p = 0.02. Estimations of SpO2 were lower during RSH than RSN, respectively, immediately prior to the commencement of the test (89.0 ± 2.0 vs 97.2 ± 1.5 %, post Sprint 8 (78.0 ± 6.3 vs 93.8 ± 3.6 % and post Sprint 16 (75.3 ± 6.3 vs 94.5 ± 2.5 %; all p < 0.01. In summary, the RSR444 is a practical protocol for the implementation of a hypoxic repeated-sprint training intervention into the training schedules of team-sport athletes. However, given the inability of amateur team-sport athletes to maintain performance in hypoxic (FiO2 = 0.140 conditions, the potential for specific training outcomes (i.e. speed to be achieved will be compromised, thus suggesting that the RSR444 should be used with caution.

  10. Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses.

    Science.gov (United States)

    Liu, Yang; Forrest, Laura L; Bainard, Jillian D; Budke, Jessica M; Goffinet, Bernard

    2013-03-01

    Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.

  11. Genetic variation in Rhodomyrtus tomentosa (Kemunting) populations from Malaysia as revealed by inter-simple sequence repeat markers.

    Science.gov (United States)

    Hue, T S; Abdullah, T L; Abdullah, N A P; Sinniah, U R

    2015-12-14

    Kemunting (Rhodomyrtus tomentosa) from the Myrtaceae family, is native to Malaysia. It is widely used in traditional medicine to treat various illnesses and possesses significant antibacterial properties. In addition, it has great potential as ornamental in landscape design. Genetic variability studies are important for the rational management and conservation of genetic material. In the present study, inter-simple sequence repeat markers were used to assess the genetic diversity of 18 R. tomentosa populations collected from ten states of Peninsular Malaysia. The 11 primers selected generated 173 bands that ranged in size from 1.6 kb to 130 bp, which corresponded to an average of 15.73 bands per primer. Of these bands, 97.69% (169 in total) were polymorphic. High genetic diversity was documented at the species level (H(T) = 0.2705; I = 0.3973; PPB = 97.69%) but there was a low diversity at population level (H(S) = 0.0073; I = 0 .1085; PPB = 20.14%). The high level of genetic differentiation revealed by G(ST) (73%) and analysis of molecular variance (63%), together with the limited gene flow among population (N(m) = 0.1851), suggests that the populations examined are isolated. Results from an unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis clearly grouped the populations into two geographic groups. This clear grouping can also be demonstrated by the significant Mantel test (r = 0.581, P = 0.001). We recommend that all the R. tomentosa populations be preserved in conservation program.

  12. The cortisol awakening response is associated with performance of a serial sequence reaction time task.

    Science.gov (United States)

    Hodyl, Nicolette A; Schneider, Luke; Vallence, Ann-Maree; Clow, Angela; Ridding, Michael C; Pitcher, Julia B

    2016-02-01

    There is emerging evidence of a relationship between the cortisol awakening response (CAR) and the neural mechanisms underlying learning and memory. The aim of this study was to determine whether the CAR is associated with acquisition, retention and overnight consolidation or improvement of a serial sequence reaction time task. Salivary samples were collected at 0, 15, 30 and 45 min after awakening in 39 healthy adults on 2 consecutive days. The serial sequence reaction time task was repeated each afternoon. Participants completed the perceived stress scale and provided salivary samples prior to testing for cortisol assessment. While the magnitude of the CAR (Z score) was not associated with either baseline performance or the timed improvement during task acquisition of the serial sequence task, a positive correlation was observed with reaction times during the stable performance phase on day 1 (r=0.373, p=0.019). Residuals derived from the relationship between baseline and stable phase reaction times on day 1 were used as a surrogate for the degree of learning: these residuals were also correlated with the CAR mean increase on day 1 (r=0.357, p=0.048). Task performance on day 2 was not associated with the CAR obtained on this same day. No association was observed between the perceived stress score, cortisol at testing or task performance. These data indicate that a smaller CAR in healthy adults is associated with a greater degree of learning and faster performance of a serial sequence reaction time task. These results support recognition of the CAR as an important factor contributing to cognitive performance throughout the day.

  13. LONGITUDINAL STUDY OF REPEATED SPRINT PERFORMANCE IN YOUTH SOCCER PLAYERS OF CONTRASTING SKELETAL MATURITY STATUS

    Directory of Open Access Journals (Sweden)

    João Valente-dos-Santos

    2012-09-01

    Full Text Available The purpose of the study was to evaluate the developmental changes in performance in a repeated-sprint ability (RSA test in young soccer players of contrasting maturity status. A total of 83 regional level Portuguese youth soccer players, aged 11- 13 years at baseline was assessed annually. Stature, body mass, 7x34.2-m sprint protocol (25-s active recovery, 20-m multi-stage continuous shuttle endurance run and counter-movement jump (CMJ without the use of the arms were measured. Fat-free mass (FFM was determined by age and gender- specific formulas. Developmental changes in total sprint time across ages were predicted using multilevel modeling. Corresponding measurements were performed on an independent cross-sectional subsample of 52 youth soccer players 11-17 years to evaluate the predictive model. CA, CA2, maturational status (SA-CA, body size (mass and stature, FFM, aerobic endurance, lower limb explosive strength and annual volume training significantly improved the statistical fit of the RSA multilevel model. In 'late' maturing athletes, the best model for predicting change in RSA was expressed by the following equation: 86.54 - 2.87 x CA + 0.05 x CA2 - 0.25 x FFM + 0.15 x body mass + 0.05 x stature - 0.05 x aerobic endurance - 0.09 x lower limb explosive strength - 0.01 x annual volume training. The best fitting models for players who were 'on time' and 'early' maturing were identical to the best model for late maturing players, less 0.64 seconds and 1.74 seconds, respectively. Multilevel modeling provided performance curves that permitted the prediction of individual RSA performance across adolescent years in regional level soccer players

  14. The Effect of Caffeine on Repeat-High-Intensity-Effort Performance in Rugby League Players.

    Science.gov (United States)

    Wellington, Brandon M; Leveritt, Michael D; Kelly, Vincent G

    2017-02-01

    Repeat-high-intensity efforts (RHIEs) have recently been shown to occur at critical periods of rugby league matches. To examine the effect that caffeine has on RHIE performance in rugby league players. Using a double-blind, placebo-controlled, crossover design, 11 semiprofessional rugby league players (age 19.0 ± 0.5 y, body mass 87.4 ± 12.9 kg, height 178.9 ± 2.6 cm) completed 2 experimental trials that involved completing an RHIE test after either caffeine (300 mg caffeine) or placebo (vitamin H) ingestion. Each trial consisted of 3 sets of 20-m sprints interspersed with bouts of tackling. During the RHIE test, 20-m-sprint time, heart rate (HR), rating of perceived exertion (RPE), and blood lactate were measured. Total time to complete the nine 20-m sprints during the caffeine condition was 1.0% faster (28.46 ± 1.4 s) than during the placebo condition (28.77 ± 1.7 s) (ES = 0.18, 90%CI -0.7 to 0.1 s). This resulted in a very likely chance of caffeine being of benefit to RHIE performance (99% likely to be beneficial). These improvements were more pronounced in the early stages of the test, with a 1.3%, 1.0%, and 0.9% improvement in sprint performance during sets 1, 2, and 3 respectively. There was no significant difference in RPE across the 3 sets (P = .47, 0.48, 1.00) or mean HR (P = .36), maximal HR (P = .74), or blood lactate (P = .50) between treatment conditions. Preexercise ingestion of 300 mg caffeine produced practically meaningful improvements in RHIE performance in rugby league players.

  15. IS1630 of Mycoplasma fermentans, a Novel IS30-Type Insertion Element That Targets and Duplicates Inverted Repeats of Variable Length and Sequence during Insertion

    Science.gov (United States)

    Calcutt, Michael J.; Lavrrar, Jennifer L.; Wise, Kim S.

    1999-01-01

    A new insertion sequence (IS) of Mycoplasma fermentans is described. This element, designated IS1630, is 1,377 bp long and has 27-bp inverted repeats at the termini. A single open reading frame (ORF), predicted to encode a basic protein of either 366 or 387 amino acids (depending on the start codon utilized), occupies most of this compact element. The predicted translation product of this ORF has homology to transposases of the IS30 family of IS elements and is most closely related (27% identical amino acid residues) to the product of the prototype of the group, IS30. Multiple copies of IS1630 are present in the genomes of at least two M. fermentans strains. Characterization and comparison of nine copies of the element revealed that IS1630 exhibits unusual target site specificity and, upon insertion, duplicates target sequences in a manner unlike that of any other IS element. IS1630 was shown to have the striking ability to target and duplicate inverted repeats of variable length and sequence during transposition. IS30-type elements typically generate 2- or 3-bp target site duplications, whereas those created by IS1630 vary between 19 and 26 bp. With the exception of two recently reported IS4-type elements which have the ability to generate variable large duplications (B. B. Plikaytis, J. T. Crawford, and T. M. Shinnick, J. Bacteriol. 180:1037–1043, 1998; E. M. Vilei, J. Nicolet, and J. Frey, J. Bacteriol. 181:1319–1323, 1999), such large direct repeats had not been observed for other IS elements. Interestingly, the IS1630-generated duplications are all symmetrical inverted repeat sequences that are apparently derived from rho-independent transcription terminators of neighboring genes. Although the consensus target site for IS30 is almost palindromic, individual target sites possess considerably less inverted symmetry. In contrast, IS1630 appears to exhibit an increased stringency for inverted repeat recognition, since the majority of target sites had no

  16. Repeat Effort Performance is Reduced 24 h following Acute Dehydration in Mixed Martial Arts Athletes.

    Science.gov (United States)

    Barley, Oliver R; Iredale, Fiona; Chapman, Dale W; Hopper, Amanda; Abbiss, Chris

    2017-09-11

    This study sought to determine the influence of acute dehydration on physical performance and physiology in Mixed Martial Arts (MMA). MMA athletes (n=14; age: 23±4 years), completed in a randomised counterbalanced order a dehydration protocol, (DHY: 3 h cycling at 60 W in 40°C to induce 5% dehydration) or thermoneutral control (25°C: CONT) exercise, followed by ad libitum fluid/food intake. Performance testing (a repeat sled push test, medicine ball chest throw and vertical jump) was completed 3 and 24 h following the intervention, while urine and blood samples were collected before, 20 min, 3 and 24 h following the intervention. Body mass was reduced (4.8±0.8%) following DHY (p<0.001) and remained lower than CONT at 3 and 24 h post (p=0.003 and p=0.024, respectively). Compared to CONT average sled push times were slower 3 and 24 h following DHY (19±15%; p=0.001; g=1.229 and 14±15%; p=0.012; g=0.671, respectively). When compared to the CONT hand grip was weaker 3 h following DHY (53±8 and 51±8 kg; p=0.044, g=0.243 respectively) and medicine ball chest throw distances were shorter 24 h following DHY (474±52 and 449±44 cm; p=0.016, g=0.253 respectively). No significant differences were observed in vertical jump (p=0.467). Urine specific gravity was higher than CONT 20 min (p=0.035) and 24 h (p=0.035) following DHY. Acute dehydration of 4.8% body mass results in reduced physical performance 3 and 24 h following. There is need for caution when athletes use dehydration for weight loss 24 h prior to competition.

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

    Science.gov (United States)

    Schmidt, Bertil; Hildebrandt, Andreas

    2017-02-02

    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.

  18. A Clustered Repeated-Sprint Running Protocol for Team-Sport Athletes Performed in Normobaric Hypoxia.

    Science.gov (United States)

    Morrison, Jaime; McLellan, Chris; Minahan, Clare

    2015-12-01

    The present study compared the performance (peak speed, distance, and acceleration) of ten amateur team-sport athletes during a clustered (i.e., multiple sets) repeated-sprint protocol, (4 sets of 4, 4-s running sprints; i.e., RSR444) in normobaric normoxia (FiO2 = 0.209; i.e., RSN) with normobaric hypoxia (FiO2 = 0.140; i.e., RSH). Subjects completed two separate trials (i. RSN, ii. RSH; randomised order) between 48 h and 72 h apart on a non-motorized treadmill. In addition to performance, we examined blood lactate concentration [La(-)] and arterial oxygen saturation (SpO2) before, during, and after the RSR444. While there were no differences in peak speed or distance during set 1 or set 2, peak speed (p = 0.04 and 0.02, respectively) and distance (p = 0.04 and 0.02, respectively) were greater during set 3 and set 4 of RSN compared with RSH. There was no difference in the average acceleration achieved in set 1 (p = 0.45), set 2 (p = 0.26), or set 3 (p = 0.23) between RSN and RSH; however, the average acceleration was greater in RSN than RSH in set 4 (p Sprint 16 (10.2 ± 2.5 vs 8.6 ± 2.6 mM; p = 0.02). Estimations of SpO2 were lower during RSH than RSN, respectively, immediately prior to the commencement of the test (89.0 ± 2.0 vs 97.2 ± 1.5 %), post Sprint 8 (78.0 ± 6.3 vs 93.8 ± 3.6 %) and post Sprint 16 (75.3 ± 6.3 vs 94.5 ± 2.5 %; all p sprint training intervention into the training schedules of team-sport athletes. However, given the inability of amateur team-sport athletes to maintain performance in hypoxic (FiO2 = 0.140) conditions, the potential for specific training outcomes (i.e. speed) to be achieved will be compromised, thus suggesting that the RSR444 should be used with caution. Key pointsThe RSR444 is a practical, multiple-set repeated-sprint running protocol designed for team-sport athletes.During performance of the RSR444 in hypoxia (FiO2 = 0.140), amateur team-sport athletes were unable to replicate the peak speed, distance covered or

  19. Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, J.V.; Cevario, S.; O`Brien, S.J. [National Cancer Institute, Frederick, MD (United States)

    1996-04-15

    The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species. 86 refs., 4 figs., 3 tabs.

  20. PEGylation enhances tumor targeting of plasmid DNA by an artificial cationized protein with repeated RGD sequences, Pronectin.

    Science.gov (United States)

    Hosseinkhani, Hossein; Tabata, Yasuhiko

    2004-05-31

    The objective of this study is to investigate feasibility of a non-viral gene carrier with repeated RGD sequences (Pronectin F+) in tumor targeting for gene expression. The Pronectin F+ was cationized by introducing spermine (Sm) to the hydroxyl groups to allow to polyionically complex with plasmid DNA. The cationized Pronectin F+ prepared was additionally modified with poly(ethylene glycol) (PEG) molecules which have active ester and methoxy groups at the terminal, to form various PEG-introduced cationized Pronectin F+. The cationized Pronectin F+ with or without PEGylation at different extents was mixed with a plasmid DNA of LacZ to form respective cationized Pronectin F+-plasmid DNA complexes. The plasmid DNA was electrophoretically complexed with cationized Pronectin F+ and PEG-introduced cationized Pronectin F+, irrespective of the PEGylation extent, although the higher N/P ratio of complexes was needed for complexation with the latter Pronectin F+. The molecular size and zeta potential measurements revealed that the plasmid DNA was reduced in size to about 250 nm and the charge was changed to be positive by the complexation with cationized Pronectin F+. For the complexation with PEG-introduced cationized Pronectin F+, the charge of complex became neutral being almost 0 mV with the increasing PEGylation extents, while the molecular size was similar to that of cationized Pronectin F+. When cationized Pronectin F+-plasmid DNA complexes with or without PEGylation were intravenously injected to mice carrying a subcutaneous Meth-AR-1 fibrosarcoma mass, the PEG-introduced cationized Pronectin F+-plasmid DNA complex specifically enhanced the level of gene expression in the tumor, to a significantly high extent compared with the cationized Pronectin F+-plasmid DNA complexes and free plasmid DNA. The enhanced level of gene expression depended on the percentage of PEG introduced, the N/P ratio, and the plasmid DNA dose. A fluorescent microscopic study revealed that the

  1. Sludge reduction by direct addition of chlorine dioxide into a sequencing batch reactor under operational mode of repeatedly alternating aeration/non-aeration.

    Science.gov (United States)

    Peng, Hong; Liu, Weiyi; Li, Yuanmei; Xiao, Hong

    2015-01-01

    The effect of direct addition of chlorine dioxide (ClO2) into a repeatedly alternating aeration/non-aeration sequencing batch reactor (SBR) on its sludge reduction and process performance was investigated. The experimental results showed that the sludge reduction efficiency was 32.9% and the observed growth yield (Yobs) of SBR was 0.11 kg VSS (volatile suspended solids) /kg COD (chemical oxygen demand) for 80 days' operation at the optimum ClO2 dosage of 2.0 mg/g TSS (total suspended solids). It was speculated that cell lysis and cryptic growth, uncoupled metabolism and endogenous metabolism were jointly responsible for the sludge reduction in this study. COD, NH3-N, total nitrogen (TN) and total phosphorus (TP) in the effluent increased on average 29.47, 4.44, 1.97 and 0.05 mg/L, respectively. However, the effluent quality still satisfied the first-class B discharge standards for municipal wastewater treatment plants in China. In that case, the sludge maintained fine viability with the specific oxygen uptake rate (SOUR) being 14.47 mg O2/(g VSS·h) and demonstrated good settleability with the sludge volume index (SVI) being 116 mL/g. The extra cost of sludge reduction at the optimum ClO2 dosage was estimated to be 2.24 CNY (or 0.36 dollar)/kg dry sludge.

  2. Genetic Diversity and Association Analysis for Salinity Tolerance,Heading Date and Plant Height of Barley Germplasm Using Simple Sequence Repeat Markers

    Institute of Scientific and Technical Information of China (English)

    Lilia Eleuch; Abderrazek Jilal; Stefania Grando; Salvatore Ceccarelli; Maria von Korff Schmising; Hisashi Tsujimoto; Amara Hajer; Abderrazek Daaloul; Michael Baum

    2008-01-01

    The objective of this study was to investigate the genetic diversity of barley accessions.Additionally,association trait analysis was conducted for grain yield under salinity,heading date and plant height.For this purpose,48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers.Four of the 22 markers (Bmac316,scssr03907,HVM67 and Bmag770) were able to differentiate all barley genotypes.Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region.The genotypes used in this study have been evaluated for agronomic performance in different environments.Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H,bin 13) in two different environments with common significant alleles (175,177),whereas the HVHOTR1 marker (2H,bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161.Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmacO415 markers in three different agro climatic locations,whereas HVCMA,scssr00103 and HVM67 were linked to heading date in the Egyptian environment only.The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398.

  3. Investigation of Clostridium difficile interspecies relatedness using multilocus sequence typing, multilocus variable-number tandem-repeat analysis and antimicrobial susceptibility testing.

    Science.gov (United States)

    Rodriguez, C; Avesani, V; Taminiau, B; Van Broeck, J; Brévers, B; Delmée, M; Daube, G

    2015-12-01

    Multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA) and antimicrobial susceptibility were performed on 37 animal and human C. difficile isolates belonging to 15 different PCR-ribotypes in order to investigate the relatedness of human and animal isolates and to identify possible transmission routes. MLVA identified a total of 21 different types while MLST only distinguished 12 types. Identical C. difficile strains were detected in the same animal species for PCR-ribotypes 014, 078, UCL 16U and UCL 36, irrespective of their origin or the isolation date. Non clonal strains were found among different hosts; however, a high genetic association between pig and cattle isolates belonging to PCR-ribotype 078 was revealed. MLVA also showed genetic differences that clearly distinguished human from animal strains. For a given PCR-ribotype, human and animal strains presented a similar susceptibility to the antimicrobials tested. All strains were susceptible to vancomycin, metronidazole, chloramphenicol and rifampicin, while PCR-ribotypes 078, UCL 5a, UCL 36 and UCL 103 were associated with erythromycin resistance. The data suggest a wide dissemination of clones at hospitals and breeding-farms or a contamination at the slaughterhouse, but less probability of interspecies transmission. However, further highly discriminatory genotyping methods are necessary to elucidate interspecies and zoonotic transmission of C. difficile.

  4. Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance

    National Research Council Canada - National Science Library

    Lim, Kian Guan; Kwoh, Chee Keong; Hsu, Li Yang; Wirawan, Adrianto

    2013-01-01

    .... Over the last 10-15 years, numerous tools have been developed for searching tandem repeats, but differences in the search algorithms adopted and difficulties with parameter settings have confounded...

  5. Effects of Early and Late Rest Intervals on Performance and Overnight Consolidation of a Keyboard Sequence

    Science.gov (United States)

    Cash, Carla Davis

    2009-01-01

    Thirty-six nonmusicians practiced a five-element key-press sequence on a digital piano, repeating the sequence as quickly and accurately as possible during twelve 30-s practice blocks alternating with 30-s pauses. Twelve learners rested for 5 min between Blocks 3 and 4, another 12 learners rested for 5 min between Blocks 9 and 10, and the…

  6. Effects of Early and Late Rest Intervals on Performance and Overnight Consolidation of a Keyboard Sequence

    Science.gov (United States)

    Cash, Carla Davis

    2009-01-01

    Thirty-six nonmusicians practiced a five-element key-press sequence on a digital piano, repeating the sequence as quickly and accurately as possible during twelve 30-s practice blocks alternating with 30-s pauses. Twelve learners rested for 5 min between Blocks 3 and 4, another 12 learners rested for 5 min between Blocks 9 and 10, and the…

  7. Performance evaluation of enterprise architecture using fuzzy sequence diagram

    Directory of Open Access Journals (Sweden)

    Mohammad Atasheneh

    2014-01-01

    Full Text Available Developing an Enterprise Architecture is a complex task and to control the complexity of the regulatory framework we need to measure the relative performance of one system against other available systems. On the other hand, enterprise architecture cannot be organized without the use of a logical structure. The framework provides a logical structure for classifying architectural output. Among the common architectural framework, the C4ISR framework and methodology of the product is one of the most popular techniques. In this paper, given the existing uncertainties in system development and information systems, a new version of UML called Fuzzy-UML is proposed for enterprise architecture development based on fuzzy Petri nets. In addition, the performance of the system is also evaluated based on Fuzzy sequence diagram.

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

    OpenAIRE

    2015-01-01

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

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

    Science.gov (United States)

    Calcutt, Michael J; Foecking, Mark F

    2015-02-26

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

  10. CRISPRs of Enterococcus faecalis and E. hirae isolates from pig feces have species-specific repeats but share some common spacer sequences.

    Science.gov (United States)

    Katyal, Isha; Chaban, Bonnie; Ng, Beata; Hill, Janet E

    2013-07-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are currently a topic of interest in microbiology due to their role as a prokaryotic immune system. Investigations of CRISPR distribution and characterization to date have focused on pathogenic bacteria, while less is known about CRISPR in commensal bacteria, where they may have a significant role in the ecology of the microbiota of humans and other animals, and act as a recorder of interactions between bacteria and viruses. A combination of PCR and sequencing was used to determine prevalence and distribution of CRISPR arrays in Enterococcus faecalis and Enterococcus hirae isolates from the feces of healthy pigs. Both type II CRISPR-Cas and Orphan CRISPR (without Cas genes) were detected in the 195 isolates examined. CRISPR-Cas was detected in 52 (46/88) and 42 % (45/107) E. faecalis and E. hirae isolates, respectively. The prevalence of Orphan CRISPR arrays was higher in E. faecalis isolates (95 %, 84/88) compared with E. hirae isolates (49 %, 53/107). Species-specific repeat sequences were identified in Orphan CRISPR arrays, and 42 unique spacer sequences were identified. Only two spacers matched previously characterized pig virome sequences, and many were apparently derived from chromosomal sequences of enterococci. Surprisingly, 17 (40 %) of the spacers were detected in both species. Shared spacer sequences are evidence of a lack of species specificity in the agents and mechanisms responsible for integration of spacers, and the abundance of spacer sequences corresponding to bacterial chromosomal sequences reflects interspecific interactions within the intestinal microbiota.

  11. Identification of Syringa oblata by Inter-Simple Sequence Repeat Markers%白花与紫花丁香ISSR-PCR鉴别研究

    Institute of Scientific and Technical Information of China (English)

    思彬彬; 赵海燕; 刘海涛

    2012-01-01

    [ Objective] To identify Syringa oblata by inter-simple sequence repeat markers. [ Method] Primers suitable for routine analysis were screened from 100 inter-simple sequence repeat primers, then, they were used in PCR and separated of 2 samples of Syringa oblata. [ Results ] Three of the one-hundred primers amplified polymorphic bands and suitable for the identification of Syringa oblata. [Conclusion] Inter-simple sequence repeat markers provide a quick, reliable molecular marker for identification of Syringa oblata.%[目的]探索用ISSR分子标记方法在核酸分子水平上鉴别白花与紫花丁香.[方法]从100条ISSR引物中筛选合适的引物对白花和紫花丁香2个样品进行PCR扩增及电泳分析,寻找特征位点.[结果]有3条ISSR引物扩增出较为明显的多态性特征条带,可单独应用于白花和紫花丁香的鉴别.[结论] ISSR作为一种简便、可靠的分子标记方法,可用于不同花色丁香的鉴别.

  12. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE Consensus Sequence Repeats in the Viral Genome.

    Directory of Open Access Journals (Sweden)

    Ashutosh Kumar

    2016-08-01

    Full Text Available Owing to the reports of microcephaly as a consistent outcome in the foetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV - microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favour of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1 sequence homology between ZIKV genome and the response element of an early neural tube developmental marker ‘retinoic acid’ in human DNA and (2 comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE consensus sequence (5′–AGGTCA–3′ in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly and other viruses available in National Institute of Health genetic sequence database (GenBank for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause foetal brain defects (for which maternal-foetal transmission during developing stage may be required. The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although bioinformatic

  13. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome

    Science.gov (United States)

    Kumar, Ashutosh; Singh, Himanshu N.; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A.

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker “retinoic acid” in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5′–AGGTCA–3′) in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and

  14. Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms.

    Science.gov (United States)

    Goremykin, V; Bobrova, V; Pahnke, J; Troitsky, A; Antonov, A; Martin, W

    1996-02-01

    We developed PCR primers against highly conserved regions of the rRNA operon located within the inverted repeat of the chloroplast genome and used these to amplify the region spanning from the 3' terminus of the 23S rRNA gene to the 5' terminus of the 5S rRNA gene. The sequence of this roughly 500-bp region, which includes the 4.5S rRNA gene and two chloroplast intergenic transcribed spacer regions (cpITS2 and cpITS3), was determined from 20 angiosperms, 7 gymnosperms, and 16 ferns (21,700 bp). Sequences for the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL) from the same or confamilial genera were analyzed in both separate and combined data sets. Due to the low substitution rate in the inverted repeat region, noncoding sequences in the cpITS region are not saturated with substitutions, in contrast to synonymous sites in rbcL, which are shown to evolve roughly six times faster than noncoding cpITS sequences. Several length polymorphisms with very clear phylogenetic distributions were detected in the data set. Results of phylogenetic analyses provide very strong bootstrap support for monophyly of both spermatophytes and angiosperms. No support for a sister group relationship between Gnetales and angiosperms in either cpITS or rbcL data was found. Rather, weak bootstrap support for monophyly of gymnosperms studied and for a basal position for the aquatic angiosperm Nymphaea among angiosperms studied was observed. Noncoding sequences from the inverted repeat region of chloroplast DNA appear suitable for study of land plant evolution.

  15. A novel approach to propagate flavivirus infectious cDNA clones in bacteria by introducing tandem repeat sequences upstream of virus genome.

    Science.gov (United States)

    Pu, Szu-Yuan; Wu, Ren-Huang; Tsai, Ming-Han; Yang, Chi-Chen; Chang, Chung-Ming; Yueh, Andrew

    2014-07-01

    Despite tremendous efforts to improve the methodology for constructing flavivirus infectious cDNAs, the manipulation of flavivirus cDNAs remains a difficult task in bacteria. Here, we successfully propagated DNA-launched type 2 dengue virus (DENV2) and Japanese encephalitis virus (JEV) infectious cDNAs by introducing seven repeats of the tetracycline-response element (7×TRE) and a minimal cytomegalovirus (CMVmin) promoter upstream of the viral genome. Insertion of the 7×TRE-CMVmin sequence upstream of the DENV2 or JEV genome decreased the cryptic E. coli promoter (ECP) activity of the viral genome in bacteria, as measured using fusion constructs containing DENV2 or JEV segments and the reporter gene Renilla luciferase in an empty vector. The growth kinetics of recombinant viruses derived from DNA-launched DENV2 and JEV infectious cDNAs were similar to those of parental viruses. Similarly, RNA-launched DENV2 infectious cDNAs were generated by inserting 7×TRE-CMVmin, five repeats of the GAL4 upstream activating sequence, or five repeats of BamHI linkers upstream of the DENV2 genome. All three tandem repeat sequences decreased the ECP activity of the DENV2 genome in bacteria. Notably, 7×TRE-CMVmin stabilized RNA-launched JEV infectious cDNAs and reduced the ECP activity of the JEV genome in bacteria. The growth kinetics of recombinant viruses derived from RNA-launched DENV2 and JEV infectious cDNAs displayed patterns similar to those of the parental viruses. These results support a novel methodology for constructing flavivirus infectious cDNAs, which will facilitate research in virology, viral pathogenesis and vaccine development of flaviviruses and other RNA viruses. © 2014 The Authors.

  16. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: Strain diversity, host range, and recombination

    NARCIS (Netherlands)

    Schouls, L.M.; Reulen, S.; Duim, B.; Wagenaar, J.A.; Willems, R.J.L.; Dingle, K.E.; Colles, F.M.; Embden, van J.D.A.

    2003-01-01

    Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic

  17. Pitch Sequence Complexity and Long-Term Pitcher Performance

    Directory of Open Access Journals (Sweden)

    Joel R. Bock

    2015-03-01

    Full Text Available Winning one or two games during a Major League Baseball (MLB season is often the difference between a team advancing to post-season play, or “waiting until next year”. Technology advances have made it feasible to augment historical data with in-game contextual data to provide managers immediate insights regarding an opponent’s next move, thereby providing a competitive edge. We developed statistical models of pitcher behavior using pitch sequences thrown during three recent MLB seasons (2011–2013. The purpose of these models was to predict the next pitch type, for each pitcher, based on data available at the immediate moment, in each at-bat. Independent models were developed for each player’s most frequent four pitches. The overall predictability of next pitch type is 74:5%. Additional analyses on pitcher predictability within specific game situations are discussed. Finally, using linear regression analysis, we show that an index of pitch sequence predictability may be used to project player performance in terms of Earned Run Average (ERA and Fielding Independent Pitching (FIP over a longer term. On a restricted range of the independent variable, reducing complexity in selection of pitches is correlated with higher values of both FIP and ERA for the players represented in the sample. Both models were significant at the α = 0.05 level (ERA: p = 0.022; FIP: p = 0.0114. With further development, such models may reduce risk faced by management in evaluation of potential trades, or to scouts assessing unproven emerging talent. Pitchers themselves might benefit from awareness of their individual statistical tendencies, and adapt their behavior on the mound accordingly. To our knowledge, the predictive model relating pitch-wise complexity and long-term performance appears to be novel.

  18. K-ABC/McCarthy Performance for Repeating and Nonrepeating Preschoolers.

    Science.gov (United States)

    Smith, Douglas K.; Lyon, Mark A.

    This study compares the McCarthy Scales of Children's Abilities (MSCA) and the Kaufman Assessment Battery for Children (K-ABC) profiles of successful and unsuccessful preschoolers with learning disabilities. Subjects, 40 preschool students, were tested at the beginning and at the end of the preschool year and were placed into repeating or…

  19. Isolation and Characterization of Simple Sequence Repeats (SSR Markers from the Moss Genus Orthotrichum Using a Small Throughput Pyrosequencing Machine

    Directory of Open Access Journals (Sweden)

    Vítězslav Plášek

    2012-06-01

    Full Text Available Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing.

  20. Kearns-Sayre syndrome case presenting a mitochondrial DNA deletion with unusual direct repeats and a rudimentary RNAse mitochondria ribonucleotide processing target sequence

    Energy Technology Data Exchange (ETDEWEB)

    Remes, A.M.; Hassinen, I.E. (Univ. of Oulu (Finland)); Peuhkurinen, K.J.; Herva, R.; Majamaa, K. (Oulu Univ. Central Hospital (Finland))

    1993-04-01

    A mitochondrial DNA deletion in a case of Kearns-Sayre syndrome is described. The deletion is bracketed by direct repeats that were unusual in that one of them was located 11--13 nucleotides from the deletion seam and both were conserved, which should not occur in slip replication or illegitimate elongation. The deleted region was demarcated on the deletion side by sequences that could be predicted to form hairpin structures. The 5[prime]-side of the deletion was flanked by a sequence homologous to a 9-nucleotide piece of the conserved sequence block II of the D-loop. This arrangement around the deletion in Kearns-Sayre syndrome bears some resemblance to the arrangement in the Pearson marrow- pancreas syndrome described by A. Rotig et al. (1991, Genomics 10: 502--504). 10 refs., 1 fig.

  1. Effects of Sequences of Socially Regulated Learning on Group Performance

    NARCIS (Netherlands)

    Molenaar, I.; Chiu, M.M.

    2015-01-01

    Past research shows that regulative activities (metacognitive or relational) can aid learning and that sequences of cognitive, metacognitive and relational activities affect subsequent cognition. Extending this research, this study examines whether sequences of socially regulated learning differ

  2. Effects of Sequences of Socially Regulated Learning on Group Performance

    NARCIS (Netherlands)

    Molenaar, I.; Chiu, M.M.

    2015-01-01

    Past research shows that regulative activities (metacognitive or relational) can aid learning and that sequences of cognitive, metacognitive and relational activities affect subsequent cognition. Extending this research, this study examines whether sequences of socially regulated learning differ acr

  3. Recombination-Independent Recognition of DNA Homology for Repeat-Induced Point Mutation (RIP Is Modulated by the Underlying Nucleotide Sequence.

    Directory of Open Access Journals (Sweden)

    Eugene Gladyshev

    2016-05-01

    Full Text Available Haploid germline nuclei of many filamentous fungi have the capacity to detect homologous nucleotide sequences present on the same or different chromosomes. Once recognized, such sequences can undergo cytosine methylation or cytosine-to-thymine mutation specifically over the extent of shared homology. In Neurospora crassa this process is known as Repeat-Induced Point mutation (RIP. Previously, we showed that RIP did not require MEI-3, the only RecA homolog in Neurospora, and that it could detect homologous trinucleotides interspersed with a matching periodicity of 11 or 12 base-pairs along participating chromosomal segments. This pattern was consistent with a mechanism of homology recognition that involved direct interactions between co-aligned double-stranded (ds DNA molecules, where sequence-specific dsDNA/dsDNA contacts could be established using no more than one triplet per turn. In the present study we have further explored the DNA sequence requirements for RIP. In our previous work, interspersed homologies were always examined in the context of a relatively long adjoining region of perfect homology. Using a new repeat system lacking this strong interaction, we now show that interspersed homologies with overall sequence identity of only 36% can be efficiently detected by RIP in the absence of any perfect homology. Furthermore, in this new system, where the total amount of homology is near the critical threshold required for RIP, the nucleotide composition of participating DNA molecules is identified as an important factor. Our results specifically pinpoint the triplet 5'-GAC-3' as a particularly efficient unit of homology recognition. Finally, we present experimental evidence that the process of homology sensing can be uncoupled from the downstream mutation. Taken together, our results advance the notion that sequence information can be compared directly between double-stranded DNA molecules during RIP and, potentially, in other processes

  4. Recombination-Independent Recognition of DNA Homology for Repeat-Induced Point Mutation (RIP) Is Modulated by the Underlying Nucleotide Sequence.

    Science.gov (United States)

    Gladyshev, Eugene; Kleckner, Nancy

    2016-05-01

    Haploid germline nuclei of many filamentous fungi have the capacity to detect homologous nucleotide sequences present on the same or different chromosomes. Once recognized, such sequences can undergo cytosine methylation or cytosine-to-thymine mutation specifically over the extent of shared homology. In Neurospora crassa this process is known as Repeat-Induced Point mutation (RIP). Previously, we showed that RIP did not require MEI-3, the only RecA homolog in Neurospora, and that it could detect homologous trinucleotides interspersed with a matching periodicity of 11 or 12 base-pairs along participating chromosomal segments. This pattern was consistent with a mechanism of homology recognition that involved direct interactions between co-aligned double-stranded (ds) DNA molecules, where sequence-specific dsDNA/dsDNA contacts could be established using no more than one triplet per turn. In the present study we have further explored the DNA sequence requirements for RIP. In our previous work, interspersed homologies were always examined in the context of a relatively long adjoining region of perfect homology. Using a new repeat system lacking this strong interaction, we now show that interspersed homologies with overall sequence identity of only 36% can be efficiently detected by RIP in the absence of any perfect homology. Furthermore, in this new system, where the total amount of homology is near the critical threshold required for RIP, the nucleotide composition of participating DNA molecules is identified as an important factor. Our results specifically pinpoint the triplet 5'-GAC-3' as a particularly efficient unit of homology recognition. Finally, we present experimental evidence that the process of homology sensing can be uncoupled from the downstream mutation. Taken together, our results advance the notion that sequence information can be compared directly between double-stranded DNA molecules during RIP and, potentially, in other processes where homologous

  5. Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)n and d(CAG/CTG)n

    Indian Academy of Sciences (India)

    Shibasish Chowdhury; Manju Bansal

    2001-12-01

    Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.

  6. Chromosomal organization of simple sequence repeats in the Pacific oyster (Crassostrea gigas): (GGAT)4, (GT)7 and (TA)10 chromosome patterns

    Indian Academy of Sciences (India)

    K. Bouilly; R. Chaves; A. Leitão; A. Benabdelmouna; H. Guedes-Pinto

    2008-08-01

    Chromosome identification is essential in oyster genomic research. Fluorescence in situ hybridization (FISH) offers new opportunities for the identification of oyster chromosomes. It has been used to locate satellite DNAs, telomeres or ribosomal DNA sequences. However, regarding chromosome identification, no study has been conducted with simple sequence repeats (SSRs). FISH was used to probe the physical organization of three particular SSRs, (GGAT)4, (GT)7 and (TA)10 onto metaphase chromosomes of the Pacific oyster, Crassostrea gigas. Hybridization signals were observed in all the SSR probes, but the distribution and intensity of signals varied according to the oligonucleotide repeat. The intercalary, centromeric and telomeric bands were observed along the chromosomes, and for each particular repeat every chromosome pair presented a similar pattern, allowing karyotypic analysis with all the SSRs tested. Our study is the first in mollusks to show the application of SSR in situ hybridization for chromosome identification and karyotyping. This technique can be a useful tool for oyster comparative studies and to understand genome organization in different oyster taxa.

  7. Repeated dose liver micronucleus assay using adult mice with multiple genotoxicity assays concurrently performed as a combination test.

    Science.gov (United States)

    Hagio, Soichiro; Furukawa, Satoshi; Abe, Masayoshi; Kuroda, Yusuke; Hayashi, Seigo; Ogawa, Izumi

    2014-06-01

    Recently, the liver micronucleus (MN) assay using young adult rats with repeated administrations has been investigated by employing a new method without partial hepatectomy or in situcollagenase perfusion as the repeated dose liver MN (RDLMN) assay by Narumi et al. (2012). In our study, in order to investigate the possibility of the RDLMN assay using young adult mice instead of rats and the feasibility of employing some genotoxicity assays along with the RDLMN assay as a combination test, two genotoxic carcinogens (N,N-diethylnitrosoamine (DEN) and cisplatin (CIS)) and a nongenotoxic carcinogen (phenobarbital sodium (PHE)) were administered to mice for 15 or 29 days. Then, the liver MN assay, peripheral blood (PB) MN assay and comet assay using the liver and kidney were concurrently performed as a combination test. DEN showed positive responses to all endpoints except MN induction in PB after 15 days of repeat administration. A cross-linking agent, CIS, showed MN induction in liver after 29 days of repeat administration, and in PB after 15 and 29 days of repeat administration, although the comet assay yielded negative responses for both organs at both sampling times. PHE yielded negative responses for all endpoints. In conclusion, it is suggested that the RDLMN assay using mice is a feasible method to be integrated into the general repeated toxicity test along with the combination assays, i.e., comet assay or PB MN assay, which would help in risk assessment for carcinogenicity by comparing the results of combination assays with each other.

  8. No Improved Performance With Repeated-Sprint Training in Hypoxia Versus Normoxia: A Double-Blind and Crossover Study.

    Science.gov (United States)

    Montero, David; Lundby, Carsten

    2017-02-01

    Few recent studies indicate that short-term repeated-sprint (RS) training in hypoxia (RSH) improves RS performance compared with identical training under normoxic conditions (RSN) in endurance-trained subjects. To determine the effects of RSH against RSN on RS performance under normoxic and moderate hypoxic conditions, using a randomized, doubleblind, crossover experimental design. Fifteen endurance-trained male subjects (age 25 ± 4 y) performed 4 wk of RS training (3 sessions/wk) in normobaric hypoxia (RSH, FiO2 = 13.8%) and normoxia (RSN, FiO2 = 20.9%) in a crossover manner. Before and after completion of training, RS tests were performed on a cycle ergometer with no prior exercise (RSNE), after an incremental exercise test (RSIE), and after a time-trial test (RSTT) in normoxia and hypoxia. Peak power outputs at the incremental exercise test and time-trial performance were unaltered by RSH in normoxia and hypoxia. RS performance was generally enhanced by RSH, as well as RSN, but there were no additional effects of RSH over RSN on peak and mean sprint power output and the number of repeated sprints performed in the RSNE, RSIE, and RSTT trials under normoxic and hypoxic conditions. The present double-blind crossover study indicates that RSH does not improve RS performance compared with RSN in normoxic and hypoxic conditions in endurance-trained subjects. Therefore, caution should be exercised when proposing RSH as an advantageous method to improve exercise performance.

  9. Comparison of Two Types of Warm-Up Upon Repeated-Sprint Performance in Experienced Soccer Players.

    Science.gov (United States)

    van den Tillaar, Roland; von Heimburg, Erna

    2016-08-01

    van den Tillaar, R and von Heimburg, E. Comparison of two types of warm-up upon repeated-sprint performance in experienced soccer players. J Strength Cond Res 30(8): 2258-2265, 2016-The aim of the study was to compare the effects of a long warm-up and a short warm-up upon repeated-sprint performance in soccer players. Ten male soccer players (age, 21.9 ± 1.9 years; body mass, 77.7 ± 8.3 kg; body height, 1.85 ± 0.03 m) conducted 2 types of warm-ups with 1 week in between: a long warm-up (20 minutes: LWup) and a short warm-up (10 minutes: SWup). Each warm-up was followed by a repeated-sprint test consisting of 8 × 30 m sprints with a new start every 30th second. The best sprint time, total sprinting time, and % decrease in time together with heart rate, lactate, and rate of perceived exertion (RPE) were measured. No significant differences in performance were found for the repeated-sprint test parameters (total sprint time: 35.99 ± 1.32 seconds [LWup] and 36.12 ± 0.96 seconds [SWup]; best sprint time: 4.32 ± 0.13 seconds [LWup] and 4.30 ± 0.10 seconds [SWup]; and % sprint decrease: 4.16 ± 2.15% [LWup] and 5.02 ± 2.07% [SWup]). No differences in lactate concentration after the warm-up and after the repeated-sprint test were found. However, RPE and heart rate were significantly higher after the long warm-up and the repeated-sprint test compared with the short warm-up. It was concluded that a short warm-up is as effective as a long warm-up for repeated sprints in soccer. Therefore, in regular training, less warm-up time is needed; the extra time could be used for important soccer skill training.

  10. Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

    Science.gov (United States)

    Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

    2016-09-01

    Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

  11. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

    Directory of Open Access Journals (Sweden)

    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  12. Sequence-specific DNA alkylation and transcriptional inhibition by long-chain hairpin pyrrole-imidazole polyamide-chlorambucil conjugates targeting CAG/CTG trinucleotide repeats.

    Science.gov (United States)

    Asamitsu, Sefan; Kawamoto, Yusuke; Hashiya, Fumitaka; Hashiya, Kaori; Yamamoto, Makoto; Kizaki, Seiichiro; Bando, Toshikazu; Sugiyama, Hiroshi

    2014-09-01

    Introducing novel building blocks to solid-phase peptide synthesis, we readily synthesized long-chain hairpin pyrrole-imidazole (PI) polyamide-chlorambucil conjugates 3 and 4 via the introduction of an amino group into a GABA (γ-turn) contained in 3, to target CAG/CTG repeat sequences, which are associated with various hereditary disorders. A high-resolution denaturing polyacrylamide sequencing gel revealed sequence-specific alkylation both strands at the N3 of adenines or guanines in CAG/CTG repeats by conjugates 3 and 4, with 11bp recognition. In vitro transcription assays using conjugate 4 revealed that specific alkylation inhibited the progression of RNA polymerase at the alkylating sites. Chiral substitution of the γ-turn with an amino group resulted in higher binding affinity observed in SPR assays. These assays suggest that conjugates 4 with 11bp recognition has the potential to cause specific DNA damage and transcriptional inhibition at the alkylating sites. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. A repeat sequence domain of the ring-exported protein-1 of Plasmodium falciparum controls export machinery architecture and virulence protein trafficking.

    Science.gov (United States)

    McHugh, Emma; Batinovic, Steven; Hanssen, Eric; McMillan, Paul J; Kenny, Shannon; Griffin, Michael D W; Crawford, Simon; Trenholme, Katharine R; Gardiner, Donald L; Dixon, Matthew W A; Tilley, Leann

    2015-12-01

    The malaria parasite Plasmodium falciparum dramatically remodels its host red blood cell to enhance its own survival, using a secretory membrane system that it establishes outside its own cell. Cisternal organelles, called Maurer's clefts, act as a staging point for the forward trafficking of virulence proteins to the red blood cell (RBC) membrane. The Ring-EXported Protein-1 (REX1) is a Maurer's cleft resident protein. We show that inducible knockdown of REX1 causes stacking of Maurer's cleft cisternae without disrupting the organization of the knob-associated histidine-rich protein at the RBC membrane. Genetic dissection of the REX1 sequence shows that loss of a repeat sequence domain results in the formation of giant Maurer's cleft stacks. The stacked Maurer's clefts are decorated with tether-like structures and retain the ability to dock onto the RBC membrane skeleton. The REX1 mutant parasites show deficient export of the major virulence protein, PfEMP1, to the red blood cell surface and markedly reduced binding to the endothelial cell receptor, CD36. REX1 is predicted to form a largely α-helical structure, with a repetitive charge pattern in the repeat sequence domain, providing potential insights into the role of REX1 in Maurer's cleft sculpting.

  14. Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium.

    Science.gov (United States)

    Ithurbide, Solenne; Bentchikou, Esma; Coste, Geneviève; Bost, Bruno; Servant, Pascale; Sommer, Suzanne

    2015-10-01

    The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequences of various lengths ranging from 1,479 bp to 10,500 bp to restore a functional tetA gene in the presence or absence of radiation-induced DNA double strand breaks. The frequency of spontaneous deletion events between the chromosomal direct repeats were the same in recA+ and in ΔrecA, ΔrecF, and ΔrecO bacteria, whereas recombination between chromosomal and plasmid DNA was shown to be strictly dependent on the RecA and RecF proteins. The presence of mutations in one of the repeated sequence reduced, in a MutS-dependent manner, the frequency of the deletion events. The distance between the repeats did not influence the frequencies of deletion events in recA+ as well in ΔrecA bacteria. The absence of the UvrD protein stimulated the recombination between the direct repeats whereas the absence of the DdrB protein, previously shown to be involved in DNA double strand break repair through a single strand annealing (SSA) pathway, strongly reduces the frequency of RecA- (and RecO-) independent deletions events. The absence of the DdrB protein also increased the lethal sectoring of cells devoid of RecA or RecO protein. γ-irradiation of recA+ cells increased about 10-fold the frequencies of the deletion events, but at a lesser extend in cells devoid of the DdrB protein. Altogether, our results suggest a major role of single strand annealing in DNA repeat deletion events in bacteria devoid of the RecA protein, and also in recA+ bacteria exposed to ionizing radiation.

  15. Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium.

    Directory of Open Access Journals (Sweden)

    Solenne Ithurbide

    2015-10-01

    Full Text Available The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequences of various lengths ranging from 1,479 bp to 10,500 bp to restore a functional tetA gene in the presence or absence of radiation-induced DNA double strand breaks. The frequency of spontaneous deletion events between the chromosomal direct repeats were the same in recA+ and in ΔrecA, ΔrecF, and ΔrecO bacteria, whereas recombination between chromosomal and plasmid DNA was shown to be strictly dependent on the RecA and RecF proteins. The presence of mutations in one of the repeated sequence reduced, in a MutS-dependent manner, the frequency of the deletion events. The distance between the repeats did not influence the frequencies of deletion events in recA+ as well in ΔrecA bacteria. The absence of the UvrD protein stimulated the recombination between the direct repeats whereas the absence of the DdrB protein, previously shown to be involved in DNA double strand break repair through a single strand annealing (SSA pathway, strongly reduces the frequency of RecA- (and RecO- independent deletions events. The absence of the DdrB protein also increased the lethal sectoring of cells devoid of RecA or RecO protein. γ-irradiation of recA+ cells increased about 10-fold the frequencies of the deletion events, but at a lesser extend in cells devoid of the DdrB protein. Altogether, our results suggest a major role of single strand annealing in DNA repeat deletion events in bacteria devoid of the RecA protein, and also in recA+ bacteria exposed to ionizing radiation.

  16. The DUB/USP17 deubiquitinating enzymes: A gene family within a tandemly repeated sequence, is also embedded within the copy number variable Beta-defensin cluster

    Directory of Open Access Journals (Sweden)

    Scott Christopher J

    2010-04-01

    Full Text Available Abstract Background The DUB/USP17 subfamily of deubiquitinating enzymes were originally identified as immediate early genes induced in response to cytokine stimulation in mice (DUB-1, DUB-1A, DUB-2, DUB-2A. Subsequently we have identified a number of human family members and shown that one of these (DUB-3 is also cytokine inducible. We originally showed that constitutive expression of DUB-3 can block cell proliferation and more recently we have demonstrated that this is due to its regulation of the ubiquitination and activity of the 'CAAX' box protease RCE1. Results Here we demonstrate that the human DUB/USP17 family members are found on both chromosome 4p16.1, within a block of tandem repeats, and on chromosome 8p23.1, embedded within the copy number variable beta-defensin cluster. In addition, we show that the multiple genes observed in humans and other distantly related mammals have arisen due to the independent expansion of an ancestral sequence within each species. However, it is also apparent when sequences from humans and the more closely related chimpanzee are compared, that duplication events have taken place prior to these species separating. Conclusions The observation that the DUB/USP17 genes, which can influence cell growth and survival, have evolved from an unstable ancestral sequence which has undergone multiple and varied duplications in the species examined marks this as a unique family. In addition, their presence within the beta-defensin repeat raises the question whether they may contribute to the influence of this repeat on immune related conditions.

  17. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

    Science.gov (United States)

    Waye, J S; Willard, H F

    1986-09-01

    The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

  18. Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.A.

    1996-06-01

    The objective of this project is the development of practical software to automate the identification of genes in anonymous DNA sequences from the human, and other higher eukaryotic genomes. A software system for automated sequence analysis, gm (gene modeler) has been designed, implemented, tested, and distributed to several dozen laboratories worldwide. A significantly faster, more robust, and more flexible version of this software, gm 2.0 has now been completed, and is being tested by operational use to analyze human cosmid sequence data. A range of efforts to further understand the features of eukaryoyic gene sequences are also underway. This progress report also contains papers coming out of the project including the following: gm: a Tool for Exploratory Analysis of DNA Sequence Data; The Human THE-LTR(O) and MstII Interspersed Repeats are subfamilies of a single widely distruted highly variable repeat family; Information contents and dinucleotide compostions of plant intron sequences vary with evolutionary origin; Splicing signals in Drosophila: intron size, information content, and consensus sequences; Integration of automated sequence analysis into mapping and sequencing projects; Software for the C. elegans genome project.

  19. EFFECT OF DYE CONCENTRATION ON SEQUENCING BATCH REACTOR PERFORMANCE

    Directory of Open Access Journals (Sweden)

    A. A. Vaigan ، M. R. Alavi Moghaddam ، H. Hashemi

    2009-01-01

    Full Text Available Reactive dyes have been identified as problematic compounds in textile industries wastewater as they are water soluble and cannot be easily removed by conventional aerobic biological treatment systems. The treatability of a reactive dye (Brill Blue KN-R by sequencing batch reactor and the influence of the dye concentration on system performance were investigated in this study. Brill Blue KN-R is one of the main dyes that are used in textile industries in Iran. Four cylindrical Plexiglas reactors were run for 36 days (5 days for acclimatization of sludge and 31 days for normal operation at different initial dye concentrations. The dye concentrations were adjusted to be 20, 25, 30 and 40 mg/L in the reactors R1, R2, R3 and R4, respectively. In all reactors, effective volume, influent wastewater flowrate and sludge retention time were 5.5 L, 3.0 L/d and 10 d, respectively. According to the obtained data, average dye removal efficiencies of R1, R2, R3 and R4 were 57% ± 2, 50.18% ± 3, 44.97% ± 3 and 30.98% ± 3, respectively. The average COD removal efficiencies of all reactors were 97% ± 1, 97.12% ± 1, 96.93% ± 1 and 97.22% ± 1, respectively. The dye removal efficiency was decreased by increasing the dye concentration with the correlation coefficient of 0.997.

  20. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles †

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  1. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  2. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Oussama Ahrazem; Benjamin Viñegla; Juan C. Linares; Lourdes Gómez-Gómez; David Candel-Perez; Tiscar, Pedro A.; Lucas-Borja, Manuel E.; Angela Rubio-Moraga

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina...

  3. 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

  4. Variability and repeatability in gestation length related to litter performance in female pigs on commercial farms.

    Science.gov (United States)

    Sasaki, Y; Koketsu, Y

    2007-07-15

    Forecasting gestation length (GL) in sows enables producers to be prepared to provide assistance at farrowing, or for timely treatment to induce parturition. The objectives of the present study were to determine GL across parities, the repeatability and correlation of the GL, and associations of GL with the three litter size variables (total pigs born, pigs born alive, and dead piglets) and longevity. This study was conducted on 94 farms and encompassed 66,254 farrowing records of 13,715 sows born during 1999. Variance components and correlation analyses were used to determine the repeatability and the correlations of GL. Mixed-effects models were used to analyze associations of GL with litter size variables and longevity. The mean of GL across parities was from 115.2 to 115.4 d. The proportions of GL 114, 115, and 116 d for all farrowing events were 19.2, 30.8, and 22.2%, respectively. The GL between parities were correlated (0.40/=117 d (P<0.01). Sows with GL

  5. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  6. Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

    Science.gov (United States)

    Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J Antonio; Castro-Escarpulli, Graciela

    2015-08-04

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes. The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in

  7. Endurance, aerobic high-intensity, and repeated sprint cycling performance is unaffected by normobaric "Live High-Train Low"

    DEFF Research Database (Denmark)

    Bejder, Jacob; Andersen, Andreas Breenfeldt; Buchardt, Rie

    2017-01-01

    The aim was to investigate whether 6 weeks of normobaric "Live High-Train Low" (LHTL) using altitude tents affect highly trained athletes incremental peak power, 26-km time-trial cycling performance, 3-min all-out performance, and 30-s repeated sprint ability. In a double-blinded, placebo...... conducted in a double-blinded, placebo-controlled cross-over design do not affect power output during an incremental test, a ~26-km time-trial test, or 3-min all-out exercise in highly trained triathletes. Furthermore, 30 s of repeated sprint ability was unaltered.......-out exercise, and 8 × 30 s of all-out sprint was evaluated before and after the intervention. Following at least 8 weeks of wash-out, the subjects crossed over and repeated the procedure. Incremental peak power output was similar after both interventions [LHTL: 375 ± 74 vs. 369 ± 70 W (pre-vs-post), placebo...

  8. Repeatability and reproducibility of measurements of the suburethral tape location obtained in pelvic floor ultrasound performed with a transvaginal probe

    Directory of Open Access Journals (Sweden)

    Maria Magdalena Dresler

    2017-06-01

    Full Text Available Introduction: Implants used to treat patients with urogynecological conditions are well visible in US examination. The position of the suburethral tape (sling is determined in relation to the urethra or the pubic symphysis. Aim of the study: The study was aimed at assessing the accuracy of measurements determining suburethral tape location obtained in pelvic US examination performed with a transvaginal probe. Material and methods: The analysis covered the results of sonographic measurements obtained according to a standardized technique in women referred for urogynecological diagnostics. Data from a total of 68 patients were used to analyse the repeatability and reproducibility of results obtained on the same day. Results: The intraclass correlation coefficient for the repeatability and reproducibility of the sonographic measurements of suburethral tape location obtained with a transvaginal probe ranged from 0.6665 to 0.9911. The analysis of the measurements confirmed their consistency to be excellent or good. Conclusions: Excellent and good repeatability and reproducibility of the measurements of the suburethral tape location obtained in a pelvic ultrasound performed with a transvaginal probe confirm the test’s validity and usefulness for clinical and academic purposes.

  9. Effects of Beetroot Juice on Recovery of Muscle Function and Performance between Bouts of Repeated Sprint Exercise

    Directory of Open Access Journals (Sweden)

    Tom Clifford

    2016-08-01

    Full Text Available This study examined the effects of beetroot juice (BTJ on recovery between two repeated-sprint tests. In an independent groups design, 20 male, team-sports players were randomized to receive either BTJ or a placebo (PLA (2 × 250 mL for 3 days after an initial repeated sprint test (20 × 30 m; RST1 and after a second repeated sprint test (RST2, performed 72 h later. Maximal isometric voluntary contractions (MIVC, countermovement jumps (CMJ, reactive strength index (RI, pressure-pain threshold (PPT, creatine kinase (CK, C-reactive protein (hs-CRP, protein carbonyls (PC, lipid hydroperoxides (LOOH and the ascorbyl free radical (A•− were measured before, after, and at set times between RST1 and RST2. CMJ and RI recovered quicker in BTJ compared to PLA after RST1: at 72 h post, CMJ and RI were 7.6% and 13.8% higher in BTJ vs. PLA, respectively (p < 0.05. PPT was 10.4% higher in BTJ compared to PLA 24 h post RST2 (p = 0.012 but similar at other time points. No group differences were detected for mean and fastest sprint time or fatigue index. MIVC, or the biochemical markers measured (p > 0.05. BTJ reduced the decrement in CMJ and RI following and RST but had no effect on sprint performance or oxidative stress.

  10. Effects of Beetroot Juice on Recovery of Muscle Function and Performance between Bouts of Repeated Sprint Exercise.

    Science.gov (United States)

    Clifford, Tom; Berntzen, Bram; Davison, Gareth W; West, Daniel J; Howatson, Glyn; Stevenson, Emma J

    2016-08-18

    This study examined the effects of beetroot juice (BTJ) on recovery between two repeated-sprint tests. In an independent groups design, 20 male, team-sports players were randomized to receive either BTJ or a placebo (PLA) (2 × 250 mL) for 3 days after an initial repeated sprint test (20 × 30 m; RST1) and after a second repeated sprint test (RST2), performed 72 h later. Maximal isometric voluntary contractions (MIVC), countermovement jumps (CMJ), reactive strength index (RI), pressure-pain threshold (PPT), creatine kinase (CK), C-reactive protein (hs-CRP), protein carbonyls (PC), lipid hydroperoxides (LOOH) and the ascorbyl free radical (A(•-)) were measured before, after, and at set times between RST1 and RST2. CMJ and RI recovered quicker in BTJ compared to PLA after RST1: at 72 h post, CMJ and RI were 7.6% and 13.8% higher in BTJ vs. PLA, respectively (p sprint time or fatigue index. MIVC, or the biochemical markers measured (p > 0.05). BTJ reduced the decrement in CMJ and RI following and RST but had no effect on sprint performance or oxidative stress.

  11. Immunogenicity and antigenicity of the N-term repeat amino acid sequence of the Plasmodium falciparum P126 antigen

    Directory of Open Access Journals (Sweden)

    Dalma Maria Banic

    1992-01-01

    Full Text Available The P126 protein, a parasitosphorus vacuole antigen of Plasmodium falciparum has beenshoen to induce protective immunity in Saimiri and Aotus monkeys. In the present work we investigated its immunogenicity. Our results suggest that the N-term of P126 is poorly immunogenic and antibody response against the P126 could be under a MHC restricted control in C57BL/6(H-2b mice, which could be problematic in ternms of a use of the P126 in a vaccine program. However, we observed that a synthetic peptide, copying the 6 octapeptide repeat corresponding to the N-term of the P126, induces an antibody response to the native molecule in C57BL/6 non-responder mice. Moreover, the vaccine-P126 recombinant induced anmtibodies against the N-term of the molecule in rabbits while the unprocessed P126 did not.

  12. The pugilistDominant Mutation of Drosophila melanogaster: A Simple-Sequence Repeat Disorder Reveals Localized Transport in the Eye.

    Directory of Open Access Journals (Sweden)

    Yikang S Rong

    Full Text Available The pugilist-Dominant mutation results from fusion of a portion of the gene encoding the tri-functional Methylene Tetrahydrofolate Dehydrogenase (E.C.1.5.1.5, E.C.3.5.4.9, E.C.6.3.4.3 to approximately one kb of a heterochromatic satellite repeat. Expression of this fusion gene results in an unusual ring pattern of pigmentation around the eye. We carried out experiments to determine the mechanism for this pattern. By using FLP-mediated DNA mobilization to place different pugD transgenes at pre-selected sites we found that variation in repeat length makes a strong contribution to variability of the pug phenotype. This variation is manifest primarily as differences in the thickness of the pigmented ring. We show that similar phenotypic variation can also be achieved by changing gene copy number. We found that the pugD pattern is not controlled by wingless, which is normally expressed in a similar ring pattern. Finally, we found that physical injury to a pugD eye can lead to pigment deposition in parts of the eye that would not have been pigmented in the absence of injury. Our results are consistent with a model in which a metabolite vital for pigment formation is imported from the periphery of the eye, and pugD limits the extent of its transport towards the center of the eye, thus revealing the existence of a hitherto unknown mechanism of localized transport in the eye.

  13. Analysing the performance of personal computers based on Intel microprocessors for sequence aligning bioinformatics applications.

    Science.gov (United States)

    Nair, Pradeep S; John, Eugene B

    2007-01-01

    Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache.

  14. Dynamic damage and stress-strain relations of ultra-high performance cementitious composites subjected to repeated impact

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Ultra-high performance cementitious composites (UHPCC) were prepared by replacing 60% of cement with ultra-fine industrial waste powders.The dynamic damage and compressive stress-strain relations of UHPCC were studied using split Hopkinson pressure bar (SHPB).The damage of UHPCC subjected to repeated impact was measured by the ultrasonic pulse velocity method.Results show that the dynamic damage of UHPCC increases linearly with impact times and the abilities of repeated impact resistance of UHPCC are improved with increasing fiber volume fraction.The stress waves on impact were recorded and the average stress,strain and strain rate of UHPCC were calculated based on the wave propagation theory.The effects of strain rate,fibers volume fraction and impact times on the stress-strain relations of UHPCC were studied.Results show that the peak stress and elastic modulus decrease while the strain rate and peak strain increase gradually with increasing impact times.

  15. 园艺作物的ISSR分子标记研究及应用%Inter-simple sequence repeat and its application in horticultural crop research

    Institute of Scientific and Technical Information of China (English)

    刘淑芹; 吴凤芝; 刘守伟

    2012-01-01

    ISSR (Inter-simple sequence repeat)是一种基于微卫星序列发展起来的新型分子标记方法,具有无需知道任何靶标序列的微卫星背景信息、遗传多态性高、稳定高效、检测快速等特点.目前,ISSR分子标记技术在园艺作物的遗传多样性研究、品种鉴定、遗传图谱构建、基因定位及分子标记辅助育种等方面得到了广泛应用,文章就ISSR标记的原理、方法、特点及其在园艺作物研究中的应用加以综述.%Inter-simple sequence repeat (ISSR) is a new molecular marker method which is based on micro-satellite technique with advantages of simple, quick, stable, reliable and higher DNA polymorphism, etc. At present, ISSR has been widely applied in genetic diversity research, genetic map construction, genetic mapping, molecular marker assisted breeding and variety purity identification of horticultural crops. The purpose of this review is to introduce principles, methods, characteristics of the ISSR and its application in the research of horticultural crops.

  16. Rhoptry-associated protein (rap-1) genes in the sheep pathogen Babesia sp. Xinjiang: Multiple transcribed copies differing by 3' end repeated sequences.

    Science.gov (United States)

    Niu, Qingli; Marchand, Jordan; Yang, Congshan; Bonsergent, Claire; Guan, Guiquan; Yin, Hong; Malandrin, Laurence

    2015-07-30

    Sheep babesiosis occurs mainly in tropical and subtropical areas. The sheep parasite Babesia sp. Xinjiang is widespread in China, and our goal is to characterize rap-1 (rhoptry-associated protein 1) gene diversity and expression as a first step of a long term goal aiming at developing a recombinant subunit vaccine. Seven different rap-1a genes were amplified in Babesia sp. Xinjiang, using degenerate primers designed from conserved motifs. Rap-1b and rap-1c gene types could not be identified. In all seven rap-1a genes, the 5' regions exhibited identical sequences over 936 nt, and the 3' regions differed at 28 positions over 147 nt, defining two types of genes designated α and β. The remaining 3' part varied from 72 to 360 nt in length, depending on the gene. This region consists of a succession of two to ten 36 nt repeats, which explains the size differences. Even if the nucleotide sequences varied, 6 repeats encoded the same stretch of amino acids. Transcription of at least four α and two β genes was demonstrated by standard RT-PCR. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. XML Genetic Structure of SSR1 & SSR2 loci from Iranian Mycobacterium Avium Subspecies Paratuberculosis Isolates by a Short Sequence Repeat Analysis Approach

    Directory of Open Access Journals (Sweden)

    Aida Chalesh (MSc

    2016-01-01

    Full Text Available Background and Objective: Paratuberculosis has been repeatedly reported from Iranian ruminant herds. The extrem fastidious nature of Mycobacterium avium subspecies paratuberculsos hinders genomic diversity studies of the pathogen. Short Sequence Repeat analysis is one of the genome-based approches recently developed to overcome this difficulty. In this study we describe the application of SSR genotyping on three Iranian MAP type strains plus the III & V vaccinal strain. Methods: All the bacteria were examined by PCR-F57 and PCR-IS900 experiments in order to authenticate their identity as MAP. SSR genotyping using SSR1 & SSR2 loci was conducted according to the Amonsin method. PCR amplicons were sequenced to guarantee the accuracy of findings. Results: At SSR1 locus two allels were identified, a larger allel of 770 bp and a smaller allel of 763 bp long. At SSR2 only a single allele, 800 bp long, was detected. Two Iranian bovine and ovine MAP isolates along with the vaccinal III & V strain shared a single SSR1/SSR2 pattern while a different SSR1/SSR2 was represented by the third (caprine Iranian MAP isolate. Conclusion: While finding a shared SSR type between the two Iranian MAP isolates and the III & V strain might represent a mutual ancestral background but this has to be assessed through further studies. Detection of two SSR genotypes between three Iranian type strains is likely a reflection of more MAP clones in Iran.

  18. Unexpected instability of family of repeats (FR, the critical cis-acting sequence required for EBV latent infection, in EBV-BAC systems.

    Directory of Open Access Journals (Sweden)

    Teru Kanda

    Full Text Available A group of repetitive sequences, known as the Family of Repeats (FR, is a critical cis-acting sequence required for EBV latent infection. The FR sequences are heterogeneous among EBV strains, and they are sometimes subject to partial deletion when subcloned in E. coli-based cloning vectors. However, the FR stability in EBV-BAC (bacterial artificial chromosome system has never been investigated. We found that the full length FR of the Akata strain EBV was not stably maintained in a BAC vector. By contrast, newly obtained BAC clones of the B95-8 strain of EBV stably maintained the full length FR during recombinant virus production and B-cell transformation. Investigation of primary DNA sequences of Akata-derived EBV-BAC clones indicates that the FR instability is most likely due to a putative secondary structure of the FR region. We conclude that the FR instability in EBV-BAC clones can be a pitfall in E. coli-mediated EBV genetics.

  19. Unexpected instability of family of repeats (FR), the critical cis-acting sequence required for EBV latent infection, in EBV-BAC systems.

    Science.gov (United States)

    Kanda, Teru; Shibata, Sachiko; Saito, Satoru; Murata, Takayuki; Isomura, Hiroki; Yoshiyama, Hironori; Takada, Kenzo; Tsurumi, Tatsuya

    2011-01-01

    A group of repetitive sequences, known as the Family of Repeats (FR), is a critical cis-acting sequence required for EBV latent infection. The FR sequences are heterogeneous among EBV strains, and they are sometimes subject to partial deletion when subcloned in E. coli-based cloning vectors. However, the FR stability in EBV-BAC (bacterial artificial chromosome) system has never been investigated. We found that the full length FR of the Akata strain EBV was not stably maintained in a BAC vector. By contrast, newly obtained BAC clones of the B95-8 strain of EBV stably maintained the full length FR during recombinant virus production and B-cell transformation. Investigation of primary DNA sequences of Akata-derived EBV-BAC clones indicates that the FR instability is most likely due to a putative secondary structure of the FR region. We conclude that the FR instability in EBV-BAC clones can be a pitfall in E. coli-mediated EBV genetics.

  20. Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

    Science.gov (United States)

    Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

    2011-07-01

    Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

  1. Effects of repeated exposure to malathion on growth, food consumption, and locomotor performance of the western fence lizard (Sceloporus occidentalis)

    Energy Technology Data Exchange (ETDEWEB)

    Holem, Ryan R. [University of Georgia, Savannah River Ecology Laboratory, Aiken, SC 29801 (United States); ENTRIX, Inc., Okemos, MI 48864 (United States); Hopkins, William A. [University of Georgia, Savannah River Ecology Laboratory, Aiken, SC 29801 (United States); Department of Fisheries and Wildlife Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (United States)], E-mail: hopkinsw@vt.edu; Talent, Larry G. [Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078 (United States)

    2008-03-15

    Effects of repeated pollutant exposure on growth, locomotor performance, and behavior have rarely been evaluated in reptiles. We administered three doses of malathion (2.0, 20, or 100 mg/kg body weight) to western fence lizards (Sceloporus occidentalis) over an 81 day period. Eight and 23% mortality occurred at 20 and 100 mg/kg (p = 0.079) and 85% of lizards in the 100 mg/kg group exhibited clinical symptoms of poisoning. Growth, food consumption, body condition index, and terrestrial locomotor performance were not significantly influenced by malathion. However, arboreal sprint velocity was significantly reduced in lizards receiving 100 mg/kg. Fifty percent of lizards in the 100 mg/kg group also refused to sprint in the arboreal setting (p = 0.085). Based on these results, arboreal locomotor performance was the most sensitive metric of exposure we evaluated. Further study of compounds such as malathion is warranted due to highly variable application rates and exposure scenarios. - Repeated exposure of western fence lizards to malathion caused reduced arboreal performance and some mortality but growth, food consumption, and terrestrial performance were not affected.

  2. Effects of acute creatine loading with or without carbohydrate on repeated bouts of maximal swimming in high-performance swimmers.

    Science.gov (United States)

    Theodorou, Apostolos S; Havenetidis, Konstantinos; Zanker, Cathy L; O'Hara, John P; King, Roderick F G J; Hood, Colin; Paradisis, Giorgios; Cooke, Carlton B

    2005-05-01

    The addition of carbohydrate (CHO) to an acute creatine (Cr) loading regimen has been shown to increase muscle total creatine content significantly beyond that achieved through creatine loading alone. However, the potential ergogenic effects of combined Cr and CHO loading have not been assessed. The purpose of this study was to compare swimming performance, assessed as mean swimming velocity over repeated maximal intervals, in high-performance swimmers before and after an acute loading regimen of either creatine alone (Cr) or combined creatine and carbohydrate (Cr + CHO). Ten swimmers (mean +/- SD of age and body mass: 17.8 +/- 1.8 years and 72.3 +/- 6.8 kg, respectively) of international caliber were recruited and were randomized to 1 of 2 groups. Each swimmer ingested five 5 g doses of creatine for 4 days, with the Cr + CHO group also ingesting approximately 100 g of simple CHO 30 minutes after each dose of creatine. Performance was measured on 5 separate occasions: twice at "baseline" (prior to intervention, to assess the repeatability of the performance test), within 48 hours after intervention, and then 2 and 4 weeks later. All subjects swam faster after either dietary loading regimen (p swimmers continued to produce faster swim times for up to 4 weeks after intervention. Our findings suggest that no performance advantage was gained from the addition of carbohydrate to a creatine-loading regimen in these high-caliber swimmers.

  3. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

    Science.gov (United States)

    Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

    2011-01-01

    Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

  4. The Role of the Y-Chromosome in the Establishment of Murine Hybrid Dysgenesis and in the Analysis of the Nucleotide Sequence Organization, Genetic Transmission and Evolution of Repeated Sequences.

    Science.gov (United States)

    Nallaseth, Ferez Soli

    The Y-chromosome presents a unique cytogenetic framework for the evolution of nucleotide sequences. Alignment of nine Y-chromosomal fragments in their increasing Y-specific/non Y-specific (male/female) sequence divergence ratios was directly and inversely related to their interspersion on these two respective genomic fractions. Sequence analysis confirmed a direct relationship between divergence ratios and the Alu, LINE-1, Satellite and their derivative oligonucleotide contents. Thus their relocation on the Y-chromosome is followed by sequence divergence rather than the well documented concerted evolution of these non-coding progenitor repeated sequences. Five of the nine Y-chromosomal fragments are non-pseudoautosomal and transcribed into heterogeneous PolyA^+ RNA and thus can be retrotransposed. Evolutionary and computer analysis identified homologous oligonucleotide tracts in several human loci suggesting common and random mechanistic origins. Dysgenic genomes represent the accelerated evolution driving sequence divergence (McClintock, 1984). Sex reversal and sterility characterizing dysgenesis occurs in C57BL/6JY ^{rm Pos} but not in 129/SvY^{rm Pos} derivative strains. High frequency, random, multi-locus deletion products of the feral Y^{ rm Pos}-chromosome are generated in the germlines of F1(C57BL/6J X 129/SvY^{ rm Pos})(male) and C57BL/6JY ^{rm Pos}(male) but not in 129/SvY^{rm Pos}(male). Equal, 10^{-1}, 10^ {-2}, and 0 copies (relative to males) of Y^{rm Pos}-specific deletion products respectively characterize C57BL/6JY ^{rm Pos} (HC), (LC), (T) and (F) females. The testes determining loci of inactive Y^{rm Pos}-chromosomes in C57BL/6JY^{rm Pos} HC females are the preferentially deleted/rearranged Y ^{rm Pos}-sequences. Disruption of regulation of plasma testosterone and hepatic MUP-A mRNA levels, TRD of a 4.7 Kbp EcoR1 fragment suggest disruption of autosomal/X-chromosomal sequences. These data and the highly repeated progenitor (Alu, GATA, LINE-1

  5. Repeated Sprint Ability in Elite Water Polo Players and Swimmers and its Relationship to Aerobic and Anaerobic Performance

    Directory of Open Access Journals (Sweden)

    Yoav Meckel

    2013-12-01

    Full Text Available The purpose of this study was to determine indices of swimming repeated sprint ability (RSA in 19 elite water polo players compared to 16 elite swimmers during a repeated sprint swimming test (RST, and to examine the relationships between these indices and aerobic and anaerobic performance capabilities in both groups. Indices of RSA were determined by the ideal sprint time (IS, the total sprint time (TS, and the performance decrement (PD recorded during an 8 x 15-m swimming RST. Single long - (800-m and short-(25-m distance swim tests were used to determined indices of aerobic and anaerobic swimming capabilities, respectively. The water polo players exhibited lower RSA swimming indices, as well as lower scores in the single short and long swim distances, compared to the swimmers. Significant relationships were found between the 25- m swim results and the IS and the TS, but not the PD of both the swimmers and the water polo players. No significant relationships were found between the 800-m swim results and any of the RSA indices in either the swimmers or the water polo players. No significant relationships were found between the 25-m and the 800-m swim results in either the swimmers or the water polo players. The results indicate that swimmers posses better RSA as well as higher anaerobic and aerobic capabilities, as reflected by the single short- and long-distance swim tests, compared to water polo players. The results also indicate that, as for running and cycling, repeated sprint swim performance is strongly related to single sprint performance.

  6. Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Yuan Tong

    2010-01-01

    Full Text Available Abstract Background Transmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs, representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. Results As a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs of 194 LRR-RLKs were cloned into the GatewayR donor vector pDONR/ZeoR and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into GatewayR destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC at Ohio State University for full accessibility by the Arabidopsis research community. Conclusions Most of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family.

  7. R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs.

    Science.gov (United States)

    Trubetskoy, A M; Okenquist, S A; Lenz, J

    1999-04-01

    A stem-loop structure at the 5' end of the R region of the long terminal repeat (LTR) of the murine leukemia virus SL3 and other type C mammalian retroviruses is important for maximum levels of expression of a reporter gene under the control of the viral LTR. This element, termed the R region stem-loop (RSL), has a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Its major effect is on posttranscriptional processing of LTR-driven transcripts. Here we tested whether the RSL affected the production of RNAs from a full-length SL3 genome. Mutation of the RSL in the 5' LTR of SL3 reduced the cytoplasmic levels of full-length viral transcripts but not those of spliced, env mRNA transcripts. Thus, the RSL specifically affected the cytoplasmic levels of the unspliced viral RNA. To test further whether the effect was specific for unspliced transcripts, a system was devised in which the expression of a reporter gene under the control of the viral LTR was tested in the presence or absence of an intron. Mutation of the RSL resulted in only about a twofold decline in the level of reporter gene expression when the transcripts contained an intron. However, when the intron was removed, mutation of the RSL reduced expression of the reporter gene about 10- to 60-fold in various cell lines. The secondary structure of the RSL was essential for its activity on the intronless transcript. Thus, the RSL appears to be important for the cytoplasmic accumulation of unspliced viral RNA and unspliced RNA from chimeric transcription units under the control of the viral LTR.

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

    Directory of Open Access Journals (Sweden)

    Turmel Monique

    2007-07-01

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

  9. Repeated sprint ability in elite water polo players and swimmers and its relationship to aerobic and anaerobic performance.

    Science.gov (United States)

    Meckel, Yoav; Bishop, David; Rabinovich, Moran; Kaufman, Leonid; Nemet, Dan; Eliakim, Alon

    2013-01-01

    The purpose of this study was to determine indices of swimming repeated sprint ability (RSA) in 19 elite water polo players compared to 16 elite swimmers during a repeated sprint swimming test (RST), and to examine the relationships between these indices and aerobic and anaerobic performance capabilities in both groups. Indices of RSA were determined by the ideal sprint time (IS), the total sprint time (TS), and the performance decrement (PD) recorded during an 8 x 15-m swimming RST. Single long - (800-m) and short-(25-m) distance swim tests were used to determined indices of aerobic and anaerobic swimming capabilities, respectively. The water polo players exhibited lower RSA swimming indices, as well as lower scores in the single short and long swim distances, compared to the swimmers. Significant relationships were found between the 25- m swim results and the IS and the TS, but not the PD of both the swimmers and the water polo players. No significant relationships were found between the 800-m swim results and any of the RSA indices in either the swimmers or the water polo players. No significant relationships were found between the 25-m and the 800-m swim results in either the swimmers or the water polo players. The results indicate that swimmers posses better RSA as well as higher anaerobic and aerobic capabilities, as reflected by the single short- and long-distance swim tests, compared to water polo players. The results also indicate that, as for running and cycling, repeated sprint swim performance is strongly related to single sprint performance. Key PointsElite water polo players demonstrated lower repeated sprint ability (RSA), aerobic and anaerobic capabilities compared to elite swimmers.A 25-m swim trial correlated significantly with ideal sprint time and total sprint time, emphasizing the important contribution of anaerobic metabolism for these exercise types in both water polo players and swimmers.800-m swim results did not correlate with RSA or 25-m

  10. Effect of Repeated/Spaced Formative Assessments on Medical School Final Exam Performance

    Directory of Open Access Journals (Sweden)

    Edward K. Chang

    2017-06-01

    Discussion: Performance on weekly formative assessments was predictive of final exam scores. Struggling medical students will benefit from extra cumulative practice exams while students who are excelling do not need extra practice.

  11. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers.

    Science.gov (United States)

    Jain, Shalu; Kumar, Ajay; Mamidi, Sujan; McPhee, Kevin

    2014-10-01

    Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.

  12. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Science.gov (United States)

    Dossa, Komivi; Yu, Jingyin; Liao, Boshou; Cisse, Ndiaga; Zhang, Xiurong

    2017-01-01

    The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries. PMID:28878802

  13. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2017-08-01

    Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

  14. Local repeat sequence organization of an intergenic spacer in the chloroplast genome of Chlamydomonas reinhardtii leads to DNA expansion and sequence scrambling: a complex mode of “copy-choice replication”?

    Indian Academy of Sciences (India)

    Mahendra D Wagle; Subhojit Sen; Basuthkar J Rao

    2001-12-01

    Parent-specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA of Chlamydomonas reinhardtii. Such parent-specific RAPD bands (genomic fingerprints) segregated uniparentally (through mt+) in a cross between a pair of polymorphic interfertile strains of Chlamydomonas (C. reinhardtii and C. minnesotti), suggesting that they originated from the chloroplast genome. Southern analysis mapped the RAPD-markers to the chloroplast genome. One of the RAPD-markers, ``P2” (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3′ end of 23S, full 5S and intergenic region between 5S and psbA. This region seems divergent enough between the two parents, such that a specific PCR designed for a parental specific chloroplast sequence within this region, amplified a marker in that parent only and not in the other, indicating the utility of RAPD-scan for locating the genomic regions of sequence divergence. Remarkably, the RAPD-product, ``P2” seems to have originated from a PCR-amplification of a much smaller (about 600 bp), but highly repeat-rich (direct and inverted) domain of the 3 kb region in a manner that yielded no linear sequence alignment with its own template sequence. The amplification yielded the same uniquely ``sequence-scrambled” product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product, a ``unique” new sequence, had lost the repetitive organization of the template genome where it had originated from and perhaps represented a ``complex path” of copy-choice replication.

  15. Repeat-until-success quantum repeaters

    Science.gov (United States)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  16. Consistency across repeated eyewitness interviews: contrasting police detectives' beliefs with actual eyewitness performance.

    Directory of Open Access Journals (Sweden)

    Alana C Krix

    Full Text Available In the legal system, inconsistencies in eyewitness accounts are often used to discredit witnesses' credibility. This is at odds with research findings showing that witnesses frequently report reminiscent details (details previously unrecalled at an accuracy rate that is nearly as high as for consistently recalled information. The present study sought to put the validity of beliefs about recall consistency to a test by directly comparing them with actual memory performance in two recall attempts. All participants watched a film of a staged theft. Subsequently, the memory group (N = 84 provided one statement immediately after the film (either with the Self-Administered Interview or free recall and one after a one-week delay. The estimation group (N = 81 consisting of experienced police detectives estimated the recall performance of the memory group. The results showed that actual recall performance was consistently underestimated. Also, a sharp decline of memory performance between recall attempts was assumed by the estimation group whereas actual accuracy remained stable. While reminiscent details were almost as accurate as consistent details, they were estimated to be much less accurate than consistent information and as inaccurate as direct contradictions. The police detectives expressed a great concern that reminiscence was the result of suggestive external influences. In conclusion, it seems that experienced police detectives hold many implicit beliefs about recall consistency that do not correspond with actual recall performance. Recommendations for police trainings are provided. These aim at fostering a differentiated view on eyewitness performance and the inclusion of more comprehensive classes on human memory structure.

  17. Tolerance to repeated nicotine administration on performance, subjective, and physiological responses in nonsmokers.

    Science.gov (United States)

    Heishman, S J; Henningfield, J E

    2000-10-01

    When administered acutely to nonsmokers, nicotine's effects on performance are inconsistent, perhaps because of suboptimal dosing or initial dysphoria that could interfere with performance. The purpose of this study was to determine if a range of nicotine doses administered for 8 days to nonsmokers would enhance psychomotor and cognitive abilities and to document the development of nicotine tolerance or sensitization. Twelve male volunteers, who reported ever smoking five cigarettes or less, participated in 8 consecutive experimental days in which they were administered four doses of nicotine polacrilex gum each day in this order: 0, 2, 4, and 8 mg. Performance, subjective, and physiological measures were assessed before and after each dose. Plasma nicotine concentration ranged from 6.9 to 11.5 ng/ml following the 8 mg dose. Nicotine increased rate of responding and decreased response time on working memory (digit recall); however, accuracy was impaired. Nicotine also decreased accuracy on visual scanning and attention (two-letter search), and the 8 mg dose impaired gross motor coordination (circular lights). Tolerance did not develop to the performance impairing effects of nicotine. Nicotine produced dose-related increases in ratings of dysphoria and negative mood, including tension, anxiety, nervousness, turning of stomach, and sedation. Tolerance developed to some, but not all, of these aversive effects. Tolerance also was not observed to the increased cardiovascular measures. Although tolerance developed to some of the aversive effects of nicotine, performance enhancement was not observed. These data do not support the hypothesis that nicotine-induced performance enhancement contributes to the reinforcing effects of tobacco use during the early stages of dependence development.

  18. Consistency across Repeated Eyewitness Interviews: Contrasting Police Detectives’ Beliefs with Actual Eyewitness Performance

    Science.gov (United States)

    Krix, Alana C.; Sauerland, Melanie; Lorei, Clemens; Rispens, Imke

    2015-01-01

    In the legal system, inconsistencies in eyewitness accounts are often used to discredit witnesses’ credibility. This is at odds with research findings showing that witnesses frequently report reminiscent details (details previously unrecalled) at an accuracy rate that is nearly as high as for consistently recalled information. The present study sought to put the validity of beliefs about recall consistency to a test by directly comparing them with actual memory performance in two recall attempts. All participants watched a film of a staged theft. Subsequently, the memory group (N = 84) provided one statement immediately after the film (either with the Self-Administered Interview or free recall) and one after a one-week delay. The estimation group (N = 81) consisting of experienced police detectives estimated the recall performance of the memory group. The results showed that actual recall performance was consistently underestimated. Also, a sharp decline of memory performance between recall attempts was assumed by the estimation group whereas actual accuracy remained stable. While reminiscent details were almost as accurate as consistent details, they were estimated to be much less accurate than consistent information and as inaccurate as direct contradictions. The police detectives expressed a great concern that reminiscence was the result of suggestive external influences. In conclusion, it seems that experienced police detectives hold many implicit beliefs about recall consistency that do not correspond with actual recall performance. Recommendations for police trainings are provided. These aim at fostering a differentiated view on eyewitness performance and the inclusion of more comprehensive classes on human memory structure. PMID:25695428

  19. Genetic Variation in Five Mediterranean Populations of Juniperus phoenicea as Revealed by Inter-Simple Sequence Repeat (ISSR) Markers

    Science.gov (United States)

    MELONI, MARILENA; PERINI, DAVIDE; FILIGHEDDU, ROSSELLA; BINELLI, GIORGIO

    2006-01-01

    • Background and Aims The assessment of the genetic variability and the identification of isolated populations within a given species represent important information to plan conservation strategies on a genetic basis. In this work, the genetic variability in five natural populations of Juniperus phoenicea, three from Sardinia, one from Cyprus and the last one in the Maritime Alps was analysed by means of ISSRs, on the hypothesis that the latter could have been a refugial one during the last glaciation. • Methods ISSRs were chosen because of their ability to detect variation without any prior sequence information. The use of three primers yielded 45 reproducible, polymorphic bands, which were utilized to estimate the basic parameters of genetic variability and diversity. • Key Results All of the populations analysed harboured an adequate amount of genetic variability, with HS = 0·1299. The proportion of genetic diversity between populations has been estimated by GST = 0·12. The three Sardinian populations are separated, as tested by AMOVA, from the Cyprus and the continental ones. • Conclusions The results indicate that geographical isolation has represented a major barrier to gene flow in Juniperus phoenicea. This work represents a first step towards a full genetic characterization of a conifer from the Mediterranean, a world biodiversity hotspot confronted with climate change, and thus contributes towards the planning of genetics-informed conservation strategies. PMID:16311272

  20. Performance Concern, Contingent Self-Worth, and Responses to Repeated Achievement Failure in Second Graders

    Science.gov (United States)

    Smiley, Patricia A.; Coulson, Sheri L.; Greene, Joelle K.; Bono, Katherine L.

    2010-01-01

    Individual differences in emotion, cognitions, and task choice following achievement failure are found among four- to seven-year-olds. However, neither performance deterioration during failure nor generalization after failure--aspects of the helpless pattern in 10-year-olds--have been reliably demonstrated in this age group. In the present study,…

  1. USEFULNESS AND METABOLIC IMPLICATIONS OF A 60-SECOND REPEATED JUMPS TEST AS A PREDICTOR OF ACROBATIC JUMPING PERFORMANCE IN GYMNASTS

    Directory of Open Access Journals (Sweden)

    Ferran Antoni Rodriguez

    2013-01-01

    Full Text Available Gymnastics floor exercises are composed of a set of four to five successive acrobatic jumps usually called a �series�. The aims of the study were: 1 to relate the acrobatic gymnastics performance of these series with a repeated jumps test of similar duration (R60, 2 to study the relation between R60 and physiological parameters (heart rate and blood lactate, and the performance obtained in different kinds of jumps, 3 to confirm whether R60, executed without a damped jumping technique, can be considered an anaerobic lactic power test. Twenty male and twenty-four female gymnasts performed three repeated jumps tests for 5 s (R5, 10 s (R10 and 60 s (R60 and vertical jumps, such as drop jumps (DJ, squat jumps (SJ and countermovement jumps (CMJ. We assessed heart rate (HR and blood lactate during R10 and R60. The average values of the maximal blood lactate concentration (Lmax after R10 (males = 2.5±0.6 mmol.l-1; females = 2.1±0.8 mmol.l-1 confirm that anaerobic glycolysis is not activated to a high level. In R60, the Lmax (males = 7.5±1.7 mmol.l-1; females = 5.9±2.1 mmol.l-1 that was recorded does not validate R60 as an anaerobic lactic power test. We confirmed the relation between the average power obtained in R60 (R60Wm and the acrobatic performance on the floor. The inclusion in the multiple regression equation of the best power in DJ and the best flight-contact ratio (FC in R5 confirms the influence of other non-metabolic components on the variability in R60 performance, at least in gymnasts.

  2. Development of chloroplast simple sequence repeats (cpSSRs) for the intraspecific study of Gracilaria tenuistipitata (Gracilariales, Rhodophyta) from different populations.

    Science.gov (United States)

    Song, Sze-Looi; Lim, Phaik-Eem; Phang, Siew-Moi; Lee, Weng-Wah; Hong, Dang Diem; Prathep, Anchana

    2014-02-04

    Gracilaria tenuistipitata is an agarophyte with substantial economic potential because of its high growth rate and tolerance to a wide range of environment factors. This red seaweed is intensively cultured in China for the production of agar and fodder for abalone. Microsatellite markers were developed from the chloroplast genome of G. tenuistipitata var. liui to differentiate G. tenuistipitata obtained from six different localities: four from Peninsular Malaysia, one from Thailand and one from Vietnam. Eighty G. tenuistipitata specimens were analyzed using eight simple sequence repeat (SSR) primer-pairs that we developed for polymerase chain reaction (PCR) amplification. Five mononucleotide primer-pairs and one trinucleotide primer-pair exhibited monomorphic alleles, whereas the other two primer-pairs separated the G. tenuistipitata specimens into two main clades. G. tenuistipitata from Thailand and Vietnam were grouped into one clade, and the populations from Batu Laut, Middle Banks and Kuah (Malaysia) were grouped into another clade. The combined dataset of these two primer-pairs separated G. tenuistipitata obtained from Kelantan, Malaysia from that obtained from other localities. Based on the variations in repeated nucleotides of microsatellite markers, our results suggested that the populations of G. tenuistipitata were distributed into two main geographical regions: (i) populations in the west coast of Peninsular Malaysia and (ii) populations facing the South China Sea. The correct identification of G. tenuistipitata strains with traits of high economic potential will be advantageous for the mass cultivation of seaweeds.

  3. Characterization of expressed Pgip genes in rice and wheat reveals similar extent of sequence variation to dicot PGIPs and identifies an active PGIP lacking an entire LRR repeat.

    Science.gov (United States)

    Janni, Michela; Di Giovanni, Michela; Roberti, Serena; Capodicasa, Cristina; D'Ovidio, Renato

    2006-11-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. A number of PGIPs have been characterized from dicot species, whereas only a few data are available from monocots. Database searches and genome-specific cloning strategies allowed the identification of four rice (Oryza sativa L.) and two wheat (Triticum aestivum L.) Pgip genes. The rice Pgip genes (Ospgip1, Ospgip2, Ospgip3 and Ospgip4) are distributed over a 30 kbp region of the short arm of chromosome 5, whereas the wheat Pgip genes, Tapgip1 and Tapgip2, are localized on the short arm of chromosome 7B and 7D, respectively. Deduced amino acid sequences show the typical LRR modular organization and a conserved distribution of the eight cysteines at the N- and C-terminal regions. Sequence comparison suggests that monocot and dicot PGIPs form two separate clusters sharing about 40% identity and shows that this value is close to the extent of variability observed within each cluster. Gene-specific RT-PCR and biochemical analyses demonstrate that both Ospgips and Tapgips are expressed in the whole plant or in a tissue-specific manner, and that OsPGIP1, lacking an entire LRR repeat, is an active inhibitor of fungal polygalacturonases. This last finding can contribute to define the molecular features of PG-PGIP interactions and highlights that the genetic events that can generate variability at the Pgip locus are not only limited to substitutions or small insertions/deletions, as so far reported, but can also involve variation in the number of LRRs.

  4. The effect of repeated periods of speed endurance training on performance, running economy and muscle adaptations

    DEFF Research Database (Denmark)

    Skovgaard, Casper; Almquist, Nicki Winfield; Bangsbo, Jens

    2017-01-01

    , with no change in P1. No changes in muscle expression of Na(+) ,K(+) -ATPase α1, α2 and β1, NHE1, SERCA1 and SERCA2, actin and CamKII were found during neither P1 nor P2. Thus, the present study demonstrates that a second period of intense training leads to improved short-term performance and further improved RE...

  5. Effect of cold water immersion on repeated 1-km cycling performance in the heat.

    Science.gov (United States)

    Peiffer, Jeremiah J; Abbiss, Chris R; Watson, Greig; Nosaka, Kazunori; Laursen, Paul B

    2010-01-01

    This study examined the effect of a short cold water immersion (CWI) intervention on rectal and muscle temperature, isokinetic strength and 1-km cycling time trial performance in the heat. Ten male cyclists performed a 1-km time trial at 35.0+/-0.3 degrees C and 40.0+/-3.0% relative humidity, followed by 20 min recovery sitting in either cold water (14 degrees C) for 5 min or in 35 degrees C air (control); a second 1-km time trial immediately followed. Peak and mean cycling power output were recorded for both time trials. Rectal and muscle temperature, and maximal isokinetic concentric torque of the knee extensors were measured before and immediately after the first and second time trials. Rectal temperature was not different between cold water immersion and control conditions at any time points. After the second time trial, however, muscle temperature was significantly lower (-1.3+/-0.7 degrees C) in cold water immersion compared with the control trial. While peak and mean power decreased from the first to second time trial in both conditions (-86+/-54 W and -24+/-16 W, respectively), maximal isokinetic concentric torque was similar between conditions at all time points. The 5 min cold water immersion intervention lowered muscle temperature but did not affect isokinetic strength or 1-km cycling performance. Copyright (c) 2008 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  6. The relationship between repeated kicking performance and maximal aerobic capacity in elite junior Australian football.

    Science.gov (United States)

    Joseph, Jacob; Woods, Carl; Joyce, Christopher

    2017-08-26

    Australian football (AF) is a physically demanding game, requiring players to engage in a range of anaerobic activities interspersed with prolonged aerobic exercise. Coupled, players have to perform a range of technical skills, the most fundamental of which being to effectively kick (dispose) the ball. The aim of this study was to ascertain the extent to which aerobic capacity influenced kicking performance in AF. Twenty four elite U18 players competing in the same U18 competition performed the Australian Football Kicking test (AFK) three times with the yo-yo IR2 completed twice (between each AFK), with no rest between all three AFKs. Linear mixed models (LMM) reported the extent to which kicking speed and accuracy scores were influenced by the level reached on the yo-yo IR2. Results indicated that players who recorded a higher level on the yo-yo IR2 produced a faster average kicking speed following each AFK (P players, kicking speed was faster and more accurate on their dominant kicking leg regardless of score on the yo-yo IR2 (P players who attain a relatively higher score on the yo-yo IR2 may be better equipped at preserving their kicking speed. Thus, coaches may wish to integrate both technical and aerobic drills in an attempt to preserve a player's capability to execute ball disposals with a high velocity.

  7. Effects of leg contrast strength training on sprint, agility and repeated change of direction performance in male soccer players.

    Science.gov (United States)

    Hammami, Mehréz; Negra, Yassine; Shephard, Roy J; Chelly, Mohamed-Souhaiel

    2017-11-01

    Contrast training is a popular technique among individuals who are involved in dynamic sports, having as its goal an increase in dynamic muscular performance. It is characterized by the use of high and low loads in the same strength training session. The present investigation aimed to determine the effects of adding 8 weeks of contrast strength training (CSTP) to regular soccer practice in U-17 male soccer players during the competitive season. We hypothesized that CSTP would enhance their performance. Subjects were divided randomly between a control group (CG, N.=12) and a contrast strength group (CSG, N.=19). The 2 groups trained together; controls followed the regular soccer program, which was replaced by a contrast strength training program for the experimental group. Performance was assessed before and after training, using 10 measures: 5-10-, 20- 30-, and 40-m sprints, a 4x5 m sprint (S4x5), a 9-3-6-3-9 m sprint with 180° turns (S180), a 9-3-6-3-9 m sprint with backward and forward running (SBF), a Repeated-Shuttle-Sprint Ability Test (RSSA), and a Repeated Change of Direction Test (RCOD). CSG showed gains relative to controls in 5-m (Psprints. There were also significant gains in S180°, SBF, and S4 x 5 agility tests (P<0.01), and all RCOD parameters (P<0.05) except RCOD-FI (P=0.055) but no significant change in any RSSA parameters. We conclude that biweekly contrast strength training can be commended to U-17 male soccer players as a means of improving many important components of athletic performance relative to standard in-season training.

  8. Emotional responses during repeated sprint intervals performed on level, downhill and uphill surfaces.

    Science.gov (United States)

    Baron, Bertrand; Guilloux, Bertrand; Begue, Mylène; Uriac, Stéphane

    2015-01-01

    The purpose of this study was to test emotional responses during sprint intervals performed on a level, down and up surface. Fifty trained participants performed a maximal effort during a 60-m sprint and 10 repetitions of 60 m running sprints on a level, down and up surface on a 5.9% slope. Running speeds, emotional responses and heart rate were measured. Self-selected speeds were correlated with the rating of perceived exertion, the affective balance, the desire to stop and the resources needed for the task in all conditions whereas the pleasure, the desire to continue and the capacity to realise the task were correlated with speeds only during level and uphill running. Mean values of emotional parameters were significantly different (P < 0.05) during running on a flat surface, downhill and uphill. When the gradient of running surface is changed, the pattern of emotional responses was just translated, i.e. most of the slope between the evolution of emotional parameters and the repetitions were not significantly different whereas Y-intercepts were different. Consented effort is highly correlated with the resources needed for the task (P < 0.001, r(2) = 0.72). We propose that the difference in the resources needed for the task between level, downhill and uphill running (F 2, 1499 = 166.5, P < 0.001, Eta(2) = 0.18) is the most important key that explains our results.

  9. Effect on Spasticity After Performance of Dynamic-Repeated-Passive Ankle Joint Motion Exercise in Chronic Stroke Patients

    Directory of Open Access Journals (Sweden)

    Chin-Li Wu

    2006-12-01

    Full Text Available Spasticity associated with abnormal muscle tone is a common motor disorder following stroke, and the spastic ankle may affect ambulatory function. The purpose of this study was to investigate the short-term effect of dynamic-repeated-passive ankle movements with weight loading on ambulatory function and spastic hypertonia of chronic stroke patients. In this study, 12 chronic stroke patients with ankle spasticity and inefficient ambulatory ability were enrolled. Stretching of the plantar-flexors of the ankle in the standing position for 15 minutes was performed passively by a constant-speed and electrically powered device. The following evaluations were done before and immediately after the dynamic-repeated-passive ankle movements. Spastic hypertonia was assessed by the Modified Ashworth Scale (MAS; range, 0–4, Achilles tendon reflexes test (DTR; range, 0–4, and ankle clonus (range, 0–5. Improvement in ambulatory ability was determined by the timed up-and-go test (TUG, the 10-minute walking test, and cadence (steps/minute. In addition, subjective experience of the influence of ankle spasticity on ambulation was scored by visual analog scale (VAS. Subjective satisfaction with the therapeutic effect of spasticity reduction was evaluated by a five-point questionnaire (1 = very poor, 2 = poor, 3 = acceptable, 4 = good, 5 = very good. By comparison of the results before and after intervention, these 12 chronic stroke patients presented significant reduction in MAS and VAS for ankle spasticity, the time for TUG and 10-minute walking speed (p < 0.01. The cadence also increased significantly (p < 0.05. In addition, subjective satisfaction with the short-term therapeutic effect was mainly good (ranging from acceptable to very good. In conclusion, 15 minutes of dynamic-repeated-passive ankle joint motion exercise with weight loading in the standing position by this simple constant-speed machine is effective in reducing ankle spasticity and improving

  10. Effect of homogenizer performance on accuracy and repeatability of mid-infrared predicted values for major milk components.

    Science.gov (United States)

    Di Marzo, Larissa; Barbano, David M

    2016-12-01

    Our objective was to determine the effect of mid-infrared (MIR) homogenizer efficiency on accuracy and repeatability of Fourier transform MIR predicted fat, true protein, and anhydrous lactose determination given by traditional filter and partial least squares (PLS) prediction models. Five homogenizers with different homogenization performance based on laser light-scattering particle size analysis were used. Repeatability and accuracy were determined by conducting 17 sequential readings on milk homogenized externally to the instrument (i.e., control) and unhomogenized milk. Milk component predictions on externally homogenized milks were affected by variation in homogenizer performance, but the magnitude of effect were small (i.e., milks were pumped through both efficient and inefficient homogenizers within a MIR milk analyzer. Variation in the in-line MIR homogenizer performance on unhomogenized milks had a much larger effect on accuracy of component testing than on repeatability. The increase of particle size distribution [d(0.9)] from 1.35 to 3.03μm (i.e., fat globule diameter above which 10% of the volume of fat is contained) due to poor homogenization affected fat tests the most; traditional filter based fat B (carbon hydrogen stretch; -0.165%), traditional filter-based fat A (carbonyl stretch; -0.074%), and fat PLS (-0.078%) at a d(0.9) of 3.03μm. Variation in homogenization efficiency also affected traditional filter-based true protein test (+0.012%), true protein PLS prediction (-0.107%), and traditional filter-based anhydrous lactose test (+0.027%) at a d(0.9) of 3.03μm. Effects of variation in homogenization on anhydrous lactose PLS predictions were small. The accuracy of both traditional filter models and PLS models were influenced by poor homogenization. The value of 1.7µm for a d(0.9) used by the USDA Federal Milk Market laboratories as a criterion to make the decision to replace the homogenizer in a MIR milk analyzer appears to be a reasonable

  11. Simple-sequence repeat markers of Cattleya coccinea (Orchidaceae), an endangered species of the Brazilian Atlantic Forest.

    Science.gov (United States)

    Novello, M; Rodrigues, J F; Pinheiro, F; Oliveira, G C X; Veasey, E A; Koehler, S

    2013-09-03

    Microsatellite markers were developed for the endangered Brazilian orchid species Cattleya coccinea to describe its genetic diversity and structure and to support conservation studies. Nine microsatellite loci were isolated and characterized using an enriched genomic library. All loci are polymorphic at least in the 2 populations sampled, except for loci Cac05 and Cac09 for the Petrópolis population. The mean number of alleles per locus was 8.8 between populations. The mean values of the observed and expected heterozygosities were 0.541 (ranging from 0 to 1) and 0.639 (ranging from 0 to 0.9), respectively. Cross-amplifications were performed in 7 additional Epidendroideae species, and at least 2 loci were successful in 3 additional Cattleya species, Epidendrum secundum, and Brasiliorchis gracilis. All markers described herein will be useful in further studies evaluating the genetic diversity, population dynamics, and conservation genetics of C. coccinea and related species.

  12. Performance Study of Screen-Printed Textile Antennas after Repeated Washing

    Directory of Open Access Journals (Sweden)

    Kazani I.

    2014-06-01

    Full Text Available The stability of wearable textile antennas after 20 reference washing cycles was evaluated by measuring the reflection coefficient of different antenna prototypes. The prototypes’ conductive parts were screen-printed on several textile substrates using two different silver-based conductive inks. The necessity of coating the antennas with a thermoplastic polyurethane (TPU coating was investigated by comparing coated with uncoated antennas. It is shown that covering the antennas with the TPU layer not only protects the screen-printed conductive area but also prevents delamination of the multilayered textile fabric substrates, making the antennas washable for up to 20 cycles. Furthermore, it is proven that coating is not necessary for maintaining antenna operation and this up to 20 washing cycles. However, connector detachment caused by friction during the washing process was the main problem of antenna performance degradation. Hence, other flexible, durable methods should be developed for establishing a stable electrical connection.

  13. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Directory of Open Access Journals (Sweden)

    Huaiyong Luo

    Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  14. Attentional and visual demands for sprint performance in non-fatigued and fatigued conditions: reliability of a repeated sprint test

    Directory of Open Access Journals (Sweden)

    Diercks Ron L

    2010-05-01

    Full Text Available Abstract Background Physical performance measures are widely used to assess physical function, providing information about physiological and biomechanical aspects of motor performance. However they do not provide insight into the attentional and visual demands for motor performance. A figure-of-eight sprint test was therefore developed to measure the attentional and visual demands for repeated-sprint performance. The aims of the study were: 1 to assess test-retest reliability of the figure-of-eight sprint test, and 2 to study the attentional and visual demands for sprint performance in a non-fatigued and fatigued condition. Methods Twenty-seven healthy athletes were included in the study. To determine test-retest reliability, a subgroup of 19 athletes performed the figure-of-eight sprint test twice. The figure-of-eight sprint test consisted of nine 30-second sprints. The sprint test consisted of three test parts: sprinting without any restriction, with an attention-demanding task, and with restricted vision. Increases in sprint times with the attention-demanding task or restricted vision are reflective of the attentional and visual demands for sprinting. Intraclass correlation coefficients (ICCs and mean difference between test and retest with 95% confidence limits (CL were used to assess test-retest reliability. Repeated-measures ANOVA were used for comparisons between the sprint times and fatigue measurements of the test parts in both a non-fatigued and fatigued condition. Results The figure-of-eight sprint test showed good test-retest reliability, with ICCs ranging from 0.75 to 0.94 (95% CL: 0.40-0.98. Zero lay within the 95% CL of the mean differences, indicating that no bias existed between sprint performance at test and retest. Sprint times during the test parts with attention-demanding task (P = 0.01 and restricted vision (P Conclusions High ICCs and the absence of systematic variation indicate good test-retest reliability of the figure

  15. Collateral damage: Spread of repeat-induced point mutation from a duplicated DNA sequence into an adjoining single-copy gene in Neurospora crassa

    Indian Academy of Sciences (India)

    Meenal Vyas; Durgadas P Kasbekar

    2005-02-01

    Repeat-induced point mutation (RIP) is an unusual genome defense mechanism that was discovered in Neurospora crassa. RIP occurs during a sexual cross and induces numerous G : C to A : T mutations in duplicated DNA sequences and also methylates many of the remaining cytosine residues. We measured the susceptibility of the erg-3 gene, present in single copy, to the spread of RIP from duplications of adjoining sequences. Genomic segments of defined length (1, 1.5 or 2 kb) and located at defined distances (0, 0.5, 1 or 2 kb) upstream or downstream of the erg-3 open reading frame (ORF) were amplified by polymerase chain reaction (PCR), and the duplications were created by transformation of the amplified DNA. Crosses were made with the duplication strains and the frequency of erg-3 mutant progeny provided a measure of the spread of RIP from the duplicated segments into the erg-3 gene. Our results suggest that ordinarily RIP-spread does not occur. However, occasionally the mechanism that confines RIP to the duplicated segment seems to fail (frequency 0.1–0.8%) and then RIP can spread across as much as 1 kb of unduplicated DNA. Additionally, the bacterial hph gene appeared to be very susceptible to the spread of RIP-associated cytosine methylation.

  16. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related genera within botryosphaeriaceae.

    Science.gov (United States)

    Baird, Richard E; Wadl, Phillip A; Allen, Thomas; McNeill, David; Wang, Xinwang; Moulton, John K; Rinehart, Timothy A; Abbas, Hamed K; Shier, Thomas; Trigiano, Robert N

    2010-09-01

    Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (US). Genetic diversity was assessed using Nei's minimum genetic distance, and the usefulness of each locus was determined by calculating the polymorphism information content (PIC). A total of 98 alleles were detected and of these 31 were unique to individual genotypes. Eight of twelve loci were highly informative with PIC values greater than 0.50. The majority of pairwise comparisons of genetic distance were greater than 0.60 indicating moderate to high genetic diversity. Dendrograms based on the genetic dissimilarities were created for the 109 isolates of which 79 were from soybean. Some clustering by host and geography was noted, but, the dendrograms generally grouped isolates independent of host or geography. Additionally, sequencing of the internal transcribed spacer region (ITS) for 10 isolates revealed that all of these isolates were 99% similar. Three SSR loci from M. phaseolina were cross amplified in other genera in the Botryosphaeriaceae. This was the first study of genotyping and assessing genetic diversity of M. phaseolina isolates collected from a widespread host and geographic range across the US with SSRs. With an additional 34 loci publically available for M. phaseolina, the results indicate that previously developed SSRs from one species can be used in future population, ecological, and genetic studies of M. phaseolina and other genera within the Botryosphaeriaceae.

  17. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    Science.gov (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  18. Development of genome-wide informative simple sequence repeat markers for molecular diversity analysis in chickpea and development of web resource

    Directory of Open Access Journals (Sweden)

    SWARUP KUMAR PARIDA

    2015-08-01

    Full Text Available Development of informative polymorphic simple sequence repeat (SSR markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically-mapped SSR markers exhibited robust amplification efficiency (73.9% and high intra- and inter-specific polymorphic potential (63.5%, thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%, and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6% and functional molecular diversity (65% potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html, which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

  19. Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers.

    Science.gov (United States)

    Dai, H J; Zhang, Y M; Sun, X Q; Xue, J Y; Li, M M; Cao, M X; Shen, X L; Hang, Y Y

    2016-01-01

    Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province.

  20. Negative affect reduces performance in implicit sequence learning.

    Directory of Open Access Journals (Sweden)

    Junchen Shang

    Full Text Available BACKGROUND: It is well documented that positive rather than negative moods encourage integrative processing of conscious information. However, the extent to which implicit or unconscious learning can be influenced by affective states remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: A Serial Reaction Time (SRT task with sequence structures requiring integration over past trials was adopted to examine the effect of affective states on implicit learning. Music was used to induce and maintain positive and negative affective states. The present study showed that participants in negative rather than positive states learned less of the regularity. Moreover, the knowledge was shown by a Bayesian analysis to be largely unconscious as participants were poor at recognizing the regularity. CONCLUSIONS/SIGNIFICANCE: The results demonstrated that negative rather than positive affect inhibited implicit learning of complex structures. Our findings help to understand the effects of affective states on unconscious or implicit processing.

  1. Negative affect reduces performance in implicit sequence learning.

    Science.gov (United States)

    Shang, Junchen; Fu, Qiufang; Dienes, Zoltan; Shao, Can; Fu, Xiaolan

    2013-01-01

    It is well documented that positive rather than negative moods encourage integrative processing of conscious information. However, the extent to which implicit or unconscious learning can be influenced by affective states remains unclear. A Serial Reaction Time (SRT) task with sequence structures requiring integration over past trials was adopted to examine the effect of affective states on implicit learning. Music was used to induce and maintain positive and negative affective states. The present study showed that participants in negative rather than positive states learned less of the regularity. Moreover, the knowledge was shown by a Bayesian analysis to be largely unconscious as participants were poor at recognizing the regularity. The results demonstrated that negative rather than positive affect inhibited implicit learning of complex structures. Our findings help to understand the effects of affective states on unconscious or implicit processing.

  2. Effects of chronic dietary selenomethionine exposure on repeat swimming performance, aerobic metabolism and methionine catabolism in adult zebrafish (Danio rerio).

    Science.gov (United States)

    Thomas, Jith K; Wiseman, Steve; Giesy, John P; Janz, David M

    2013-04-15

    In a previous study we reported impaired swimming performance and greater stored energy in adult zebrafish (Danio rerio) after chronic dietary exposure to selenomethionine (SeMet). The goal of the present study was to further investigate effects of chronic exposure to dietary SeMet on repeat swimming performance, oxygen consumption (MO2), metabolic capacities (standard metabolic rate [SMR], active metabolic rate [AMR], factorial aerobic scope [F-AS] and cost of transport [COT]) and gene expression of energy metabolism and methionine catabolism enzymes in adult zebrafish. Fish were fed SeMet at measured concentrations of 1.3, 3.4, 9.8 or 27.5 μg Se/g dry mass (d.m.) for 90 d. At the end of the exposure period, fish from each treatment group were divided into three subgroups: (a) no swim, (b) swim, and (c) repeat swim. Fish from the no swim group were euthanized immediately at 90 d and whole body triglycerides, glycogen and lactate, and gene expression of energy metabolism and methionine catabolism enzymes were determined. Individual fish from the swim group were placed in a swim tunnel respirometer and swimming performance was assessed by determining the critical swimming speed (U(crit)). After both Ucrit and MO2 analyses, fish were euthanized and whole body energy stores and lactate were determined. Similarly, individual fish from the repeat swim group were subjected to two U(crit) tests (U(crit-1) and U(crit-2)) performed with a 60 min recovery period between tests, followed by determination of energy stores and lactate. Impaired swim performance was observed in fish fed SeMet at concentrations greater than 3 μg Se/g in the diet. However, within each dietary Se treatment group, no significant differences between single and repeat U(crits) were observed. Oxygen consumption, SMR and COT were significantly greater, and F-AS was significantly lesser, in fish fed SeMet. Whole body triglycerides were proportional to the concentration of SeMet in the diet. While

  3. Bov-B long interspersed repeated DNA (LINE) sequences are present in Vipera ammodytes phospholipase A2 genes and in genomes of Viperidae snakes.

    Science.gov (United States)

    Kordis, D; Gubensek, F

    1997-06-15

    Ammodytin L is a myotoxic Ser49 phospholipase A2 (PLA2) homologue, which is tissue-specifically expressed in the venom glands of Vipera ammodytes. The complete DNA sequence of the gene and its 5' and 3' flanking regions has been determined. The gene consists of five exons separated by four introns. Comparative analysis of the ammodytin L and ammodytoxin C genes shows that all intron and flanking sequences are considerably more conserved (93-97%) than the mature protein-coding exons. The pattern of nucleotide substitutions in protein-coding exons is not random but occurs preferentially on the first and the second positions of codons, which suggests positive Darwinian evolution for a new function. An Ruminantia specific ART-2 retroposon, recently recognised as a 5'-truncated Bov-B long interspersed repeated DNA (LINE) sequence, was identified in the fourth intron of both genes. This result suggests that ammodytin L and ammodytoxin C genes are derived by duplication of a common ancestral gene. The phylogenetic distribution of Bov-B LINE among vertebrate classes shows that, besides the Ruminantia, it is limited to Viperidae snakes (Vipera ammodytes, Vipera palaestinae, Echis coloratus, Bothrops alternatus, Trimeresurus flavoviridis and Trimeresurus gramineus). The copy number of the 3' end of Bov-B LINE in the Vipera ammodytes genome is between 62,000 and 75,000. The absence of Bov-B LINE at orthologous positions in other snake PLA2 genes indicates that its retrotransposition in the V. ammodytes PLA2 gene locus has occurred quite recently, about 5 My ago. The amplification of Bov-B LINEs in snakes may have occurred before the divergence of the Viperinae and Crotalinae subfamilies. Due to its wide distribution in Viperidae snakes it may be a valuable phylogenetic marker. The neighbor-joining phylogenetic tree shows two clusters of truncated Bov-B LINE, a Bovidae and a snake cluster, indicating an early horizontal transfer of this transposable element.

  4. Performing Repeated Quantitative Small-Animal PET with an Arterial Input Function Is Routinely Feasible in Rats.

    Science.gov (United States)

    Huang, Chi-Cheng; Wu, Chun-Hu; Huang, Ya-Yao; Tzen, Kai-Yuan; Chen, Szu-Fu; Tsai, Miao-Ling; Wu, Hsiao-Ming

    2017-04-01

    Performing quantitative small-animal PET with an arterial input function has been considered technically challenging. Here, we introduce a catheterization procedure that keeps a rat physiologically stable for 1.5 mo. We demonstrated the feasibility of quantitative small-animal (18)F-FDG PET in rats by performing it repeatedly to monitor the time course of variations in the cerebral metabolic rate of glucose (CMRglc). Methods: Aseptic surgery was performed on 2 rats. Each rat underwent catheterization of the right femoral artery and left femoral vein. The catheters were sealed with microinjection ports and then implanted subcutaneously. Over the next 3 wk, each rat underwent (18)F-FDG quantitative small-animal PET 6 times. The CMRglc of each brain region was calculated using a 3-compartment model and an operational equation that included a k*4Results: On 6 mornings, we completed 12 (18)F-FDG quantitative small-animal PET studies on 2 rats. The rats grew steadily before and after the 6 quantitative small-animal PET studies. The CMRglc of the conscious brain (e.g., right parietal region, 99.6 ± 10.2 μmol/100 g/min; n = 6) was comparable to that for (14)C-deoxyglucose autoradiographic methods. Conclusion: Maintaining good blood patency in catheterized rats is not difficult. Longitudinal quantitative small-animal PET imaging with an arterial input function can be performed routinely. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

  5. Effect of Small-Sided Games and Repeated Shuffle Sprint Training on Physical Performance in Elite Handball Players.

    Science.gov (United States)

    Dello Iacono, Antonio; Ardigò, Luca P; Meckel, Yoav; Padulo, Johnny

    2016-03-01

    This study was designed to compare the effects of small-sided games (SSGs) and repeated shuffle sprint (RSS) training on repeated sprint ability (RSA) and countermovement jump (CMJ) tests performances of elite handball players. Eighteen highly trained players (24.8 ± 4.4 years) were assigned to either SSG or RSS group training protocols twice a week for 8 weeks. The SSG training consisted of 5 small-sided handball games with 3-a-side teams excluding goalkeepers. The RSS consisted of 2 sets of 14-17 of 20-m shuttle sprints and 9-m jump shots interspersed by 20-second recoveries. Before and after training, the following performance variables were assessed: speed on 10-m and 20-m sprint time, agility and RSA time, CMJ height, standing throw, and jump shot speed. Significant pre-to-post treatment improvements were found in all the assessed variables following both training protocols (multivariate analysis of variance, p ≤ 0.05). There was a significantly greater improvement on 10-m sprint, CMJ, and jump shooting, after the RSS in comparison with SSG training (+4.4% vs. +2.4%, +8.6% vs. +5.6%, and +5.5% vs. +2.7%, respectively). Conversely, agility and standing throwing showed lower improvements after RSS in comparison with SSG (+1.0% vs. +7.8% and +1.6% vs. +9.0%, respectively). These results indicate that these training methods are effective for fitness development among elite adult handball players during the last period of the competitive season. Specifically, SSG seems to be more effective in improving agility and standing throw, whereas RSS seems preferable in improving 10-m sprint, CMJ, and jump shot.

  6. Changes in repeated-sprint performance in relation to change in locomotor profile in highly-trained young soccer players.

    Science.gov (United States)

    Buchheit, Martin; Mendez-Villanueva, Alberto

    2014-01-01

    The aim of this study was to examine the effects of changes in maximal aerobic (MAS) and sprinting (MSS) speeds and the anaerobic reserve (ASR) on repeated-sprint performance. Two hundred and seventy highly-trained soccer players (14.5 ± 1.6 year) completed three times per season (over 5 years) a maximal incremental running test to approach MAS, a 40-m sprint with 10-m splits to assess MSS and a repeated-sprint test (10 × 30-m sprints), where best (RSb) and mean (RSm) sprint times, and percentage of speed decrement (%Dec) were calculated. ASR was calculated as MSS-MAS. While ∆RSb were related to ∆MSS and ∆body mass (r(2) = 0.42, 90%CL[0.34;0.49] for the overall multiple regression, n = 334), ∆RSm was also correlated with ∆MAS and ∆sum of 7 skinfolds (r(2) = 0.43 [0.35;0.50], n = 334). There was a small and positive association between ∆%Dec and ∆MAS (r(2) = 0.02 [-0.07;0.11], n = 334). Substantial ∆MSS and ∆MAS had a predictive value of 70 and 55% for ∆RSm, respectively. Finally, ∆ASR per se was not predictive of ∆RSm (Cohen's = +0.8 to -0.3 with increased ASR), but the greater magnitude of ∆RSm improvement was observed when MSS, MAS and ASR increased together (0.8 vs. +0.4 with ASR increased vs. not, additionally to MSS and MAS). Low-cost field tests aimed at assessing maximal sprinting and aerobic speeds can be used to monitor ∆RS performance.

  7. Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

    DEFF Research Database (Denmark)

    Mak, Sarah Siu Tze Mak; Gopalakrishnan, Shyam Sunder; Carøe, Christian

    2017-01-01

    on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples. Results: The data generated was largely comparable between sequencing platforms...... in single strand DNA damage rate (δS, slight lower for the BGISEQ-500, p = 0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p = 0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant......Background: Ancient DNA research has been revolutionised following development of “Next Generation” Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities...

  8. Design and Performance Evaluation of Sequence Partition Algorithms

    Institute of Scientific and Technical Information of China (English)

    Bing Yang; Jing Chen; En-Yue Lu; Si-Qing Zheng

    2008-01-01

    Tradeoffs between time complexities and solution optimalities are important when selecting algorithms for an NP-hard problem in different applications. Also, the distinction between theoretical upper bound and actual solution optimality for realistic instances of an NP-hard problem is a factor in selecting algorithms in practice. We consider the problem of partitioning a sequence of n distinct numbers into minimum number of monotone (increasing or decreasing) case. We introduce a new algorithm, the modified version of the Yehuda-Fogel algorithm, that computes a solution of no on three algorithms, a known approximation algorithm of approximation ratio 1.71 and time complexity O(n3), a known greedy algorithm of time complexity O(n1.5 log n), and our new modified Yehuda-Fogel algorithm. Our results show that the solutions computed by the greedy algorithm and the modified Yehuda-Fogel algorithm are close to that computed by the approximation algorithm even though the theoretical worst-case error bounds of these two algorithms are not proved to be within a constant time of the optimal solution. Our study indicates that for practical use the greedy algorithm and the modified Yehuda-Fogel algorithm can be good choices if the running time is a major concern.

  9. Relationship between plaque score and video-monitored brushing performance after repeated instruction--a controlled, randomised clinical trial.

    Science.gov (United States)

    Schlueter, N; Klimek, J; Ganss, C

    2013-03-01

    Aim of this prospective, randomised, controlled clinical trial was to use the modified bass technique (MBT) and a specific brushing sequence to investigate whether two types of instruction methods lead to differences in plaque reduction and whether plaque reduction is related to technique adoption. Ninety-eight participants were randomly assigned to three groups: (1) control, no instruction; (2) verbal instruction by means of a leaflet; and (3) verbal instruction supported by demonstration, no leaflet. Brushing performance was video monitored. Plaque score (Turesky modified QHI (T-QHI)) was measured at baseline, afterwards participants received instructions. After 2 weeks, T-QHI was measured for a second time, and participants were re-instructed. After another 2 weeks, T-QHI was measured for a third time. At baseline, T-QHI did not differ between groups ((1) 1.99 ± 0.51, (2) 1.90 ± 0.51, (3) 1.93 ± 0.56). The second measurement revealed an improvement of T-QHI in the instructed groups and in the non-instructed control group ((1) 1.80 ± 0.47, (2) 1.58 ± 0.58, (3) 1.64 ± 0.58; n.s. between groups); in the intervention groups, remotivation achieved no further improvement ((1) 1.72 ± 0.48, (2) 1.52 ± 0.58, (3) 1.50 ± 0.69; n.s. between groups and compared to second measurement). Improvement of T-QHI was not related to proper performance of technique or brushing sequence. Those who fully adopted the brushing technique, the sequence or both did not have lower plaque scores. Technical performance and effectiveness were not linked. Within the study setting, the MBT was not effective in reducing plaque scores. The general recommendation of the MBT should be re-evaluated in further studies.

  10. Periodic performance of the chaotic spread spectrum sequence on finite precision

    Institute of Scientific and Technical Information of China (English)

    Zhu Canyan; Zhang Lihua; Wang Yiming; Liu Jiasheng; Mao Lingfeng

    2008-01-01

    It is well known that the periodic performance of spread spectrum sequence heavily affects the correlative and secure characteristics of communication systems.The chaotic binary sequence is paid more and more attention since it is one kind of applicable spread spectrum sequences.However,there are unavoidable short cyclic problems for chaotic binary sequences in finite precision.The chaotic binary sequence generating methods are studied first.Then the short cyclic behavior of the chaotic sequences is analyzed in detail,which are generated by quantification approaches with finite word-length.At the same time,a chaotic similar function is defined for presenting the cyclic characteristics of the sequences.Based on these efforts,an improved method with scrambling control for generating chaotic binary sequences is proposed.To quantitatively describe the improvement of periodic performance of the sequences,an orthogonal estimator is also defined.Some simulating results are provided.From the theoretical deduction and the experimental results,it is concluded that the proposed method can effectively increase the period and raise the complexity of the chaotic sequences to some extent.

  11. Effects of heat exposure and 3% dehydration achieved via hot water immersion on repeated cycle sprint performance.

    Science.gov (United States)

    Kraft, Justin A; Green, James M; Bishop, Phillip A; Richardson, Mark T; Neggers, Yasmin H; Leeper, James D

    2011-03-01

    This study examined effects of heat exposure with and without dehydration on repeated anaerobic cycling. Males (n = 10) completed 3 trials: control (CT), water-bath heat exposure (∼39°C) to 3% dehydration (with fluid replacement) (HE), and similar heat exposure to 3% dehydration (DEHY). Hematocrit increased significantly from pre to postheat immersion in both HE and DEHY. Participants performed 6 × 15s cycle sprints (30s active recovery). Mean Power (MP) was significantly lower vs. CT (596 ± 66 W) for DEHY (569 ± 72 W), and the difference approached significance for HE (582 ± 76 W, p = 0.07). Peak Power (PP) was significantly lower vs. CT (900 ± 117 W) for HE (870 ± 128 W) and approached significance for DEHY (857 ± 145 W, p = 0.07). Postsprint ratings of perceived exertion was higher during DEHY (6.4 ± 2.0) and HE (6.3 ± 1.6) than CT (5.7 ± 2.1). Combined heat and dehydration impaired MP and PP (decrements greatest in later bouts) with HE performance intermediate to CT and DEHY.

  12. Genetic variability and geographic differentiation in Thymus daenensis subsp. daenensis, an endangered medicinal plant, as revealed by inter simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Rahimmalek, Mehdi; Bahreininejad, Babak; Khorrami, Mojtaba; Tabatabaei, Badraldin Ebrahim Sayed

    2009-12-01

    Thymus daenensis is an aromatic medicinal plant endemic to Iran. We used inter simple sequence repeat (ISSR) markers to detect genetic polymorphism in this herb using 17 T. daenensis accessions collected from different geographic regions in Iran. The 15 primers chosen for analysis revealed 256 bands, of which 228 (88.9%) were polymorphic. Jaccard's similarity indices based on ISSR profiles were subjected to UPGMA cluster analysis. The generated dendrogram revealed two major groups. The Tc group included the accessions collected from the center of the Zagros Mountains, and the Te group was collected from the extremes of the Zagros range. A principal coordinate analysis confirmed the results of clustering. The results showed that the divergence of accessions based on the Zagros Mountains is more logical in comparison with classification on the basis of provincial borders. Gene diversity and expected heterozygosity were greater in the Tc group than in the Te group, suggesting that the germplasm collected from the center of the Zagros Mountains is more variable.

  13. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci.

    Science.gov (United States)

    Li, Ying-Hui; Li, Wei; Zhang, Chen; Yang, Liang; Chang, Ru-Zhen; Gaut, Brandon S; Qiu, Li-Juan

    2010-10-01

    • The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. • In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. • The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. • G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.

  14. 根瘤菌基因组内简单重复序列的分析%Analysis of Simple Sequence Repeats in Rhizobium Genomes

    Institute of Scientific and Technical Information of China (English)

    高亚梅; 韩毅强; 汤辉; 孙东梅; 王彦杰; 王伟东

    2008-01-01

    [目的]分析根瘤菌基因组中的简单重复序列(simple sequence repeats,SSRs),为其在根瘤菌遗传多样性研究中的应用提供有益的信息.[方法]利用公共的微生物串联重复序列数据库资源,对已测序的3种根瘤菌基因组中SSRs的结构类型,分布,丰度等进行系统的比较分析.[结果]大豆慢生根瘤菌(Bradyrhizobium japonicum)、百脉根根瘤菌(blesorhizobium loti)和苜蓿中华根瘤菌(Sinorhizobium meliloti)基因组中的SSRs分别为1 410个、859个和638个,3种根瘤菌基因组中长重复的四、五、六核苷酸基序更为丰富,变异性更高.数目最少的为单碱基重复.[结论]3种根瘤菌的SSR在结构类型和分布规律上均具有一定的相似性.

  15. Effects of genotoxicity and its consequences at the population level in sexual and asexual Artemia assessed by analysis of inter-simple sequence repeats (ISSR).

    Science.gov (United States)

    Sukumaran, Sandhya; Grant, Alastair

    2013-09-18

    There is considerable evidence that genetic damage in organisms occurs in the environment as a result of exposure to genotoxins and ionising radiation, but we have limited understanding of the extent to which this results in adverse consequences at a population level. We used inter-simple sequence repeat (ISSR) markers to quantify genotoxic effects of the mutagen ethylmethane sulfonate (EMS) on a sexual (Artemia franciscana) and an asexual (Artemia parthenogenetica) species of brine shrimp. The method provides information similar to that obtained with assessment of RAPD (random amplification of polymorphic DNA) but is more robust. Genetic damage was transmitted to the F1 generation in both Artemia species, but the sexual species showed a greater degree of recovery, as shown by higher values of genomic template stability. There was a strong correlation between DNA damage and effects on individual fitness parameters: size, survival, reproduction and population growth. These effects persisted into the F2 generation in A. parthenogenetica, but in the sexual A. franciscana only effects on fecundity continued beyond the exposed generation, even though there were substantial alterations in ISSR patterns in the F1 generation. Genetic biomarkers can thus be indicative of effects at the population level, but sexually reproducing species have a considerable assimilative capacity for the effects of genotoxins.

  16. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers.

    Science.gov (United States)

    Wang, Hui; Khera, Pawan; Huang, Bingyan; Yuan, Mei; Katam, Ramesh; Zhuang, Weijian; Harris-Shultz, Karen; Moore, Kim M; Culbreath, Albert K; Zhang, Xinyou; Varshney, Rajeev K; Xie, Lianhui; Guo, Baozhu

    2016-05-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  17. Optimization of Inter-Simple Sequence Repeats(ISSR) Reaction System for Agaricus blazei%姬松茸ISSR特异扩增体系的研究

    Institute of Scientific and Technical Information of China (English)

    林新坚; 江秀红; 蔡海松; 郑永标; 林陈强

    2007-01-01

    为了建立稳定的姬松茸(Agaricus blazei Murill)简单序列重复区间(Inter-Simple Sequence Repeats,ISSR)分子标记技术体系,笔者通过单因子试验分别研究了模板DNA、Mg2+浓度、dNTP、引物浓度和Taq酶用量对姬松茸ISSR-PCR扩增的影响,确定了姬松茸ISSR分析的最佳PCR条件为:25μL反应体系中,模板DNA 20 ng,引物0.75μmol/L,dNTP 200μmol/L,Mg2+2.0 mmol/L,Taq DNA polymerase 1.5 U.并应用该优化体系筛选到6个适合姬松茸ISSR-PCR扩增的引物,为利用ISSR标记技术研究姬松茸的种质资源提供了参考.

  18. Establishment of the Inter-simple Sequence Repeats Reaction System in Plum Germplasm%李种质资源ISSR反应体系的建立

    Institute of Scientific and Technical Information of China (English)

    乔玉山; 章镇; 房经贵; 沈志军; 赵密珍

    2003-01-01

    以5′-(AC)9A-3′为引物对牛心李(Prunus salicina cv.Niuxinli)ISSR(inter-simple sequence repeats)反应体系的优化研究表明,25μLISSR反应体系中,Taq酶、Mg2+、引物、模板DNA和dNTPs 5种主要成分的最适浓度分别是:0.3 U、1.5 mmol/L、0.2μmol/L、20 ng和0.16 mmol/L.利用该优化体系,以5′-(AC)9T-3′为引物,构建了中国李18个品种的ISSR指纹图谱,该引物可将这些品种完全区别开来;以5′-(AC)9C-3′为引物,构建了李属6类种质资源的ISSR指纹图谱,该引物区分率为100%.

  19. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers

    Institute of Scientific and Technical Information of China (English)

    Hui Wang; Xinyou Zhang; Rajeev K. Varshney; Lianhui Xie; Baozhu Guo; Pawan Khera; Bingyan Huang; Mei Yuan; Ramesh Katam; Weijian Zhuang; Karen Harris-Shultz; Kim M. Moore; Albert K. Culbreath

    2016-01-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendro-gram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  20. Interactions between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin TMPyP4 and DNA G-quadruplex of telomeric repeated sequence TTAGGG

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The binding properties between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the parallel DNA G-quadruplex (G4) of telomeric repeated sequence 5′-TTAGGG-3′ have been characterized by means of circular dichroism,steady-state absorption,steady-state fluorescence and picosecond time-resolved fluorescence spectroscopies. The binding constant and the saturated binding number were determined as 1.29×106 (mol/L)-1 and 3,respectively,according to steady-state absorption spec-troscopy. Based on the findings by the use of time-resolved fluorescence spectroscopic technique,it is deduced that TMPyP4 binds to a DNA G-quadruplex with both the thread-intercalating and end-stacking modes and at the saturated binding state,one TMPyP4 molecule intercalates into the intervals of G-tetrads while the other two stack to the ends of the DNA G-quadruplex.

  1. Heterozygosities and genetic relationship of tea cultivars revealed by simple sequence repeat markers and implications for breeding and genetic mapping programs.

    Science.gov (United States)

    Tan, L Q; Zhang, C C; Qi, G N; Wang, L Y; Wei, K; Chen, S X; Zou, Y; Wu, L Y; Cheng, H

    2015-03-06

    Genetic maps are essential tools for quantitative trait locus analysis and marker-assisted selection breeding. In order to select parents that are highly heterozygous for genetic mapping, the heterozygosity (HS) of 24 tea cultivars (Camellia sinensis) was analyzed with 72 simple sequence repeat markers. In total, 359 alleles were obtained with an average of 4.99 per marker. The HS varied greatly from 37.5 to 71.0% with an average of 51.3%. On average, tea cultivars from Fujian Province showed a higher level of heterozygosity (59.8%) than those from Zhejiang (48.5%) and Yunnan (44.5%), and the 12 national tea cultivars were generally more heterozygous than the 12 provincial cultivars. Unweighted pair-group analysis using the arithmetic average grouping divided the 24 cultivars into 2 groups that are consistent with the morphological classification. All dual combinations of the 24 cultivars were studied to calculate the percentage of mappable markers when using pseudo-testcross mapping strategy, and results showed that this value also varied greatly from 51.4 to 90.3%. The genetic relationships and HS differences among different cultivars were discussed, and tea cultivars with high HS were recommended as cross parents for genetic mapping programs.

  2. Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato.

    Science.gov (United States)

    Yada, Benard; Brown-Guedira, Gina; Alajo, Agnes; Ssemakula, Gorrettie N; Owusu-Mensah, Eric; Carey, Edward E; Mwanga, Robert O M; Yencho, G Craig

    2017-03-01

    Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H(2)) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = -0.59, P content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.

  3. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

    Science.gov (United States)

    Allegre, Mathilde; Argout, Xavier; Boccara, Michel; Fouet, Olivier; Roguet, Yolande; Bérard, Aurélie; Thévenin, Jean Marc; Chauveau, Aurélie; Rivallan, Ronan; Clement, Didier; Courtois, Brigitte; Gramacho, Karina; Boland-Augé, Anne; Tahi, Mathias; Umaharan, Pathmanathan; Brunel, Dominique; Lanaud, Claire

    2012-01-01

    Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.

  4. Applied Research Based on the Fibonacci Sequence NBA Center Performance Evaluation

    Directory of Open Access Journals (Sweden)

    Mingyou Gao

    2013-04-01

    Full Text Available The purpose of this paper study is the application of the “Fibonacci sequence” a new perspective and dimension, select five NBA excellent center players performance evaluation, and thus the size and ranking of the performance of the five players. Five players the pros and cons of the career data with the size of the Fibonacci sequence study the performance of players and then compare to see if consistent harmonious Fibonacci sequence of the universe, thus can be extended to other good players in the league performance evaluation, which provide a way for the players performance evaluation.

  5. Cyclotriveratrylene (CTV) as a new chiral triacid scaffold capable of inducing triple helix formation of collagen peptides containing either a native sequence or Pro-Hyp-Gly repeats.

    Science.gov (United States)

    Rump, Erik T; Rijkers, Dirk T S; Hilbers, Hans W; de Groot, Philip G; Liskamp, Rob M J

    2002-10-18

    A new triacid scaffold is described based on the cone-shaped cyclotriveratrylene (CTV) molecule that facilitates the triple helical folding of peptides containing either a unique blood platelet binding collagen sequence or collagen peptides composed of Pro-Hyp-Gly repeats. The latter were synthesized by segment condensation using Fmoc-Pro-Hyp-Gly-OH. Peptides were coupled to this CTV scaffold and also coupled to the Kemp's triacid (KTA) scaffold. After assembly of peptide H-Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu(OAll)-Arg-Gly-Val-Glu (OAll)-Gly-[Pro-Hyp-Gly]2-NH2 (13) by an orthogonal synthesis strategy to both triacid scaffolds, followed by deprotection of the allyl groups, the molecular constructs spontaneously folded into a triple helical structure. In contrast, the non-assembled peptides did not. The melting temperature (Tm) of (+/-) CTV[CH2C(O)N(H)Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu-Arg-Gly-Val-Glu-Gly- [Pro-Hyp-Gly]2-NH2]3 (14) is 19 degrees C, whereas KTA[Gly-Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu-Arg-Gly-Val-Glu-Gly- [Pro-Hyp-Gly]2-NH2]3 (15) has a Tm of 20 degrees C. Thus, it was shown for the first time that scaffolds were also effective in stabilizing the triple helix of native collagen sequences. The different stabilizing properties of the two CTV enantiomers could be measured after coupling of racemic CTV triacid to the collagen peptide, and subsequent chromatographic separation of the diastereomers. After assembly of the two chiral CTV scaffolds to the model peptide H-Gly-Gly-(Pro-Hyp-Gly)5-NH2 (24), the (+)-enantiomer of CTV 28b was found to serve as a better triple helix-inducing scaffold than the (-)-enantiomer 28a. In addition to an effect of the chirality of the CTV scaffold, a certain degree of flexibility between the CTV cone and the folded peptide was also shown to be of importance. Restricting the flexibility from two to one glycine residues resulted in a significant difference between the two collagen mimics 20a and 20b, whereas the difference was

  6. Sequence specific motor performance gains after memory consolidation in children and adolescents.

    Directory of Open Access Journals (Sweden)

    Shoshi Dorfberger

    Full Text Available Memory consolidation for a trained sequence of finger opposition movements, in 9- and 12-year-old children, was recently found to be significantly less susceptible to interference by a subsequent training experience, compared to that of 17-year-olds. It was suggested that, in children, the experience of training on any sequence of finger movements may affect the performance of the sequence elements, component movements, rather than the sequence as a unit; the latter has been implicated in the learning of the task by adults. This hypothesis implied a possible childhood advantage in the ability to transfer the gains from a trained to the reversed, untrained, sequence of movements. Here we report the results of transfer tests undertaken to test this proposal in 9-, 12-, and 17-year-olds after training in the finger-to-thumb opposition sequence (FOS learning task. Our results show that the performance gains in the trained sequence partially transferred from the left, trained hand, to the untrained hand at 48-hours after a single training session in the three age-groups tested. However, there was very little transfer of the gains from the trained to the untrained, reversed, sequence performed by either hand. The results indicate sequence specific post-training gains in FOS performance, as opposed to a general improvement in performance of the individual, component, movements that comprised both the trained and untrained sequences. These results do not support the proposal that the reduced susceptibility to interference, in children before adolescence, reflects a difference in movement syntax representation after training.

  7. Effects of Three Different Resistance Training Frequencies on Jump, Sprint, and Repeated Sprint Ability Performance in Professional Futsal Players.

    Science.gov (United States)

    Paz-Franco, Adrián; Rey, Ezequiel; Barcala-Furelos, Roberto

    2017-02-21

    The aim of this study was to examine the effect of 3 different resistance training frequencies (one strength training session per week (1W), two strength training sessions per week (2W) or one strength training session every second week (0.5W)) on jump, sprint and repeated sprint performance (RSA) in professional futsal players. Thirty-five futsal players were randomized into 1 of 3 groups, the 1W group (n= 12), 2W group (n= 12), or the 0.5W group (n= 11). The players performed the same resistance training during 6 weeks and only training frequency differed between the groups. Within-group analysis showed significant improvements in jump (p≤0.001, Effect Size (ES)= 0.13-0.35), sprint (p≤0.001, ES= 0.48-0.71), and RSA (p≤0.01, ES= 0.22-0.63) from pretest to posttest in 1W and 2W. However, no significant (p>0.05) pre-post changes were observed for the 0.5W in any variable. In the between-groups analysis, significant better results were found in jump (p≤0.01), sprint (p≤0.01), and RSA performance (p≤0.01) in the 1W group and 2W group in comparison with 0.5W group. Also, jump (p≤0.05) and 5 m sprint (p≤0.05) performances was significantly better in the 2W group in comparison with 1W group. In conclusion, the current study showed that 6 weeks of RT one or two times per week in addition to typical futsal training, produced significant improvements in jump, sprint and RSA performance. Additionally, RT one every second week may be sufficient to maintain physical fitness in professional futsal players. This information may be useful for coaches when planning training contents during congested fixture schedules or in periods where the emphasis need to be put on other qualities and spend as little time as possible on maintaining or increasing physical performance.

  8. The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor.

    Science.gov (United States)

    Schnare, M N; Collings, J C; Spencer, D F; Gray, M W

    2000-09-15

    In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from approximately 11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an approximately 55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A' pre-rRNA processing sites within the 5' external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5' ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C. fasciculata and Trypanosoma brucei involves 3'-terminal addition of three A residues that are not present in the corresponding DNA sequences.

  9. Training Sequences and their Effects on Task Performance and User Outcomes

    DEFF Research Database (Denmark)

    Sanford, Clive Carlton

    2007-01-01

    This article introduces the concept of information technology (IT) training sequencesand examines how sequencing of conceptual and procedural training impact IT task performance, user satisfaction and users' self-efficacy. Using assimilation theory, we develop four hypotheses related to training...... sequences. These hypotheses were then tested in a database design context using a quasi-experimental study involving student subjects. Empirical results demonstrate improved far-transfer andnear-transfer task performance and higher self-efficacy for subjects trained in the conceptual-procedural sequence vs...

  10. Sequencing on products of Oncomelania hupensis through simple sequence repeat anchored polymerase chain reaction amplification%湖北钉螺微卫星锚定PCR产物序列分析

    Institute of Scientific and Technical Information of China (English)

    郭俊涛; 周艺彪; 韦建国; 赵根明

    2008-01-01

    目的 分析4个种群湖北钉螺中微卫星序列及其两侧序列的特点.方法 以(CA)8RY为引物对湖北钉螺基因组DNA进行微卫星锚定PCR(SSR-PCR)扩增,对全部159个扩增产物进行T克隆并测定其中82个片段的核苷酸序列.结果 SSR-PCR的扩增产物是湖北钉螺基因组DNA上的散在区域,不是微卫星序列,但扩增产物中含有微卫星序列,测序的82个片段中36个克隆片段含有微卫星序列.微卫星序列其侧翼序列有一定的保守性,同一个微卫星的侧翼序列多数情况下是相同的.(GA/CT)n、(TTAGGG/CCCTAA)n两类微卫星在4个钉螺种群中均有发现,(CAA)n仅在福建福清种群中发现,(TCTCTG)n仅在安徽贵池种群中发现,(GAA~TTC)n、(CAA/TTG)n、(CAT)n三种微卫星序列仅在四川普格种群中发现.结论 SSR-PCR扩增的不是微卫星,其结果的分析应当类似于随机扩增多态性DNA.因此SSR-PCR不能十分有效体现微卫星作为分子标记的优势,应当根据微卫星的侧翼序列设计针对微卫星的引物,对微卫星进行PCR扩增并进行分析.%Objective To analyze the sequence of microsatellite and the flanking sequence from four populations of Oncomelania hupensis. Methods We cloned 159 SSR-PCR amplification products of a commonly used primer, (CA)8RY, using O. hupensis genomie DNA as template, and sequenced 82 products Results The sequences obtained were novel O. hupensis genomic sequences but not repeat simple sequence. It was observed that 36 out of 82 clones contained microsatellites between priming sites.The flanking sequences of certain microsatellite were invariant. Both (GA/CT). and (TTAGGG/CCCAA)n were found in four populations of O. hupensis. However, (CAA)n were found only in O. hupensis from Fuqing,Fujian province and (TCTCTG), were found only in O. hupensis from Guichi,Anhui province and (GAA/TTC)n, (CAA/TTG)n, (CAT), were found only in O.hupensis from Puge,Sichuan province. Conclusion The results obtained by

  11. Experimental Assessment on the Flexural Bonding Performance of Concrete Beam with GFRP Reinforcing Bar under Repeated Loading

    Directory of Open Access Journals (Sweden)

    Minkwan Ju

    2015-01-01

    Full Text Available This study intends to investigate the flexural bond performance of glass fiber-reinforced polymer (GFRP reinforcing bar under repeated loading. The flexural bond tests reinforced with GFRP reinforcing bars were carried out according to the BS EN 12269-1 (2000 specification. The bond test consisted of three loading schemes: static, monotonic, and variable-amplitude loading to simulate ambient loading conditions. The empirical bond length based on the static test was 225 mm, whereas it was 317 mm according to ACI 440 1R-03. Each bond stress on the rib is released and bonding force is enhanced as the bond length is increased. Appropriate level of bond length may be recommended with this energy-based analysis. For the monotonic loading test, the bond strengths at pullout failure after 2,000,000 cycles were 10.4 MPa and 6.5 MPa, respectively: 63–70% of the values from the static loading test. The variable loading test indicated that the linear cumulative damage theory on GFRP bonding may not be appropriate for estimating the fatigue limit when subjected to variable-amplitude loading.

  12. Effect of Red Bull energy drink on repeated Wingate cycle performance and bench-press muscle endurance.

    Science.gov (United States)

    Forbes, Scott C; Candow, Darren G; Little, Jonathan P; Magnus, Charlene; Chilibeck, Philip D

    2007-10-01

    The purpose of this study was to determine the effects of Red Bull energy drink on Wingate cycle performance and muscle endurance. Healthy young adults (N = 15, 11 men, 4 women, 21 +/- 5 y old) participated in a crossover study in which they were randomized to supplement with Red Bull (2 mg/kg body mass of caffeine) or isoenergetic, isovolumetric, noncaffeinated placebo, separated by 7 d. Muscle endurance (bench press) was assessed by the maximum number of repetitions over 3 sets (separated by 1-min rest intervals) at an intensity corresponding to 70% of baseline 1-repetition maximum. Three 30-s Wingate cycling tests (load = 0.075 kp/kg body mass), with 2 min recovery between tests, were used to assess peak and average power output. Red Bull energy drink significantly increased total bench-press repetitions over 3 sets (Red Bull = 34 +/- 9 vs. placebo = 32 +/- 8, P %%%lt; 0.05) but had no effect on Wingate peak or average power (Red Bull = 701 +/- 124 W vs. placebo = 700 +/- 132 W, Red Bull = 479 +/- 74 W vs. placebo = 471 +/- 74 W, respectively). Red Bull energy drink significantly increased upper body muscle endurance but had no effect on anaerobic peak or average power during repeated Wingate cycling tests in young healthy adults.

  13. Acute effects of a caffeine-taurine energy drink on repeated sprint performance of American college football players.

    Science.gov (United States)

    Gwacham, Nnamdi; Wagner, Dale R

    2012-04-01

    Consumption of energy drinks is common among athletes; however, there is a lack of research on the efficacy of these beverages for short-duration, intense exercise. The purpose of this research was to investigate the acute effects of a low-calorie caffeine-taurine energy drink (AdvoCare Spark) on repeated sprint performance and anaerobic power in National Collegiate Athletic Association Division I football players. Twenty football players (age 19.7 ± 1.8 yr, height 184.9 ± 5.3 cm, weight 100.3 ± 21.7 kg) participated in a double-blind, randomized crossover study in which they received the energy drink or an isoenergetic, isovolumetric, non-caffeinated placebo in 2 trials separated by 7 days. The Running Based Anaerobic Sprint Test, consisting of six 35-m sprints with 10 s of rest between sprints, was used to assess anaerobic power. Sprint times were recorded with an automatic electronic timer. The beverage treatment did not significantly affect power (F = 3.84, p = .066) or sprint time (F = 3.06, p = .097). However, there was a significant interaction effect between caffeine use and the beverage for sprint times (F = 4.62, p = .045), as well as for anaerobic power (F = 5.40, p = .032), indicating a confounding effect. In conclusion, a caffeine-taurine energy drink did not improve the sprint performance or anaerobic power of college football players, but the level of caffeine use by the athletes likely influenced the effect of the drink.

  14. Influence of equipment and settings on myocardial performance index repeatability and definition of settings to achieve optimal reproducibility.

    Science.gov (United States)

    Lobmaier, S M; Cruz-Lemini, M; Valenzuela-Alcaraz, B; Ortiz, J U; Martinez, J M; Gratacos, E; Crispi, F

    2014-06-01

    To compare left myocardial performance index (MPI) values and reproducibility using different settings and ultrasound equipment in order to standardize optimal machine settings. Left MPI was prospectively evaluated by one observer performing conventional Doppler in 62 fetuses (28-36 weeks of gestational age) using different settings (changing sweep speed, gain and wall motion filter (WMF)) and two different ultrasound devices (Siemens Antares, Siemens; Voluson 730 Expert, GE Medical Systems). Intraclass coefficients of agreement (ICCs) were calculated using Bland-Altman analysis. Using baseline settings on the Siemens, mean (SD) MPI was 0.44 (0.05) with an ICC of 0.81. Decreasing the sweep speed resulted in decreasing average MPI values (0.43) and decreasing ICC (0.61). Lowering gain also influenced average MPI values (0.46) and ICC (0.76). Raising gain resulted in similar MPI values (0.45) with better ICC (0.90) compared with baseline settings. Raising wall motion filter (WMF) provided the best ICC (0.94) compared with the other settings. Changing the ultrasound equipment resulted in an ICC of 0.64. The optimal settings to achieve the highest reproducibility in measurement of MPI were sweep speed 8, gain 60 dB and WMF 281 Hz for Siemens Antares and sweep speed 5, gain -10 dB and WMF 210 Hz for Voluson 730 Expert. Changing ultrasound settings or equipment may affect the calculation and repeatability of measurement of MPI values. Strict standardization of methods decreases the variability of this parameter for fetal cardiac function assessment. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.

  15. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    Directory of Open Access Journals (Sweden)

    Lauren R. Schoukroun-Barnes

    2015-03-01

    Full Text Available The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM. Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes.

  16. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers.

    Science.gov (United States)

    Wu, Kun; Yang, Minmin; Liu, Hongyan; Tao, Ye; Mei, Ju; Zhao, Yingzhong

    2014-03-19

    Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic

  17. Performance evaluation of the next-generation sequencing approach for molecular diagnosis of hereditary hearing loss.

    Science.gov (United States)

    Sivakumaran, Theru A; Husami, Ammar; Kissell, Diane; Zhang, Wenying; Keddache, Mehdi; Black, Angela P; Tinkle, Brad T; Greinwald, John H; Zhang, Kejian

    2013-06-01

    To evaluate the performance of a next-generation sequencing (NGS)-based targeted resequencing genetic test, OtoSeq, to identify the sequence variants in the genes causing sensorineural hearing loss (SNHL). Retrospective study. Tertiary children's hospital. A total of 8 individuals presenting with prelingual hearing loss were used in this study. The coding and flanking intronic regions of 24 well-studied SNHL genes were enriched using microdroplet polymerase chain reaction and sequenced on an Illumina HiSeq 2000 sequencer. The filtered high-quality sequence reads were mapped to reference sequence, and variants were detected using NextGENe software. A total of 1148 sequence variants were detected in 8 samples in 24 genes. Using in-house developed NGS data analysis criteria, we classified 810 (~71%) of these variants as potential true variants that include previously detected pathogenic mutations in 5 patients. To validate our strategy, we Sanger sequenced the target regions of 5 of the 24 genes, accounting for about 29.2% of all target sequence. Our results showed >99.99% concordance between NGS and Sanger sequencing in these 5 genes, resulting in an analytical sensitivity and specificity of 100% and 99.997%, respectively. We were able to successfully detect single base substitutions, small deletions, and insertions of up to 22 nucleotides. This study demonstrated that our NGS-based mutation screening strategy is highly sensitive and specific in detecting sequence variants in the SNHL genes. Therefore, we propose that this NGS-based targeted sequencing method would be an alternative to current technologies for identifying the multiple genetic causes of SNHL.

  18. Performance analysis of the periodic sequence DSSS system against CW interference

    Institute of Scientific and Technical Information of China (English)

    Anquan WEI; Lianfeng SHEN

    2008-01-01

    Based on the brief