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Sample records for simple sequence repeat-based

  1. Novel expressed sequence tag- simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  2. Abundance, composition and distribution of simple sequence ...

    Indian Academy of Sciences (India)

    Abundance, composition and distribution of simple sequence repeats and dinucleotide compositional bias within WSSV genomes. MALATHI SHEKAR, INDRANI KARUNASAGAR and IDDYA KARUNASAGAR*. Department of Fishery Microbiology, UNESCO Centre for Marine Biotechnology,. Karnataka Veterinary, Animal ...

  3. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Prakash

    2006-12-18

    Dec 18, 2006 ... Simple sequence repeats (SSRs) or microsatellites are the repetitive sequence motifs of 1–6 bp (Schlotterer 2000). They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes (Heller et al. 1982; Ellegren 2004). The origin, evolution and ubiquitous occurrence ...

  4. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  5. Simple sequence proteins in prokaryotic proteomes

    Directory of Open Access Journals (Sweden)

    Ramachandran Srinivasan

    2006-06-01

    Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

  6. Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated ...

    African Journals Online (AJOL)

    ONOS

    2010-08-09

    Aug 9, 2010 ... simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet. 100: 1311-1320. Kantety RV, Zeng X, Bennetzen JL, Zehr BE (1995). Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Mol. Breed.

  7. Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated ...

    African Journals Online (AJOL)

    Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated rice species from Ethiopia. ... African Journal of Biotechnology ... The genetic diversity of three wild rice populations of Ethiopia along with three cultivated rice populations were studied using Inter simple sequence repeats (ISSRs) as a molecular marker.

  8. Development of simple sequence repeat markers in cymbopogon species.

    Science.gov (United States)

    Kumar, Jitendra; Verma, Vijeshwar; Shahi, Ashok Kumar; Qazi, Gulam Nab; Balyan, Harindra Singh

    2007-03-01

    The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding.

  9. Development of simple sequence repeat (SSR) markers that are ...

    African Journals Online (AJOL)

    Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, 'Tsuda' and 'Yurugi Akamaru'. Out of 90 EST-SSRs for ...

  10. A simple criterion on degree sequences of graphs

    National Research Council Canada - National Science Library

    Tripathi, Amitabha; Tyagi, Himanshu

    2008-01-01

    ... sequences are due to Havel  [7] , and independently, Hakimi  [5] , and jointly due to Erdős and Gallai  [4] . The result of Havel–Hakimi has been extended by Kleitman and Wang  [9] , and that of Erdős and Gallai by Eggleton  [3] , and by Tripathi and Vijay [11] . We give a simple criterion to characterize graphic sequences. Our characterization reli...

  11. Conservation of polymorphic simple sequence loci in cetacean species.

    Science.gov (United States)

    Schlötterer, C; Amos, B; Tautz, D

    1991-11-07

    Length polymorphisms within simple-sequence loci occur ubiquitously in non-coding eukaryotic DNA and can be highly informative in the analysis of natural populations. Simple-sequence length polymorphisms (SSLP) in the long-finned pilot whale Globicephala melas (Delphinidae) have provided useful information on the mating system as well as on the genetic structure of populations. We have therefore tested whether the polymerase chain reaction primers designed for Globicephala could also be used to uncover variability in other whale species. Homologous loci could indeed be amplified from a diverse range of whales, including all toothed (Odontoceti) and baleen whales (Mysticeti) tested. Cloning and sequencing these loci from 11 different species revealed an unusually high conservation of sequences flanking the simple-sequence stretches, averaging 3.2% difference over 35-40 Myr. This represents the lowest divergence rate for neutral nucleotide positions found for any species group so far and raises the possible need for a re-evaluation of the age of the modern whales. On the other hand, the high conservation of non-coding sequences in whales simplifies the application of SSLP DNA fingerprinting in cetacean species, as primers designed for one species will often uncover variability in other species.

  12. Development of specific simple sequence repeat (SSR) markers for ...

    African Journals Online (AJOL)

    The bulk segregant analysis (BSA) using simple sequence repeat (SSR) markers were deployed to identify the location and genetic effect of this gene. We have generated new set of SSR markers to identify progenies carrying TGMS gene in a cross TGMS/PTT1. The TGMS gene was located on chromosome 2 with 0.0 cM ...

  13. Inter-simple sequence repeats (ISSR) and morphological diversity in ...

    African Journals Online (AJOL)

    Morphological characteristics as well as inter-simple sequence repeats (ISSR) molecular markers were used to study the species relationship in Onosma species (Boraginaceae) in Iran. Principal component analysis (PCA) showed that morphological characters like caule leaf size and shape, bract shape, corolla shape, ...

  14. Inter simple sequence repeat (ISSR) markers as reproducible and ...

    African Journals Online (AJOL)

    Rose is one of the most important cultivated ornamental plants in the world. A molecular approach using inter-simple sequence repeat (ISSR) markers was applied to seven species of Rosa. To obtain clear and reproducible bands on 2% agarose gels, 9 ISSR primers and 5 parameters (annealing temperature, DNA ...

  15. Validating simple sequence repeat (SSR) markers for introgression ...

    African Journals Online (AJOL)

    Low hybridization efficiency (22.5%) was achieved using the anther dehiscence method. Such low hybridization efficiency requires use of molecular markers to easily identify plants harbouring the required genotypes. Key words: Stay-green, drought tolerance, quantitative trait loci (QTL), simple sequence repeat (SSR) ...

  16. Evaluation of genetic diversity in rice using simple sequence repeats ...

    African Journals Online (AJOL)

    The dendrogram revealed 8 major distinct clusters. Higher range of similarity values for related genotypes using simple sequence repeats (SSR) provides greater confidence for the assessment of genetic diversity and relationships. The polymorphism information content (PIC) value for the SSR loci ranged from 0.36 to 0.98.

  17. Analysis of B-genome derived simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    A study was conducted to investigate the genetic variability between 40 Musa genotypes maintained at the Musa germplasm collection of the International Institute for Tropical Agriculture, Ibadan using nine B-genome derived simple sequence repeat (SSR) markers. The nine primers produced reproducible and discrete ...

  18. Comparative effectiveness of inter-simple sequence repeat and ...

    African Journals Online (AJOL)

    iisr

    2013-10-10

    Oct 10, 2013 ... whereas RAPD markers showed segregation based on geographical location as well as species based. Key words: Garcinia, genetic diversity, inter-simple sequence repeats, randomly amplified polymorphic DNA, principal component analysis. INTRODUCTION. Garcinia is a large genus with 240 species ...

  19. Genetic relationships revealed by simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    Genetic relationships revealed by simple sequence repeat (SSR) markers among Ghanaian cassava cultivars released by different research groups. ... Genetic diversity was observed within populations (HS = 0.552) and, therefore, suggesting a low rate of inter-population gene flow among the individuals constituting the ...

  20. Use of simple sequence repeat (SSR) markers for screening blue ...

    African Journals Online (AJOL)

    The findings suggest the need for caution to be taken during introduction of exotic germplasm and recognize the value of resistance trait to susceptible Brazilian germplasm when breeding for blue disease resistance. Key words: Cotton blue disease, cotton single nucleotide polymorphisms (SNPs), simple sequence repeat

  1. Inter simple sequence repeat analysis of genetic diversity of five ...

    African Journals Online (AJOL)

    This paper studied the genetic diversity of five cultivated pepper species using inter simple sequence repeat (ISSR) analysis. The amplicons of 13 out of 15 designed primers were stable polymorphic and therefore were used as genetic biomarkers. 135 total clear bands were obtained, of which 102 were polymorphic bands ...

  2. Using inter simple sequence repeat (ISSR) markers to study genetic ...

    African Journals Online (AJOL)

    enoh

    2012-04-10

    Apr 10, 2012 ... Inter simple sequence repeat (ISSRs) are semi arbitrary markers amplified by. PCR in the presence of one primer complementary to a target microsatellite. Amplification in the presence of non- anchored primers also has been called microsatellite- primed PCR (Karp et al., 1997). Each band corresponds.

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

    African Journals Online (AJOL)

    ... as recurrent parent was investigated using 128 simple sequence repeat (SSR) primers covered on chromosome number 1-12. The results reveal that 36 HRM primers showed distinct polymorphism among the donor and recurrent parents studied indicating the robust nature of microsatellites in revealing polymorphism.

  4. Evolution Analysis of Simple Sequence Repeats in Plant Genome.

    Science.gov (United States)

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

  5. Prediction of potential drug targets based on simple sequence properties

    Directory of Open Access Journals (Sweden)

    Lai Luhua

    2007-09-01

    Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

  6. 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.

  7. MSDB: A Comprehensive Database of Simple Sequence Repeats.

    Science.gov (United States)

    Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

    2017-06-01

    Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    Science.gov (United States)

    Lewers, Kim S; Saski, Chris A; Cuthbertson, Brandon J; Henry, David C; Staton, Meg E; Main, Dorrie S; Dhanaraj, Anik L; Rowland, Lisa J; Tomkins, Jeff P

    2008-06-20

    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. 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. 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.

  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. 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.

  11. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

    Science.gov (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

    2014-04-08

    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

  12. a stable simple sequence repeat marker for resistance to white ...

    African Journals Online (AJOL)

    ACSS

    ADN extraits pour une analyse moléculaire. Huit marqueurs SSR et dix ISSRs ont été utilisés. Ces marqueurs ont été essayés sur des lignées parentales et produits de backcross afin de déterminer la différence entre résistants. (score 1) et susceptibles (score 5). Simple analyse de marqueurs a été réalisée au travers du ...

  13. Scoredist: a simple and robust protein sequence distance estimator.

    Science.gov (United States)

    Sonnhammer, Erik L L; Hollich, Volker

    2005-04-27

    Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used. We propose a correction-based protein sequence estimator called Scoredist. It uses a logarithmic correction of observed divergence based on the alignment score according to the BLOSUM62 score matrix. We evaluated Scoredist and a number of optimal matrix methods using three evolutionary models for both training and testing Dayhoff, Jones-Taylor-Thornton, and Muller-Vingron, as well as Whelan and Goldman solely for testing. Test alignments with known distances between 0.01 and 2 substitutions per position (1-200 PAM) were simulated using ROSE. Scoredist proved as accurate as the optimal matrix methods, yet substantially more robust. When trained on one model but tested on another one, Scoredist was nearly always more accurate. The Jukes-Cantor and Kimura correction methods were also tested, but were substantially less accurate. The

  14. Scoredist: A simple and robust protein sequence distance estimator

    Directory of Open Access Journals (Sweden)

    Hollich Volker

    2005-04-01

    Full Text Available Abstract Background Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used. Results We propose a correction-based protein sequence estimator called Scoredist. It uses a logarithmic correction of observed divergence based on the alignment score according to the BLOSUM62 score matrix. We evaluated Scoredist and a number of optimal matrix methods using three evolutionary models for both training and testing Dayhoff, Jones-Taylor-Thornton, and Müller-Vingron, as well as Whelan and Goldman solely for testing. Test alignments with known distances between 0.01 and 2 substitutions per position (1–200 PAM were simulated using ROSE. Scoredist proved as accurate as the optimal matrix methods, yet substantially more robust. When trained on one model but tested on another one, Scoredist was nearly always more accurate. The Jukes-Cantor and Kimura correction methods were also

  15. 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

    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. 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. 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. This EST collection offers a resource for studying functional genes, including transcripts expressed in banana-Mf interactions. Markers are

  16. 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

  17. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

    OpenAIRE

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-01-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence re...

  18. 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...

  19. Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines.

    Science.gov (United States)

    Slate, Jon; Hale, Matthew C; Birkhead, Timothy R

    2007-02-14

    Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries. A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length > or =20 bp and purity > or =90% and 144 simple sequence repeats of length > or =30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7. We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.

  20. Simple sequence repeats in zebra finch (Taeniopygia guttata expressed sequence tags: a new resource for evolutionary genetic studies of passerines

    Directory of Open Access Journals (Sweden)

    Birkhead Timothy R

    2007-02-01

    Full Text Available Abstract Background Passerines (perching birds are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST Genbank entries. Results A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs or microsatellites of length ≥20 bp and purity ≥90% and 144 simple sequence repeats of length ≥30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7. Conclusion We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.

  1. Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm.

    Science.gov (United States)

    Zhao, Yongli; Keremane, Manjunath; Prakash, Channapatna S; He, Guohao

    2017-01-01

    The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

  2. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development.

    Science.gov (United States)

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-12-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence repeat markers for identification of Zanthoxylum. In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that Zanthoxylum is relatively recent and estimated to have diverged from Citrus ca. 36.5-37.7 million years ago. We also detected a whole-genome duplication event in Zanthoxylum that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by Ka/Ks. Simple sequence repeat analysis divided 31 Zanthoxylum cultivars and landraces into three major groups. This Zanthoxylum reference transcriptome provides crucial information for the evolutionary study of the Zanthoxylum genus and the Rutaceae family, and facilitates the establishment of more effective Zanthoxylum breeding programs.

  3. Development of expressed sequence tag-simple sequence repeat markers for Chrysanthemum morifolium and closely related species.

    Science.gov (United States)

    Liu, H; Zhang, Q X; Sun, M; Pan, H T; Kong, Z X

    2015-07-13

    With the development of chrysanthemum breeding in recent years, an increasing number of wild species in genera related to Chrysanthemum were introduced to extend the genetic resources and facilitate the genetic improvement of chrysanthemums via hybridization. However, few simple sequence repeat (SSR) markers are available for marker-assisted breeding and population genetic studies of chrysanthemum and closely related species. Expressed sequence tags (ESTs) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers. In this study, 25 EST-SSRs were successfully developed from Chrysanthemum EST sequences for Chrysanthemum morifolium and closely related species. In total, 4164 unigene sequences were assembled from 7180 ESTs of chrysanthemum in GenBank, which were subsequently used to screen for the presence of microsatellites with the SSRIT software. The screening criteria were 8, 5, 4, and 3 repeating units for di-, tri-, tetra-, and penta- and higher-order nucleotides, respectively. Moreover, 310 SSR loci from 296 sequences were identified, and 198 primer pairs for SSR amplification were designed with the Primer Premier 5.0 software, of which 25 SSR loci showed polymorphic amplification in 52 species and varieties belonging to Chrysanthemum, Ajania, and Opisthopappus. The application of EST-SSR markers to the identification of intergeneric hybrids between Chrysanthemum and Ajania was demonstrated. Therefore, EST-SSRs can be developed for species that lack gene sequences or ESTs by utilizing ESTs of closely related species.

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

    OpenAIRE

    Lewers, Kim S; Saski, Chris A; Cuthbertson, Brandon J; Henry, David C; Staton, Meg E; Main, Dorrie S; Dhanaraj, Anik L; Rowland, Lisa J; Tomkins, Jeff P

    2008-01-01

    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 ge...

  5. Simple protocol for population (Sanger sequencing for Zika virus genomic regions

    Directory of Open Access Journals (Sweden)

    Gabriela Bastos Cabral

    2017-11-01

    Full Text Available BACKGROUND A number of Zika virus (ZIKV sequences were obtained using Next-generation sequencing (NGS, a methodology widely applied in genetic diversity studies and virome discovery. However Sanger method is still a robust, affordable, rapid and specific tool to obtain valuable sequences. OBJECTIVE The aim of this study was to develop a simple and robust Sanger sequencing protocol targeting ZIKV relevant genetic regions, as envelope protein and nonstructural protein 5 (NS5. In addition, phylogenetic analysis of the ZIKV strains obtained using the present protocol and their comparison with previously published NGS sequences were also carried out. METHODS Six Vero cells isolates from serum and one urine sample were available to develop the procedure. Primer sets were designed in order to conduct a nested RT-PCR and a Sanger sequencing protocols. Bayesian analysis was used to infer phylogenetic relationships. FINDINGS Seven complete ZIKV envelope protein (1,571 kb and six partial NS5 (0,798 Kb were obtained using the protocol, with no amplification of NS5 gene from urine sample. Two NS5 sequences presented ambiguities at positions 495 and 196. Nucleotide analysis of a Sanger sequence and consensus sequence of previously NGS study revealed 100% identity. ZIKV strains described here clustered within the Asian lineage. MAIN CONCLUSIONS The present study provided a simple and low-cost Sanger protocol to sequence relevant genes of the ZIKV genome. The identity of Sanger generated sequences with published consensus NGS support the use of Sanger method for ZIKV population studies. The regions evaluated were able to provide robust phylogenetic signals and may be used to conduct molecular epidemiological studies and monitor viral evolution.

  6. Simple protocol for population (Sanger) sequencing for Zika virus genomic regions.

    Science.gov (United States)

    Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Souza, Renato Pereira de; Cunha, Mariana Sequetin; Luchs, Adriana; Figueiredo, Cristina Adelaide; Brígido, Luís Fernando de Macedo

    2018-01-01

    A number of Zika virus (ZIKV) sequences were obtained using Next-generation sequencing (NGS), a methodology widely applied in genetic diversity studies and virome discovery. However Sanger method is still a robust, affordable, rapid and specific tool to obtain valuable sequences. The aim of this study was to develop a simple and robust Sanger sequencing protocol targeting ZIKV relevant genetic regions, as envelope protein and nonstructural protein 5 (NS5). In addition, phylogenetic analysis of the ZIKV strains obtained using the present protocol and their comparison with previously published NGS sequences were also carried out. Six Vero cells isolates from serum and one urine sample were available to develop the procedure. Primer sets were designed in order to conduct a nested RT-PCR and a Sanger sequencing protocols. Bayesian analysis was used to infer phylogenetic relationships. Seven complete ZIKV envelope protein (1,571 kb) and six partial NS5 (0,798 Kb) were obtained using the protocol, with no amplification of NS5 gene from urine sample. Two NS5 sequences presented ambiguities at positions 495 and 196. Nucleotide analysis of a Sanger sequence and consensus sequence of previously NGS study revealed 100% identity. ZIKV strains described here clustered within the Asian lineage. The present study provided a simple and low-cost Sanger protocol to sequence relevant genes of the ZIKV genome. The identity of Sanger generated sequences with published consensus NGS support the use of Sanger method for ZIKV population studies. The regions evaluated were able to provide robust phylogenetic signals and may be used to conduct molecular epidemiological studies and monitor viral evolution.

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

    African Journals Online (AJOL)

    Inter-simple sequence repeat (ISSR)-PCR technique was used to assess genetic variation and phylogenetic relationships between Lymnaea natalensis collected from Giza, Ismailia, Damietta, and Beheira governorates in Egypt and compared with lab-bred snail in addition to characterization of watercourses from these ...

  8. Inter-simple sequence repeat (ISSR) markers in the evaluation of ...

    African Journals Online (AJOL)

    DNA samples of six hybrids of Capsicum annuum and Capsicum frutescens were analyzed with ten inter-simple sequence repeat (ISSR) primers, which produced 52 polymorphic bands out of 87 bands with polymorphism average of 60%. ISSR patterns scored five distinguishable species-specific bands; two for C.

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

    Science.gov (United States)

    Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

    2015-10-26

    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 sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

  10. Marker-assisted sex differentiation in date palm using simple sequence repeats

    OpenAIRE

    Elmeer, Khaled; Mattat, Imene

    2012-01-01

    Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Our objective was to identify microsatellite markers that could be used to differentiate between male and female date palm (Phoenix dactylifera). The date palm is a dioecious plant whose sex cannot be determined until it reaches a reproductive age between 5 and 10 years. An early selection and/or differentiation of young seedlings into males and females could enhance breeding and assist ...

  11. Transferability of Simple Sequence Repeat (SSR) Markers Developed in Litchi chinensis to Blighia sapida (Sapindaceae)

    OpenAIRE

    Ekué, Marius; Gailing, Oliver; Finkeldey,Reiner

    2009-01-01

    Ackee (Blighia sapida, Sapindaceae) is a multipurpose fruit tree species of high economic importance, native to the Guinean forests of West Africa, and belongs to the same family as that of lychee (Litchi chinensis). In this study, a set of 12 primer pairs for simple sequence repeats (SSRs) previously developed for lychee has been evaluated for polymorphism in 16 ackee trees from different populations. Seven primer pairs have been found to be transferable, and four have revealed polymorphisms...

  12. Temporal and spatiotemporal coherence in simple-cell responses: a generative model of natural image sequences.

    Science.gov (United States)

    Hurri, Jarmo; Hyvärinen, Aapo

    2003-08-01

    We present a two-layer dynamic generative model of the statistical structure of natural image sequences. The second layer of the model is a linear mapping from simple-cell outputs to pixel values, as in most work on natural image statistics. The first layer models the dependencies of the activity levels (amplitudes or variances) of the simple cells, using a multivariate autoregressive model. The second layer shows the emergence of basis vectors that are localized, oriented and have different scales, just like in previous work. But in our new model, the first layer learns connections between the simple cells that are similar to complex cell pooling: connections are strong among cells with similar preferred location, frequency and orientation. In contrast to previous work in which one of the layers needed to be fixed in advance, the dynamic model enables us to estimate both of the layers simultaneously from natural data.

  13. Development of Genomic Simple Sequence Repeats (SSR) by Enrichment Libraries in Date Palm.

    Science.gov (United States)

    Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

    2017-01-01

    Development of highly informative markers such as simple sequence repeats (SSR) for cultivar identification and germplasm characterization and management is essential for date palms genetic studies. The present study documents the development of SSR markers and assesses genetic relationships of commonly grown date palm (Phoenix dactylifera L.) cultivars in different geographical regions of Saudi Arabia. A total of 93 novel simple sequence repeat (SSR) markers were screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs are dinucleotide, 25% trinucleotide, 3% tetranucleotide, and 1% pentanucleotide motives and show 100% polymorphism. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis illustrates that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) reveals genetic variation among and within cultivars of 27% and 73%, respectively, according to the geographical distribution of the cultivars. Developed microsatellite markers are of additional value to date palm characterization, tools which can be used by researchers in population genetics, cultivar identification, as well as genetic resource exploration and management. The cultivars tested exhibited a significant amount of genetic diversity and could be suitable for successful breeding programs. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

  14. Simple sequence repeat markers for kānuka (Kunzeaspp.; Myrtaceae) present in New Zealand.

    Science.gov (United States)

    Goeke, Dagmar F; Mitchell, Caroline M; Lange, Claudia; Houliston, Gary J

    2017-04-01

    We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on kānuka ( Kunzea spp.; Myrtaceae). A shotgun sequencing library was constructed from leaf material of K. robusta using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand Kunzea species. Each of these loci cross-amplified in all tested species. The amplified di-, tri-, and pentanucleotide repeats resulted in eight to 24 alleles per locus for a total of 220 specimens. The mean observed and expected heterozygosity per locus ranged from 0.18 to 0.77 and 0.33 to 0.82, respectively. The SSR markers we produced are valuable for phylogenetic and population studies on all endemic Kunzea spp. and may also be useful for studies on closely related Kunzea species from Australia.

  15. 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.

  16. Development, characterization, and annotation of potential simple sequence repeats by transcriptome sequencing in pears (Pyrus pyrifolia Nakai).

    Science.gov (United States)

    Zhou, H; Cai, B H; Lü, Z Q; Gao, Z H; Qiao, Y S

    2016-09-23

    Simple sequence repeats (SSRs), one of the most powerful molecular markers, can be used for DNA fingerprinting, variety identification, genetic mapping, and marker-assisted selection. Using the pear's (Pyrus pyrifolia Nakai) 75,764 unigenes (55,676,271 bp) obtained by deep transcriptome sequencing, a total of 10,622 novel SSRs were identified in 9154 unigenes, accounting for 14.02% of all unigenes. The average length and distribution of these SSRs was about 16 bp and 5.24 kb, respectively. Dinucleotide repeat motifs were the main type, with a frequency of 55.87%, followed by trinucleotides (24.45%). There were 159 kinds of repeat motifs existing in the pear transcriptome. AG/CT was the most frequent motif, accounting for 49.64%. All 9154 SSR-containing unigenes were functionally annotated using Nr (NCBI non-redundant protein database), Nt (NCBI non-redundant nucleotide database), and the Swiss-Prot database, and were classified further by Gene Ontology and Clusters of Orthologous Groups. In addition, a total of 4300 primer pairs were designed from all SSR loci obtained. Of these, 40 primers were randomly selected for PCR amplification and polyacrylamide gel (PAGE) analysis. Among the 40 primer pairs, 31 were successfully separated via PAGE. These findings also confirm that mining SSRs using next-generating sequencing technologies is a fast, effective, and reliable approach.

  17. A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores

    Directory of Open Access Journals (Sweden)

    Olivier Bastien

    2008-01-01

    Full Text Available Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model computes a P-value assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Using a simple approach combined with recent results in reliability theory, we demonstrate here that the Karlin-Altshul model can be derived with no reference to the extreme events theory. Sequences were considered as systems in which components are amino acids and having a high redundancy of Information reflected by their alignment scores. Evolution of the information shared between aligned components determined the Shared Amount of Information (SA.I. between sequences, i.e. the score. The Gumbel distribution parameters of aligned sequences scores find here some theoretical rationale. The first is the Hazard Rate of the distribution of scores between residues and the second is the probability that two aligned residues do not lose bits of information (i.e. conserve an initial pairing score when a mutation occurs.

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

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

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

  19. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis

    Science.gov (United States)

    Simple sequence repeats (SSR) or microsatellite markers are one of the most informative and versatile DNA-based markers. The use of next-generation sequencing technologies allow whole genome sequencing and make it possible to develop large numbers of SSRs through bioinformatic analysis of genome da...

  20. SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

    Science.gov (United States)

    Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

    2014-01-01

    Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig's scalability over many computing nodes and illustrate its use with example scripts. Available under the open source MIT license at http://sourceforge.net/projects/seqpig/

  1. SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

    Science.gov (United States)

    Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

    2014-01-01

    Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts. Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ Contact: andre.schumacher@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24149054

  2. 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.

  3. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis

    Science.gov (United States)

    Zheng, Jin-shuang; Sun, Cheng-zhen; Zhang, Shu-ning; Hou, Xi-lin; Bonnema, Guusje

    2016-01-01

    A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis. PMID:27507974

  4. Characterization and phylogenetic relationships among microsporidia infecting silkworm, Bombyx mori, using inter simple sequence repeat (ISSR) and small subunit rRNA (SSU-rRNA) sequence analysis

    National Research Council Canada - National Science Library

    Rao, S N; Nath, B S.u.r.e.n.d.r.a; Saratchandra, B

    2005-01-01

    This study is the first report on the genetic characterization and relationships among different microsporidia infecting the silkworm, Bombyx mori, using inter simple sequence repeat PCR (ISSR-PCR) analysis...

  5. Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Ayesh, Basim M

    2017-01-01

    Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

  6. Identification of apple cultivars on the basis of simple sequence repeat markers.

    Science.gov (United States)

    Liu, G S; Zhang, Y G; Tao, R; Fang, J G; Dai, H Y

    2014-09-12

    DNA markers are useful tools that play an important role in plant cultivar identification. They are usually based on polymerase chain reaction (PCR) and include simple sequence repeats (SSRs), inter-simple sequence repeats, and random amplified polymorphic DNA. However, DNA markers were not used effectively in the complete identification of plant cultivars because of the lack of known DNA fingerprints. Recently, a novel approach called the cultivar identification diagram (CID) strategy was developed to facilitate the use of DNA markers for separate plant individuals. The CID was designed whereby a polymorphic maker was generated from each PCR that directly allowed for cultivar sample separation at each step. Therefore, it could be used to identify cultivars and varieties easily with fewer primers. In this study, 60 apple cultivars, including a few main cultivars in fields and varieties from descendants (Fuji x Telamon) were examined. Of the 20 pairs of SSR primers screened, 8 pairs gave reproducible, polymorphic DNA amplification patterns. The banding patterns obtained from these 8 primers were used to construct a CID map. Each cultivar or variety in this study was distinguished from the others completely, indicating that this method can be used for efficient cultivar identification. The result contributed to studies on germplasm resources and the seedling industry in fruit trees.

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

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    Todd P Michael

    2007-08-01

    Full Text Available 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.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.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.

  8. 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.

  9. Mating Type and Simple Sequence Repeat Markers Indicate a Clonal Population of Phyllosticta citricarpa in Florida.

    Science.gov (United States)

    Wang, Nan-Yi; Zhang, Ke; Huguet-Tapia, Jose C; Rollins, Jeffrey A; Dewdney, Megan M

    2016-11-01

    Phyllosticta citricarpa, the citrus black spot pathogen, was first identified in Florida in March 2010. Subsequently, this pathogen has become established in Florida but can be easily confused with the endemic nonpathogenic citrus endophyte P. capitalensis. In this study, the mating-type (MAT) loci of P. citricarpa and P. capitalensis were identified via draft genome sequencing and were characterized at the structural and sequence levels. P. citricarpa was determined to have an idiomorphic, heterothallic MAT locus structure, whereas P. capitalensis was found to have a single MAT locus consistent with a homothallic mating system. A survey of P. citricarpa isolates from Florida revealed that only the MAT1-2 idiomorph existed in the Floridian population. In contrast, isolates collected from Australia exhibited a 1:1 ratio of MAT1-1 and MAT1-2 isolates. Development and analysis of simple sequence repeat markers revealed a single multilocus genotype (MLG) in the Floridian population (n = 70) and 11 MLG within the Australian population (n = 24). These results indicate that isolates of P. citricarpa from Florida are likely descendent from a single clonal lineage and are reproducing asexually. The disease management focus in Florida will need to be concentrated on the production and dispersal of pycnidiospores.

  10. Comparative mapping between quercus and castanea using simple-sequence repeats (SSRs).

    Science.gov (United States)

    Barreneche, T; Casasoli, M; Russell, K; Akkak, A; Meddour, H; Plomion, C; Villani, F; Kremer, A

    2004-02-01

    Simple sequence repeat (SSR) markers from Quercus and Castanea were used for comparative mapping between Quercus robur (L.) and Castanea sativa (Mill.). We tested the transferability of SSRs developed in Quercus to Castanea and vice-versa. In total, 47% (25) of the Quercus SSRs and 63% (19) of the Castanea SSRs showed a strong amplification product in the non-source species. From these 44 putative comparative anchor tags, 19 (15 from Quercus and 4 from Castanea) were integrated in two previously established genetic linkage maps for the two genera. SSR loci were sequenced to confirm the orthology of the markers. The combined information from both genetic mapping and sequence analysis were used to determine the homeology between seven linkage groups, aligned on the basis of pairs or triplets of common markers, while two additional groups were matched using a single microsatellite marker. Orthologous loci identified between Q. robur and C. sativa will be useful as anchor loci for comparative mapping studies within the Fagaceae family.

  11. Transferability of Simple Sequence Repeat (SSR) Markers Developed in Litchi chinensis to Blighia sapida (Sapindaceae).

    Science.gov (United States)

    Ekué, Marius R M; Gailing, Oliver; Finkeldey, Reiner

    2009-01-01

    Ackee (Blighia sapida, Sapindaceae) is a multipurpose fruit tree species of high economic importance, native to the Guinean forests of West Africa, and belongs to the same family as that of lychee (Litchi chinensis). In this study, a set of 12 primer pairs for simple sequence repeats (SSRs) previously developed for lychee has been evaluated for polymorphism in 16 ackee trees from different populations. Seven primer pairs have been found to be transferable, and four have revealed polymorphisms. However, the average number of alleles per locus has dropped from 4.9 for lychee to 3.7 for ackee. Characterization of the four polymorphic markers in 279 individuals belonging to14 different ackee populations from Benin has revealed that the numbers of alleles per locus range from two to 14 with a mean number of 5.8. The observed and expected heterozygosities range between 0.020 to 0.359 and 0.020 to 0.396, respectively.

  12. Eye Movement Sequences during Simple versus Complex Information Processing of Scenes in Autism Spectrum Disorder

    Directory of Open Access Journals (Sweden)

    Sheena K. Au-Yeung

    2011-01-01

    Full Text Available Minshew and Goldstein (1998 postulated that autism spectrum disorder (ASD is a disorder of complex information processing. The current study was designed to investigate this hypothesis. Participants with and without ASD completed two scene perception tasks: a simple “spot the difference” task, where they had to say which one of a pair of pictures had a detail missing, and a complex “which one's weird” task, where they had to decide which one of a pair of pictures looks “weird”. Participants with ASD did not differ from TD participants in their ability to accurately identify the target picture in both tasks. However, analysis of the eye movement sequences showed that participants with ASD viewed scenes differently from normal controls exclusively for the complex task. This difference in eye movement patterns, and the method used to examine different patterns, adds to the knowledge base regarding eye movements and ASD. Our results are in accordance with Minshew and Goldstein's theory that complex, but not simple, information processing is impaired in ASD.

  13. 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; Lamontanara, A; Orsini, L; Serra, I A; Mazzuca, S; Procaccini, G

    2016-12-20

    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.

  14. A simple strategy for reducing false negatives in calling variants from single-cell sequencing data.

    Directory of Open Access Journals (Sweden)

    Cong Ji

    Full Text Available Due to the growth of interest in single-cell genomics, computational methods for distinguishing true variants from artifacts are highly desirable. While special attention has been paid to false positives in variant or mutation calling from single-cell sequencing data, an equally important but often neglected issue is that of false negatives derived from allele dropout during the amplification of single cell genomes. In this paper, we propose a simple strategy to reduce the false negatives in single-cell sequencing data analysis. Simulation results show that this method is highly reliable, with an error rate of 4.94×10-5, which is orders of magnitude lower than the expected false negative rate (~34% estimated from a single-cell exome dataset, though the method is limited by the low SNP density in the human genome. We applied this method to analyze the exome data of a few dozen single tumor cells generated in previous studies, and extracted cell specific mutation information for a small set of sites. Interestingly, we found that there are difficulties in using the classical clonal model of tumor cell growth to explain the mutation patterns observed in some tumor cells.

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

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    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.

  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. 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.

  18. 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. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Diversity Analysis of Polyporus umbellatus in China Using Inter-simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Liu, Meng-Meng; Xing, Yong-Mei; Guo, Shun-Xing

    2015-01-01

    Polyporus (P.) umbellatus, an endangered medicinal fungus in China, is distributed throughout most areas of the country. Thirty-seven natural P. umbellatus samples collected from 12 provinces in China were subjected to the inter-simple sequence repeat (ISSR) assay to investigate the genetic diversity within and among the 11 natural populations. Nine ISSR primers selected from 100 primers produced 88 discernible DNA bands, with 46 being polymorphic. The frequency of polymorphism varied from 19.57 to 93.48% with an average of 61.26% across all populations. At the population level, the within-population variance was much greater (92.04%) than the between-population variance (7.96%) as revealed by analysis of molecular variance. Eleven P. umbellatus populations were grouped into two major clusters, and the clustering pattern displayed four groups using the unweighted pair-group method with an arithmetic mean dendrogram. Principal coordinate analysis further indicated that the genetic diversity of P. umbellatus strains was unevenly distributed and displayed a clustered distribution pattern instead. Within these clusters, subgrouping (Henan and Hubei) and cluster II (Jilin and Heilongjiang) related to the geographic distribution were evident. The present study provides the first global overview of P. umbellatus diversity analysis in China, which may open up new opportunities in comparative genetic research on this medicinal fungus in other countries.

  20. Development of Simple Sequence Repeat (SSR Markers of Sesame (Sesamum indicum from a Genome Survey

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    Xin Wei

    2014-04-01

    Full Text Available 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.

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

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    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.

  2. 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

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

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    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.

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

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    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.

  5. Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Yuan, C Y; Zhang, C; Wang, P; Hu, S; Chang, H P; Xiao, W J; Lu, X T; Jiang, S B; Ye, J Z; Guo, X H

    2014-04-25

    Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins.

  6. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    Science.gov (United States)

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-07-17

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus.

  7. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

    Science.gov (United States)

    Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

    2018-01-01

    Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

  8. Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

    Directory of Open Access Journals (Sweden)

    A.D. Chowdhury

    2016-11-01

    Full Text Available Salt stress is a major problem in most of the rice growing areas in the world. A major QTL Saltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice. This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated with salt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1 to 9 score at EC = 10 dSm-1 under controlled environmental conditions. Seven new breeding lines including three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 and can be good sources of new genes/alleles for salt tolerance. Simple sequence repeat (SSR marker RM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information content value varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54 lines were clearly separated into two major clusters. Fourteen haplotypes were identified based on Saltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminate between the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assisted selection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 on chromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

  9. 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.

  10. 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.

  11. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

    Directory of Open Access Journals (Sweden)

    Shirasawa Kenta

    2012-06-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp.

  12. Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review.

    Science.gov (United States)

    Kaur, Shubhneet; Panesar, Parmjit S; Bera, Manab B; Kaur, Varinder

    2015-01-01

    Sequencing of rice genome has facilitated the understanding of rice evolution and has been utilized extensively for mining of DNA markers to facilitate marker-assisted breeding. Simple sequence repeat (SSR) markers that are tandemly repeated nucleotide sequence motifs flanked by unique sequences are presently the maker of choice in rice improvement due to their abundance, co-dominant inheritance, high levels of allelic diversity, and simple reproducible assay. The current level of genome coverage by SSR markers in rice is sufficient to employ them for genotype identification and marker-assisted selection in breeding for mapping of genes and quantitative trait loci analysis. This review provides comprehensive information on the mapping and applications of SSR markers in investigation of rice cultivars to study their genetic divergence and marker-assisted selection of important agronomic traits.

  13. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

    CERN Document Server

    Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    2015-01-01

    Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately $\\sim 150$ bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.

  14. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.

    Directory of Open Access Journals (Sweden)

    Shuhei Isami

    Full Text Available Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.

  15. Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

    OpenAIRE

    McPherson, Hannah; van der Merwe, Marlien; Delaney, Sven K; Edwards, Mark A; Henry, Robert J; McIntosh, Emma; Rymer, Paul D; Milner, Melita L; Siow, Juelian; Rossetto, Maurizio

    2013-01-01

    Background With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. Results The chloroplast genome of Toona ...

  16. Simple and efficient identification of rare recessive pathologically important sequence variants from next generation exome sequence data.

    Science.gov (United States)

    Carr, Ian M; Morgan, Joanne; Watson, Christopher; Melnik, Svitlana; Diggle, Christine P; Logan, Clare V; Harrison, Sally M; Taylor, Graham R; Pena, Sergio D J; Markham, Alexander F; Alkuraya, Fowzan S; Black, Graeme C M; Ali, Manir; Bonthron, David T

    2013-07-01

    Massively parallel ("next generation") DNA sequencing (NGS) has quickly become the method of choice for seeking pathogenic mutations in rare uncharacterized monogenic diseases. Typically, before DNA sequencing, protein-coding regions are enriched from patient genomic DNA, representing either the entire genome ("exome sequencing") or selected mapped candidate loci. Sequence variants, identified as differences between the patient's and the human genome reference sequences, are then filtered according to various quality parameters. Changes are screened against datasets of known polymorphisms, such as dbSNP and the 1000 Genomes Project, in the effort to narrow the list of candidate causative variants. An increasing number of commercial services now offer to both generate and align NGS data to a reference genome. This potentially allows small groups with limited computing infrastructure and informatics skills to utilize this technology. However, the capability to effectively filter and assess sequence variants is still an important bottleneck in the identification of deleterious sequence variants in both research and diagnostic settings. We have developed an approach to this problem comprising a user-friendly suite of programs that can interactively analyze, filter and screen data from enrichment-capture NGS data. These programs ("Agile Suite") are particularly suitable for small-scale gene discovery or for diagnostic analysis. © 2013 WILEY PERIODICALS, INC.

  17. 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.

  18. Genetic diversity analysis of Bt cotton genotypes in Pakistan using simple sequence repeat markers.

    Science.gov (United States)

    Ullah, I; Iram, A; Iqbal, M Z; Nawaz, M; Hasni, S M; Jamil, S

    2012-03-14

    The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties.

  19. Cultivar identification, pedigree verification, and diversity analysis among Peach (Prunus persica L. Batsch) Cultivars based on Simple Sequence Repeat markers

    Science.gov (United States)

    The genetic relationships and pedigree inferences among peach (Prunus persica (L.) Batsch) accessions and breeding lines used in genetic improvement were evaluated using 15 simple sequence repeat (SSR) markers. A total of 80 alleles were detected among the 37 peach accessions with an average of 5.53...

  20. Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree.

    Science.gov (United States)

    McPherson, Hannah; van der Merwe, Marlien; Delaney, Sven K; Edwards, Mark A; Henry, Robert J; McIntosh, Emma; Rymer, Paul D; Milner, Melita L; Siow, Juelian; Rossetto, Maurizio

    2013-03-14

    With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.

  1. Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species.

    Science.gov (United States)

    Healey, Adam; Furtado, Agnelo; Cooper, Tal; Henry, Robert J

    2014-01-01

    Next-generation sequencing technologies rely on high quality DNA that is suitable for library preparation followed by sequencing. Some plant species store large amounts of phenolics and polysaccharides within their leaf tissue making genomic DNA extraction difficult. While many DNA extraction methods exist that contend with the presence of phenolics and polysaccharides, these methods rely on long incubations, multiple precipitations or commercially available kits to produce high molecular weight and contaminant-free DNA. In this protocol, we describe simple modifications to the established CTAB- based extraction method that allows for reliable isolation of high molecular weight genomic DNA from difficult to isolate plant species Corymbia (a eucalypt) and Coffea (coffee). The simplified protocol does not require multiple clean up steps or commercial based kits, and the isolated DNA passed stringent quality control standards for whole genome sequencing on Illumina HiSeq and TruSeq sequencing platforms.

  2. Hybrid quantum repeater based on resonant qubit-field interactions

    Science.gov (United States)

    Bernád, József Zsolt

    2017-11-01

    We propose a hybrid quantum repeater based on ancillary coherent field states and material qubits coupled to optical cavities. For this purpose, resonant qubit-field interactions and postselective field measurements are determined which are capable of realizing all necessary two-qubit operations for the actuation of the quantum repeater. We explore both theoretical and experimental possibilities of generating near-maximally-entangled qubit pairs (F >0.999 ) over long distances. It is shown that our scheme displays moderately low repeater rates, between 5 ×10-4 and 23 pairs per second, over distances up to 900 km, and it relies completely on current technology of cavity quantum electrodynamics.

  3. A simple protocol for the automation of DNA cycle sequencing reactions and polymerase chain reactions.

    Science.gov (United States)

    Civitello, A B; Richards, S; Gibbs, R A

    1992-01-01

    Automated DNA sequencing methods using robotic workstations have been previously reported, however it is often an arduous task to import these technologies into a laboratory. We describe protocols making use of a Beckman Biomek 1000 robotic workstation to prepare polymerase chain reactions (PCRs) and "cycle sequencing" reactions to be performed in a Perkin Elmer Cetus System 9600 thermocycler. The combination of these two instruments allows a high throughput of PCR and DNA sequencing reactions. The programs described are freely available via anonymous file transfer protocol (FTP).

  4. A simple method for the parallel deep sequencing of full influenza A genomes

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen

    2011-01-01

    Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool....... This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus...

  5. 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

    regions of known sequences within the current DNA databases. An ISSR fragment of 580 bp, produced by the (GACA)4TC primer present on LG6, showed a 95% identity to the Avena sativa L. transposon and repetitive DNA linked to the receptor kinase gene. A 780 bp fragment generated by (TG)8RT primer...

  6. Assessment of in silico BAC-based simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) ... According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is ...

  7. Efficient and exact sampling of simple graphs with given arbitrary degree sequence.

    Directory of Open Access Journals (Sweden)

    Charo I Del Genio

    Full Text Available Uniform sampling from graphical realizations of a given degree sequence is a fundamental component in simulation-based measurements of network observables, with applications ranging from epidemics, through social networks to Internet modeling. Existing graph sampling methods are either link-swap based (Markov-Chain Monte Carlo algorithms or stub-matching based (the Configuration Model. Both types are ill-controlled, with typically unknown mixing times for link-swap methods and uncontrolled rejections for the Configuration Model. Here we propose an efficient, polynomial time algorithm that generates statistically independent graph samples with a given, arbitrary, degree sequence. The algorithm provides a weight associated with each sample, allowing the observable to be measured either uniformly over the graph ensemble, or, alternatively, with a desired distribution. Unlike other algorithms, this method always produces a sample, without back-tracking or rejections. Using a central limit theorem-based reasoning, we argue, that for large , and for degree sequences admitting many realizations, the sample weights are expected to have a lognormal distribution. As examples, we apply our algorithm to generate networks with degree sequences drawn from power-law distributions and from binomial distributions.

  8. 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

  9. Comparative analysis of genetic diversity among species of Chrysanthemum and its related genera using inter-simple sequence repeat and sequence-related amplified polymorphism markers.

    Science.gov (United States)

    Zhang, X; Zhang, F; Zhao, H; Guan, Z; Chen, S; Jiang, J; Fang, W; Chen, F

    2014-10-20

    In this study, inter-simple sequence repeats (ISSRs) and sequence-related amplified polymorphism (SRAP) were applied to assess the genetic diversity in 38 species of Chrysanthemum and related genera. A total of 204 and 567 bands were amplified by 24 ISSR and 25 SRAP primers, of which 196 (97%) and 557 (99%) were polymorphic, respectively. The ISSR-based genetic similarity ranged from 0.016 to 0.886 and averaged 0.201, while the SRAP-based genetic similarity varied from 0.010 to 0.811 and averaged 0.122. Both the ISSR and SRAP techniques revealed similar clustering patterns and grouped species of Chrysanthemum and Ajania together. The results of principal coordinate analysis corroborated the unweighted pair group method with arithmetic average clustering. Additionally, results from ISSR and SRAP data were significantly correlated (r = 0.89, P chrysanthemum in future distant interspecific breeding.

  10. 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.

  11. Genetic integrity of somaclonal variants in tea (Camellia sinensis (L.) O Kuntze) as revealed by inter simple sequence repeats.

    Science.gov (United States)

    Thomas, Jibu; Vijayan, Deepu; Joshi, Sarvottam D; Joseph Lopez, S; Raj Kumar, R

    2006-05-17

    Adoption of inter simple sequence repeats (ISSR) technique to analyze the genetic variability of somatic embryo derived tea plants was evaluated. Morphological characterisation of the field grown plants revealed no identical character aligning with the parent, UPASI-10. Out of 40 primers, 15 exhibited concurrent polymorphism were selected for the study. Genetic variability of somaclones derived from single line cotyledonary culture ranged from 33.0 to 55.0%. A unique fragment of 1.2Kb was visible in majority of the accessions whereas the fragments below the length of 0.6Kb were noticed only in 50% of the variants. Out of 120 interactions attempted using Pearson's coefficient correlation, only 9.2% of somaclones exhibited significant similarity at genetic level. Dendrogram constructed based on simple matching coefficient revealed a distance of 2.257-3.317 between the final clusters. This strengthens the existence of wide genetic variation among the somaclones.

  12. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    OpenAIRE

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Amon...

  13. Evaluation of genetic diversity amongst Descurainia sophia L. genotypes by inter-simple sequence repeat (ISSR) marker

    OpenAIRE

    Saki, Sahar; Bagheri, Hedayat; Deljou, Ali; Zeinalabedini, Mehrshad

    2015-01-01

    Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversi...

  14. Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag–simple sequence repeat bands in Panax ginseng Meyer

    Directory of Open Access Journals (Sweden)

    Nam-Hoon Kim

    2014-04-01

    Conclusion: Our data imply that the recent genome duplication has resulted in two highly similar paralogous regions in the ginseng genome. The two paralogous sequences could be differentiated by large SSR number variations and one or two additional SNPs or InDels in every 100 bp of genic region, which can serve as a reliable identifier for each locus.

  15. Morphometric Characterization of the Modification Sequence of Simple Impact Craters on the Moon and Mars.

    Science.gov (United States)

    Watters, W. A.; Fassett, C.

    2016-12-01

    We have characterized and compared the shape distributions of simple impact craters spanning a range of preservation states and diameters on Mars (500 m ≤ D ≤ 5 km; N = 1,165; latitude range: ± 30°) and the Moon (800 m ≤ D ≤ 5 km; N= 8,200 maria craters). The goal of this work is to identify relationships between morphometric parameters that are characteristic of surface processes on both worlds. The digital elevation models (DEMs) of martian craters were generated from stereo image pairs acquired by the HiRISE and CTX cameras using the Ames Stereo Pipeline. For the lunar craters, we used team-released DEMs derived from stereo imagery acquired by the Terrain Camera on the Kaguya spacecraft. We examined the dependence of several morphometric parameters upon diameter (D) as well as the ratio of rim-to-floor depth and rim-crest diameter (d/D); the latter quantity is expected to decrease over time. The average cavity shape of martian simple craters is paraboloidal (power-law exponent α = 2.05 ± 0.52) whereas lunar craters exhibit a relatively conical shape (α = 1.29 ± 0.22), consistent with previous work. On neither body does α exhibit a strong dependence on d/D. We also computed the length scale of crater rim curvature (λ), which is also largely independent of d/D for the global population of martian craters. This quantity exhibits a dependence that is broadly consistent with topographic diffusion for lunar craters. Diameter-normalized rim height h/D is strongly correlated with d/D for lunar craters, and shows a relatively weak correlation for martian craters, as expected from widespread aeolian infilling of cavities. Radial elevation profiles generated from numerical simulations of linear diffusion were fit to measured rim profiles of the martian craters to estimate the model parameter κτ (diffusivity × time). The median age of craters in this population was independently estimated from crater counting statistics of the context geologic units to be

  16. De novo assembly and characterization of the root transcriptome and development of simple sequence repeat markers in Paphiopedilum concolor.

    Science.gov (United States)

    Li, D M; Zhao, C Y; Liu, X R; Liu, X F; Lin, Y J; Liu, J W; Chen, H M; L, F B

    2015-06-11

    Paphiopedilum orchids (Orchidaceae) have attracted much attention from botanists and horticulturists because of their peculiar leaves and beautiful flowers. Furthermore, the dry roots of Paphiopedilum plants have well-known medicinal uses. However, it is unknown how sensitive and plastic the root genes are to environmental changes or how these environmental changes regulate the biosynthesis of active ingredients. In this study, we chose Paphiopedilum concolor for root sequencing, as it is widely used as a parent in breeding experiments. A total of 3.77 Gb of sequence data were generated by Illumina paired-end sequencing. De novo assemblies yielded 72,952 contigs, 67,434 scaffolds, 64,304 unigenes with average lengths of 937, 1022, and 1047 bp, respectively. Based on Basic Local Alignment Search Tool with known protein sequences, 40,815 (63.5%) unigenes were annotated with an E-value cutoff of 1.0E-5. Among the unigenes, 24,605 were classified in the Gene Ontology database, 17,361 were assigned to Cluster of Orthologous Groups, and 14,170 were annotated in Kyoto Encyclopedia of Genes and Genomes. Among these annotations, over 1195 unigenes related to secondary metabolic pathways, as well as 609 unigenes involved in plant hormone synthesis and signal transduction, were identified. In addition, 5322 potential simple sequence repeats (SSRs) were identified, and 4989 primer pairs for 3975 sequences containing SSRs were obtained. This study provides valuable insights into the mechanisms of genes that regulate root growth and development and provides a comprehensive resource for genes related to secondary metabolism in roots and for marker-assisted studies in Paphiopedilum.

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

    Science.gov (United States)

    Joy, Nisha; Asha, Srinivasan; Mallika, Vijayan; Soniya, Eppurathu Vasudevan

    2013-01-01

    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.

  18. 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.

  19. De novo Transcriptome Sequencing Reveals a Considerable Bias in the Incidence of Simple Sequence Repeats towards the Downstream of ‘Pre-miRNAs’ of Black Pepper

    Science.gov (United States)

    Joy, Nisha; Asha, Srinivasan; Mallika, Vijayan; Soniya, Eppurathu Vasudevan

    2013-01-01

    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. PMID:23469176

  20. Neural representations and mechanisms for the performance of simple speech sequences.

    Science.gov (United States)

    Bohland, Jason W; Bullock, Daniel; Guenther, Frank H

    2010-07-01

    Speakers plan the phonological content of their utterances before their release as speech motor acts. Using a finite alphabet of learned phonemes and a relatively small number of syllable structures, speakers are able to rapidly plan and produce arbitrary syllable sequences that fall within the rules of their language. The class of computational models of sequence planning and performance termed competitive queuing models have followed K. S. Lashley [The problem of serial order in behavior. In L. A. Jeffress (Ed.), Cerebral mechanisms in behavior (pp. 112-136). New York: Wiley, 1951] in assuming that inherently parallel neural representations underlie serial action, and this idea is increasingly supported by experimental evidence. In this article, we developed a neural model that extends the existing DIVA model of speech production in two complementary ways. The new model includes paired structure and content subsystems [cf. MacNeilage, P. F. The frame/content theory of evolution of speech production. Behavioral and Brain Sciences, 21, 499-511, 1998 ] that provide parallel representations of a forthcoming speech plan as well as mechanisms for interfacing these phonological planning representations with learned sensorimotor programs to enable stepping through multisyllabic speech plans. On the basis of previous reports, the model's components are hypothesized to be localized to specific cortical and subcortical structures, including the left inferior frontal sulcus, the medial premotor cortex, the basal ganglia, and the thalamus. The new model, called gradient order DIVA, thus fills a void in current speech research by providing formal mechanistic hypotheses about both phonological and phonetic processes that are grounded by neuroanatomy and physiology. This framework also generates predictions that can be tested in future neuroimaging and clinical case studies.

  1. 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.

  2. COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes.

    Science.gov (United States)

    Maccari, Giuseppe; Gemignani, Federica; Landi, Stefano

    2010-07-15

    The complete sequencing of the human genome shows that only 1% of the entire genome encodes for proteins. The major part of the genome is made up of non-coding DNA, regulatory elements and junk DNA. Transcriptional regulation plays a central role in a multitude of critical cellular processes and responses, and it is a central force in the development and differentiation of multicellular organisms. Identifying regulatory elements is one of the major tasks in this challenge. To accomplish this task, we developed a solid and simple suite that allows direct access to genomic database and immediate result check. We introduce COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for motif search in entire genomes. Motifs can be partially degenerated and interrupted by spacers of variable length. We demonstrate through real biological data mining the simplicity and robustness of this tool. The test was performed on two well-known protein domains and a highly variable cis-acting element. COMPASSS successfully identifies both protein domains and cis-acting semi-conserved elements. The COMPASSS suite is available for Windows free of charge from our web sites: compasss.sourceforge.net/; www.stefanolandi.eu/

  3. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures.

    Science.gov (United States)

    Nithin, Chandran; Patwa, Nisha; Thomas, Amal; Bahadur, Ranjit Prasad; Basak, Jolly

    2015-06-12

    MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.

  4. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

    Science.gov (United States)

    Ståhlberg, Anders; Krzyzanowski, Paul M; Jackson, Jennifer B; Egyud, Matthew; Stein, Lincoln; Godfrey, Tony E

    2016-06-20

    Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. 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.

  6. A Simple Mandibular Distraction Protocol to Avoid Tracheostomy in Patients With Pierre Robin Sequence.

    Science.gov (United States)

    Ching, Jessica A; Daggett, Justin D; Alvarez, Sergio A; Conley, Cathy L; Ruas, Ernesto J

    2017-03-01

      Recent treatment goals for Pierre Robin sequence (PRS) focus on avoiding tracheostomy through modalities such as mandibular distraction osteogenesis (MDO). We primarily evaluated the efficacy of our straightforward MDO treatment protocol for resolution of PRS-associated airway obstruction while secondarily analyzing patient characteristics associated with success or failure of MDO.   A retrospective chart review before and after treatment.   Tertiary institutional center and private practice setting.   All patients were diagnosed with PRS and treated with MDO, according to the MDO treatment protocol, by a single surgeon with the same operative technique from 1999 to 2013. A sample size of n = 38 met the inclusion criteria. Data assessed included tracheostomy status (pre-MDO, post-MDO, or none), microlaryngoscopy and bronchoscopy (MLB) findings, multipositional airway study results, clinical resolution of airway obstruction following MDO, and patient characteristics.   Resolution of airway obstruction with avoidance of a tracheostomy.   Prior to referral for MDO, five patients required urgent tracheostomy. Of patients without a pre-MDO tracheostomy (n = 33), two patients required tracheostomy post-MDO, while 94% avoided tracheostomy with clinical resolution of airway obstruction (n = 31). On secondary analysis, anatomic abnormalities diagnosed by MLB were associated with a higher rate of tracheostomy (P = .037), confirming the utility of preoperative evaluation with MLB; otherwise, no patient characteristics demonstrated significance in patient selection. Follow-up ranged from 6 months to 10 years (mean = 6.45 years, median = 7.61 years).   Our treatment protocol demonstrates MDO is highly effective for resolving severe airway obstruction related to PRS. Based on secondary analysis, our simplified protocol does not require amendment.

  7. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free- living actinobacterium

    Energy Technology Data Exchange (ETDEWEB)

    Young, Michael; Artsatbanov, Vladislav; Beller, Harry R.; Chandra, Govind; Chater, Keith F.; Dover, Lynn G.; Goh, Ee-Been; Kahan, Tamar; Kaprelyants, Arseny S.; Kyrpides, Nikos; Lapidus, Alla; Lowry, Stephen R.; Lykidis, Athanasios; Mahillon, Jacques; Markowitz, Viktor; Mavrommatis, Konstantinos; Mukamolova, Galina V.; Oren, Aharon; Rokem, J. Stefan; Smith, Margaret C. M.; Young, Danielle I.; Greenblatt, Charles L.

    2009-11-01

    Micrococcus luteus (NCTC2665, Fleming strain) has one of the smallest genomes of free living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content 73%) predicted to encode 2403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 IS elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and fourteen response regulators, indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to {Beta}-lactam antibiotics may result from the presence of a reduced set of penicillin binding proteins and the absence of a wblC gene, which plays an important role in antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose, and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three gene cluster essential for this metabolism has been identified in the genome.

  8. Molecular Analysis of Date Palm Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSRs).

    Science.gov (United States)

    El Sharabasy, Sherif F; Soliman, Khaled A

    2017-01-01

    The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.

  9. 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.

  10. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  11. Genome-Wide Characterization of Simple Sequence Repeat (SSR Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Directory of Open Access Journals (Sweden)

    Jing Xiao

    Full Text Available Chinese jujube (Ziziphus jujuba, an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  12. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  13. 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.

  14. Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli

    Science.gov (United States)

    Shu, Jinshuai; Liu, Yumei; Li, Zhansheng; Zhang, Lili; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

    2015-01-01

    We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens. Thereafter, mtSSR2 was used to identify another 34 broccoli accessions, with an accuracy rate of 100%. Analysis of the polymorphic sequences revealed that the mtSSR2 open reading frame of carpelloid stamen sterile sources had a deletion of 51 bases (encoding 18 amino acids) compared with normal stamen materials. The open reading frame is located in the coding region of orf125 and orf108 of the mitochondrial genomes in Brassica crops and had the highest similarity with Raphanus sativus and Brassica carinata. The current study has not only identified a useful molecular marker to detect the cytoplasm of carpelloid stamens during broccoli breeding, but it also provides evidence that the mitochondrial genome is maternally inherited and provides a basis for studying the effect of the cytoplasm on flower organ development in plants. PMID:26407159

  15. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  16. Molecular characterization of three common olive (Olea europaea L.) cultivars in Palestine, using simple sequence repeat (SSR) markers

    Science.gov (United States)

    Obaid, Ramiz; Abu-Qaoud, Hassan; Arafeh, Rami

    2014-01-01

    Eight accessions of olive trees from three common varieties in Palestine, Nabali Baladi, Nabali Mohassan and Surri, were genetically evaluated using five simple sequence repeat (SSR) markers. A total of 17 alleles from 5 loci were observed in which 15 (88.2%) were polymorphic and 2 (11.8%) were monomorphic. An average of 3.4 alleles per locus was found ranging from 2.0 alleles with the primers GAPU-103 and DCA-9 to 5.0 alleles with U9932 and DCA-16. The smallest amplicon size observed was 50 bp with the primer DCA-16, whereas the largest one (450 bp) with the primer U9932. Cluster analysis with the unweighted pair group method with arithmetic average (UPGMA) showed three clusters: a cluster with four accessions from the ‘Nabali Baladi’ cultivar, another cluster with three accessions that represents the ‘Nabali Mohassen’ cultivar and finally the ‘Surri’ cultivar. The similarity coefficient for the eight olive tree samples ranged from a maximum of 100% between two accessions from Nabali Baladi and also in two other samples from Nabali Mohassan, to a minimum similarity coefficient (0.315) between the Surri and two Nabali Baladi accessions. The results in this investigation clearly highlight the genetic dissimilarity between the three main olive cultivars that have been misidentified and mixed up in the past, based on conventional morphological characters. PMID:26019564

  17. A set of highly informative rat simple sequence length polymorphism (SSLP markers and genetically defined rat strains

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    Yamasaki Ken-ichi

    2006-04-01

    Full Text Available Abstract Background The National Bio Resource Project for the Rat in Japan (NBRP-Rat is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI strains. To evaluate their value as models of human diseases, we are characterizing them using 109 phenotypic parameters, such as clinical measurements, internal anatomy, metabolic parameters, and behavioral tests, as part of the Rat Phenome Project. Here, we report on a set of 357 simple sequence length polymorphism (SSLP markers and 122 rat strains, which were genotyped by the marker set. Results The SSLP markers were selected according to their distribution patterns throughout the whole rat genome with an average spacing of 7.59 Mb. The average number of informative markers between all possible pairs of strains was 259 (72.5% of 357 markers, showing their high degree of polymorphism. From the genetic profile of these rat inbred strains, we constructed a rat family tree to clarify their genetic background. Conclusion These highly informative SSLP markers as well as genetically and phenotypically defined rat strains are useful for designing experiments for quantitative trait loci (QTL analysis and to choose strategies for developing new genetic resources. The data and resources are freely available at the NBRP-Rat web site 1.

  18. 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.

  19. Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya.

    Science.gov (United States)

    Chiu, C T; Wang, C W; Chen, F C; Chin, S W; Liu, C C; Lee, M J; Chung, W C; Chien, Y W; Chang, H J; Lee, C Y

    2015-03-30

    The papaya (Carica papaya L.) is one of the most important economic tropical fruits in the world, and the hermaphrodite is the preferred type in field cultures. We analyzed the sexual ratio of offspring from the cultivar 'Taiwan Seed Station No. 7' (T7) by a self-cross and its cross with Taichung Sunrise (TS). Female progeny from the T7 self-crossing were not observed. This finding may be caused by a lethal gene that is linked to females. In this study, we selected 192 simple sequence repeats (SSRs) to analyze the polymorphism between T7 and TS. A total of 37 SSRs were identified for T7 and TS. In addition, 14 SSRs served as the molecular makers for identification of T7, TS and their hybrid offsprings. Thus, the results show that the genetic similarity between T7 and TS is rather high. This suggests that T7 may be a mutant of TS. Phylogenetic analysis from the SSR polymorphisms of the above parent strains and 15 F1 offspring revealed the genetic distance of the F1 offspring located between T7 and TS. The results of this study may provide an opportunity for elucidating the genetic characteristics of all hermaphrodites via identification of molecular makers.

  20. 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

  1. Genetic Diversity of Arabica Coffee (Coffea arabica L. in Nicaragua as Estimated by Simple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Mulatu Geleta

    2012-01-01

    Full Text Available Coffea arabica L. (arabica coffee, the only tetraploid species in the genus Coffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT and the within-population gene diversity (HS were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13; P<0.001. The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved through ex situ conservation of a low number of populations from each variety.

  2. Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening

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    Channabasavaiah B. Gurumurthy

    2015-01-01

    Full Text Available Marker assisted speed congenics technique is commonly used to facilitate backcrossing of mouse strains in nearly half the time it normally takes otherwise. Traditionally, the technique is performed by analyzing PCR amplified regions of simple sequence length polymorphism (SSLP markers between the recipient and donor strains: offspring with the highest number of markers showing the recipient genome across all chromosomes is chosen for the next generation. Although there are well-defined panels of SSLP makers established between certain pairs of mice strains, they are incomplete for most strains. The availability of well-established marker sets for speed congenic screens would enable the scientific community to transfer mutations across strain backgrounds. In this study, we tested the suitability of over 400 SSLP marker sets among 10 mouse strains commonly used for generating genetically engineered models. The panel of markers presented here can readily identify the specified strains and will be quite useful in marker assisted speed congenic screens. Moreover, unlike newer single nucleotide polymorphism (SNP array methods which require sophisticated equipment, the SSLP markers panel described here only uses PCR and agarose gel electrophoresis of amplified products; therefore it can be performed in most research laboratories.

  3. Evaluation of genetic diversity amongst Descurainia sophia L. genotypes by inter-simple sequence repeat (ISSR) marker.

    Science.gov (United States)

    Saki, Sahar; Bagheri, Hedayat; Deljou, Ali; Zeinalabedini, Mehrshad

    2016-01-01

    Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.

  4. THE USE OF INTER SIMPLE SEQUENCE REPEATS (ISSR) IN DISTINGUISHING NEIGHBORING DOUGLAS-FIR TREES AS A MEANS TO IDENTIFYING TREE ROOTS WITH ABOVE-GROUND BIOMASS

    Science.gov (United States)

    We are attempting to identify specific root fragments from soil cores with individual trees. We successfully used Inter Simple Sequence Repeats (ISSR) to distinguish neighboring old-growth Douglas-fir trees from one another, while maintaining identity among each tree's parts. W...

  5. miREval 2.0: a web tool for simple microRNA prediction in genome sequences.

    Science.gov (United States)

    Gao, Dadi; Middleton, Robert; Rasko, John E J; Ritchie, William

    2013-12-15

    We have developed miREval 2.0, an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms. miREval 2.0 uses multiple published in silico approaches to detect miRNAs in sequences of interest. This tool can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data. http://mimirna.centenary.org.au/mireval/.

  6. Determining Phylogenetic Relationships Among Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Haider, Nadia

    2017-01-01

    Investigation of genetic variation and phylogenetic relationships among date palm (Phoenix dactylifera L.) cultivars is useful for their conservation and genetic improvement. Various molecular markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeat (SSR), representational difference analysis (RDA), and amplified fragment length polymorphism (AFLP) have been developed to molecularly characterize date palm cultivars. PCR-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) are powerful tools to determine the relatedness of date palm cultivars that are difficult to distinguish morphologically. In this chapter, the principles, materials, and methods of RAPD and ISSR techniques are presented. Analysis of data generated from these two techniques and the use of these data to reveal phylogenetic relationships among date palm cultivars are also discussed.

  7. KERAGAMAN GENETIK DRINGO (Acorus calamus L. YANG DIGUNAKAN SEBAGAI TUMBUHAN OBAT PADA BEBERAPA ETNIS DI INDONESIA BERDASARKAN INTER-SIMPLE SEQUENCE REPEATS (ISSR

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    Dyah Subositi

    2015-12-01

    Full Text Available Dringo (Acorus calamus L. used as medicinal plant in Indonesian ethnic groups. Those information based on Ristoja 2012 research. The objective of Ristoja was to provide a database of local ethnomedicine knowledge, herbal formula and medicinal plant in Indonesia. Inter Simple Sequence Repeats (ISSR markers were used to assess the genetic diversity of Dringo from 20 selected ethnic groups in Indonesia. Ten selected ISSR primers generated 82 amplified fragments with 51,2% were polymorphic. Dice coefficient was used to calculate similarity index and UPGMA was used to construct a dendogram. The genetic similarity index among accessions ranged from 76,7-100% thus indicating that low level of genetic diversity in dringo. Genetic diversity database can be useful for medicinal plant mapping and conservation especially for in situ conservation. Keywords: Dringo (Acorus calamus L., database, genetic diversity, Inter Simple Sequence Repeats (ISSR

  8. FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing.

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    Isaac Kinde

    Full Text Available Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair designed to amplify a discrete subset of repeated regions. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.

  9. Simple species identification of Trichinella isolates by amplification and sequencing of the 5S ribosomal DNA intergenic spacer region.

    Science.gov (United States)

    De Bruyne, Aymeric; Yera, Hélène; Le Guerhier, Franck; Boireau, Pascal; Dupouy-Camet, Jean

    2005-09-05

    We developed a PCR-based assay using a single primer pair to amplify the 5S ribosomal DNA intergenic spacer region to identify Trichinella isolates. In our method, amplified products are directly sequenced on both strands and compared to GenBank sequences. Using this method, we were able to identify Trichinella spiralis, T. britovi and T. nativa. This method permits rapid species identification of Trichinella isolates; however, further evaluation is required before recommending this approach for routine use.

  10. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

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    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  11. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Science.gov (United States)

    Atanassov, Ivan I; Atanassov, Ilian I; Etchells, J Peter; Turner, Simon R

    2009-01-01

    Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data. PMID:19863796

  12. A set of simple PCR markers converted from sequence specific RFLP markers on tomato Chromosomes 9 to 12

    NARCIS (Netherlands)

    Bai, Y.; Feng, X.; Hulst, van der R.G.M.; Lindhout, W.H.

    2004-01-01

    A set of 24 simple PCR markers was generated for tomato chromosomes 9, 10, 11 and 12. Polymorphism was sought for between Lycopersicon esculentum and one of six other Lycopersicon species (L. parviflorum, L. cheesmanii, L. hirsutum, L. pennellii, L. peruvianum, and L. chilense). PCR primers, which

  13. Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms Discovery for High Throughput Genotyping across the Species

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    José Miguel Blanca

    2011-07-01

    Full Text Available Melon ( L. ranks among the highest-valued fruit crops worldwide. Some genomic tools are available for this crop, including a Sanger transcriptome. We report the generation of 689,054 high-quality expressed sequence tags (ESTs from two 454 sequencing runs, using normalized and nonnormalized complementary DNA (cDNA libraries prepared from four genotypes belonging to the two subspecies and the main commercial types. 454 ESTs were combined with the Sanger available ESTs and de novo assembled into 53,252 unigenes. Over 63% of the unigenes were functionally annotated with Gene Ontology (GO terms and 21% had known orthologs of (L. Heynh. Annotation distribution followed similar tendencies than that reported for , suggesting that the dataset represents a fairly complete melon transcriptome. Furthermore, we identified a set of 3298 unigenes with microsatellite motifs and 14,417 sequences with single nucleotide variants of which 11,655 single nucleotide polymorphism met criteria for use with high-throughput genotyping platforms, and 453 could be detected as cleaved amplified polymorphic sequence (CAPS. A set of markers were validated, 90% of them being polymorphic in a number of variable accessions. This transcriptome provides an invaluable new tool for biological research, more so when it includes transcripts not described previously. It is being used for genome annotation and has provided a large collection of markers that will allow speeding up the process of breeding new melon varieties.

  14. Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood.

    Science.gov (United States)

    Lefterova, Martina I; Budvytiene, Indre; Sandlund, Johanna; Färnert, Anna; Banaei, Niaz

    2015-07-01

    Malaria is the leading identifiable cause of fever in returning travelers. Accurate Plasmodium species identification has therapy implications for P. vivax and P. ovale, which have dormant liver stages requiring primaquine. Compared to microscopy, nucleic acid tests have improved specificity for species identification and higher sensitivity for mixed infections. Here, we describe a SYBR green-based real-time PCR assay for Plasmodium species identification from whole blood, which uses a panel of reactions to detect species-specific non-18S rRNA gene targets. A pan-Plasmodium 18S rRNA target is also amplified to allow species identification or confirmation by sequencing if necessary. An evaluation of assay accuracy, performed on 76 clinical samples (56 positives using thin smear microscopy as the reference method and 20 negatives), demonstrated clinical sensitivities of 95.2% for P. falciparum (20/21 positives detected) and 100% for the Plasmodium genus (52/52), P. vivax (20/20), P. ovale (9/9), and P. malariae (6/6). The sensitivity of the P. knowlesi-specific PCR was evaluated using spiked whole blood samples (100% [10/10 detected]). The specificities of the real-time PCR primers were 94.2% for P. vivax (49/52) and 100% for P. falciparum (51/51), P. ovale (62/62), P. malariae (69/69), and P. knowlesi (52/52). Thirty-three specimens were used to test species identification by sequencing the pan-Plasmodium 18S rRNA PCR product, with correct identification in all cases. The real-time PCR assay also identified two samples with mixed P. falciparum and P. ovale infection, which was confirmed by sequencing. The assay described here can be integrated into a malaria testing algorithm in low-prevalence areas, allowing definitive Plasmodium species identification shortly after malaria diagnosis by microscopy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD and simple sequence repeat (SSR analyses

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    Fatih Mehmet Tok

    2016-09-01

    Full Text Available The genetic diversity and pathogenicity/virulence among 60 eggplant Sclerotinia sclerotiorum isolates collected from six different geographic regions of Turkey were analysed using mycelial compatibility groupings (MCGs, random amplified polymorphic DNA (RAPD and simple sequence repeat (SSR polymorphism. By MCG tests, the isolates were classified into 22 groups. Out of 22 MCGs, 36% were represented each by a single isolate. The isolates showed great variability for virulence regardless of MCG and geographic origin. Based on the results of RAPD and SSR analyses, 60 S. sclerotiorum isolates representing 22 MCGs were grouped in 2 and 3 distinct clusters, respectively. Analyses using RAPD and SSR markers illustrated that cluster groupings or genetic distance of S. sclerotiorum populations from eggplant were not distinctly relative to the MCG, geographical origin and virulence diversity. The patterns obtained revealed a high heterogeneity of genetic composition and suggested the occurrence of clonal and sexual reproduction of S. sclerotiorum on eggplant in the areas surveyed.

  16. Simple Machines Made Simple.

    Science.gov (United States)

    St. Andre, Ralph E.

    Simple machines have become a lost point of study in elementary schools as teachers continue to have more material to cover. This manual provides hands-on, cooperative learning activities for grades three through eight concerning the six simple machines: wheel and axle, inclined plane, screw, pulley, wedge, and lever. Most activities can be…

  17. A simple algorithm locates beta-strands in the amyloid fibril core of alpha-synuclein, Abeta, and tau using the amino acid sequence alone.

    Science.gov (United States)

    Zibaee, Shahin; Makin, O Sumner; Goedert, Michel; Serpell, Louise C

    2007-05-01

    Fibrillar inclusions are a characteristic feature of the neuropathology found in the alpha-synucleinopathies such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Familial forms of alpha-synucleinopathies have also been linked with missense mutations or gene multiplications that result in higher protein expression levels. In order to form these fibrils, the protein, alpha-synuclein (alpha-syn), must undergo a process of self-assembly in which its native state is converted from a disordered conformer into a beta-sheet-dominated form. Here, we have developed a novel polypeptide property calculator to locate and quantify relative propensities for beta-strand structure in the sequence of alpha-syn. The output of the algorithm, in the form of a simple x-y plot, was found to correlate very well with the location of the beta-sheet core in alpha-syn fibrils. In particular, the plot features three peaks, the largest of which is completely absent for the nonfibrillogenic protein, beta-syn. We also report similar significant correlations for the Alzheimer's disease-related proteins, Abeta and tau. A substantial region of alpha-syn is capable [corrected] of converting from its disordered conformation into a long [corrected] alpha-helical protein. We have developed the aforementioned algorithm to locate and quantify the alpha-helical hydrophobic moment in the amino acid sequence of alpha-syn. As before, the output of the algorithm, in the form of a simple x-y plot, was found to correlate very well with the location of alpha-helical structure in membrane bilayer-associated alpha-syn.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

    Science.gov (United States)

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    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.

  2. 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.

  3. Anisakis simplex complex: ecological significance of recombinant genotypes in an allopatric area of the Adriatic Sea inferred by genome-derived simple sequence repeats.

    Science.gov (United States)

    Mladineo, Ivona; Trumbić, Željka; Radonić, Ivana; Vrbatović, Anamarija; Hrabar, Jerko; Bušelić, Ivana

    2017-03-01

    The genus Anisakis includes nine species which, due to close morphological resemblance even in the adult stage, have previously caused many issues in their correct identification. Recently observed interspecific hybridisation in sympatric areas of two closely related species, Anisakis simplex sensu stricto (s.s.) and Anisakis pegreffii, has raised concerns whether a F1 hybrid generation is capable of overriding the breeding barrier, potentially giving rise to more resistant/pathogenic strains infecting humans. To assess the ecological significance of anisakid genotypes in the Adriatic Sea, an allopatric area for the two above-mentioned species, we analysed data from PCR-RFLP genotyping of the ITS region and the sequence of the cytochrome oxidase 2 (cox2) mtDNA locus to discern the parental genotype and maternal haplotype of the individuals. Furthermore, using in silico genome-wide screening of the A. simplex database for polymorphic simple sequence repeats or microsatellites in non-coding regions, we randomly selected potentially informative loci that were tested and optimised for multiplex PCR. The first panel of microsatellites developed for Anisakis was shown to be highly polymorphic, sensitive and amplified in both A. simplex s.s. and A. pegreffii. It was used to inspect genetic differentiation of individuals showing mito-nuclear mosaicism which is characteristic for both species. The observed low level of intergroup heterozygosity suggests that existing mosaicism is likely a retention of an ancestral polymorphism rather than a recent recombination event. This is also supported by allopatry of pure A. simplex s.s. and A. pegreffii in the geographical area under study. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  4. Genetic Variation in Safflower (Carthamus tinctorious L. for Seed Quality-Related Traits and Inter-Simple Sequence Repeat (ISSR Markers

    Directory of Open Access Journals (Sweden)

    Abdolmajid M. Rezaei

    2011-04-01

    Full Text Available Safflower (Carthamus tinctorious L. is an oilseed crop that is valued as a source of high quality vegetable oil. The genetic diversity of 16 safflower genotypes originated from different geographical regions of Iran and some with exotic origin were evaluated. Eight different seed quality-related traits including fatty acid composition of seed oil (stearic acid, palmitic acid, oleic acid and linoleic acid, the contents of, oil, protein, fiber and ash in its seeds, as well as 20 inter-simple sequence repeat (ISSR polymorphic primers were used in this study. Analysis of variance showed significant variation in genotypes for the seed quality-related traits. Based on ISSR markers, a total of 204 bands were amplified and 149 bands (about 70% of these were polymorphic. Cluster analysis based on either biochemical or molecular markers classified the genotypes into four groups, showing some similarities between molecular and biochemical markers for evaluated genotypes. A logical similarity between the genotype clusters based on molecular data with their geographical origins was observed.

  5. [Genetic diversity analysis of Fusarium oxysporum f. sp. cubense populations from China using Inter-Simple Sequence Repeats-PCR (ISSR-PCR) technique].

    Science.gov (United States)

    Zhang, He; Zhang, Xin; Pu, Jinji; Qi, Yanxiang; Lu, Ying; Yu, Qunfang; Zhang, Huiqiang; Xie, Yixian

    2015-06-04

    We used Inter-Simple Sequence Repeats (ISSR) markers to reveal the genetic diversity of 95 Fusarium oxysporum f. sp. cubense ( FOC ) isolates from banana in China, for the rational control of the disease. Eight primers were chosen for analyzing FOC isolates to study their genetic diversity by ISSR-PCR. All isolates were clustered using Unweighted Pair-Group Method with Arithmetic means (UPGMA) analysis by NTSYSpc v2.10e software. A total of 52 sites were generated, among them 92.3% were polymorphic. Genetic distance was 0.57 to 1.00 based on the Nei's standard. Isolates were grouped into six distinct clusters (A, B, C, D, E and F) based on ISSR analysis using a genetic distance threshold of 0.68, the proportion of 51.06%, 39.58%, 5.20%, 2.08%, 1.04%, and 1.04%, respectively. There were high levels of genetic variation among the FOC isolates, and the ISSR clustering groups had obvious correlation with hosts and races of the pathogen.

  6. [Simple sequence repeat variation and small-scale spatial autocorrelation analysis on smooth-shell populations of Oncomelania hupensis in Sichuan province].

    Science.gov (United States)

    Guo, Jun-tao; Zhou, Yi-biao; Zhang, Zhi-jie; Liu, Gang-ming; Yihuo, Wu-li; Wang, Hai-yin; Zhao, Gen-ming

    2009-05-01

    To analysis the spatial autocorrelation on the small-scale distribution of the genetic variation in the population of Oncomelania hupensis in Puge county, Sichuan province, using simple sequence repeat (SSR) marker. 5 pairs of SSR primer were used to amplify the genomic DNA of Oncomelania hupensis, and the alleles with frequency ranging from 15% to 85% were used to calculate Moran's I spatial autocorrelation coefficients in 14 distance band based on equal numbers of paired samples. A total of 274 alleles were scored by 5 pairs of SSR primer, the average polymorphic information content of the 274 alleles were 0.965 which indicated a high level of genetic diversity. 39 alleles showed different patterns of positive spatial autocorrelation of genetic variation, which was non-random spatial structure. When the distance band increased, the spatial auto-correlativity decreased based on the average Moran's I value at 14 distance band. The alleles which showed a negative spatial autocorrelation were not found in any distance band. The spatial distribution of the genetic variation of SSR showed positive spatial autocorrelation in the population of Oncomelania hupensis, and the spatial auto-correlativity decreased with the increase of distance band.

  7. 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.

  8. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Genomic instability measured by inter-(simple sequence repeat) PCR and high-resolution microsatellite instability are prognostic of colorectal carcinoma survival after surgical resection.

    Science.gov (United States)

    Brenner, Bruce M; Swede, Helen; Jones, Beth A; Anderson, Garth R; Stoler, Daniel L

    2012-01-01

    During the multiyear progression to colorectal cancer, numerous genomic alterations arise in events ranging from single base mutations to gains or losses of entire chromosomes. A single genetic change might not stand out as an independent predictor of outcome. The goal of this study was to determine if more comprehensive measurements of genomic instability provide clinically relevant prognostic information. Our study included 65 sporadic colorectal cancer patients diagnosed from 1987 to 1991 with last follow-up ascertained in 2006. We estimated an overall tally of alterations using the genome-wide sampling technique of inter-(simple sequence repeat [SSR]) polymerase chain reaction (PCR), and evaluated its relationship with all-cause survival. We also extended and sensitized the Bethesda criteria for microsatellite instability (MSI), by analyzing 348 microsatellite markers instead of the normal five. We expanded the MSI categories into four levels: MSI stable (MSS), very low-level MSI, moderately low-level MSI, and classical high-level MSI. Tumors with genomic instability above the median value of 2.6% as measured by inter-SSR PCR, were associated with far greater risk of death compared to tumors with lower levels of genomic instability. Adverse outcome was most pronounced for patients presenting with stage 3 disease. A gradient of increased survival was observed across increasing MSI levels but did not reach statistical significance. Our findings suggest genomic instabilities quantified by inter-SSR PCR and increased precision in MSI values may be clinically useful tools for estimating prognosis in colorectal cancer.

  10. The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

    Science.gov (United States)

    2011-01-01

    Background Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested. Results From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%), Vigna (25.9%), Glycine (19.8%), Medicago (10.2%), Dipterix (6%) and Arachis (1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM. Conclusions A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to

  11. 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

  12. Genetic diversity of Centella asiatica in China analyzed by inter-simple sequence repeat (ISSR) markers: combination analysis with chemical diversity.

    Science.gov (United States)

    Zhang, Xiao-Gang; Han, Ting; He, Zhi-Gao; Zhang, Qiao-Yan; Zhang, Lei; Rahman, Khalid; Qin, Lu-Ping

    2012-01-01

    Centella asiatica is an important plant species used in traditional Chinese medicine. To help the efficient use and conservation of this species, the genetic diversity of C. asiatica populations in China was investigated using inter-simple sequence repeat (ISSR) markers. Fourteen natural populations comprising 162 individuals were included to estimate genetic diversity. At the species level, genetic diversity was relatively high (P = 66.33%, H = 0.2183, I = 0.3305). At the population level, the genetic diversity of JH (Jinhua, Zhejiang Province, China) and JJ (Jiujiang, Jiangxi Province, China) populations was relatively high (P = 43.88%, 38.78%, H = 0.1610, 0.1301, I = 0.2376, 0.1957, respectively), whereas the genetic diversity of GA (Guang'an, Sichuan Province, China) and EM (E'mei, Sichuan Province, China) was relatively low (P = 10.2%, 5.1%, H = 0.0383, 0.0211, I = 0.0570, 0.0309, respectively). On the basis of Nei's G(st) value, more genetic differentiation among populations was determined (G(st) = 0.6573). In addition, the 14 populations were clustered into four groups in view of abundant ISSR data, which further defined the genetic relationship among populations. Interestingly, the genetic clustering result was similar to previous chemical clustering results based on high-performance liquid chromatography (HPLC) data, which would also classify the 14 populations into four groups. Thus, we combined the clustering results and compared their difference. The combined analysis and genetic diversity data provide a scientific basis for conserving populations of relatively high genetic diversity such as JH and JJ populations and establishing good agricultural practices (GAP) for C. asiatica.

  13. Identification of a major quantitative trait locus conditioning resistance to greenbug biotype E in sorghum PI 550610 using simple sequence repeat markers.

    Science.gov (United States)

    Wu, Y Q; Huang, Yinghua; Porter, David R; Tauer, C G; Hollaway, Lindsey

    2007-10-01

    Greenbug, Schizaphis graminum (Rondani), represents the most important pest insect of sorghum, Sorghum bicolor (L.) Moench, in the Great Plains of the United States. Biotype E is the most widespread and dominant type not only in sorghum and wheat, Triticum aestivum L., fields, but also on many noncultivated grass species. This study was designed to determine sorghum accession PI 550610 resistance to greenbug biotype E, to map the resistance quantitative trait loci (QTLs) by using an established simple sequence repeat (SSR) linkage map and to identify SSR markers closely linked to the major resistance QTLs. In greenhouse screening tests, seedlings of PI 550610 showed strong resistance to the greenbug at a level similar to resistant accession PI550607. For QTL mapping, one F2 population containing 277 progeny and one population containing 233 F2:3 families derived from Westland A line x PI 550610 were used to genotype 132 polymorphic SSR markers and to phenotype seedling resistance to greenbug feeding. Phenotypic evaluation of sorghum seedling damage at 7, 12, 17, and 21 d postinfestation in the F2:3 families revealed that resistance variation was normally distributed. Single marker analysis indicated 16 SSRs spread over five chromosomes were significant for greenbug resistance. Composite interval and multiple interval mapping procedures indicated that a major QTL resided in the interval of 6.8 cM between SSR markers Xtxp358 and Xtxp289 on SBI-09. The results will be valuable in the development of new greenbug biotype E resistant sorghum cultivars and for the further characterization of major genes by map-based cloning.

  14. A Survey of Agreement Rate between Simple MTC and Post Contrast T1 Sequence MRI for Diagnosing Active Multiple Sclerosis Plaques

    Directory of Open Access Journals (Sweden)

    N. Farshchian

    2016-07-01

    Full Text Available Introduction & Objective: MS is the most common disabling neurological disorder. Identifying new active MS plaques at the onset and clinical status and faster onset of treatment as well as evaluating the response to treatment is important and MRI with contrast is the best indicator for these measures. Materials & Methods: This study was cross-sectional including 62 patients with diagnosed MS. Whose clinical symptoms suggested the recurrence of MS. They were referred to the radiol-ogy department to undergo brain MRI with injection for the diagnosis of active plaques by a neurologist,The Data were analyzed using statistical tests and SPSS 21 software. Results: Based on the sequences of post contrast T1, pre contrast MTC and post contrast MTC 74, 272 and 271 plaques were respectively discovered. Detection of active MS plaques on T1 sequences after injection were in poor accordance and had significant difference with MTC before and after injection. Moreover, detection of active MS plaques on MTC sequences be-fore injection were in good accordance and did not show significant difference with MTC se-quences after injection. Conclusion: Based on these results, it seems that the purpose of MRI in MS patients is deter-mining the amount of active plaques. Sequences of pre contrast and post contrast MTC are significantly more than sequences of post contrast T1. Therefore, using sequences of MTC can be helpful in MRI. (Sci J Hamadan Univ Med Sci 2016; 23 (2:97-102

  15. Simple machines

    CERN Document Server

    Graybill, George

    2007-01-01

    Just how simple are simple machines? With our ready-to-use resource, they are simple to teach and easy to learn! Chocked full of information and activities, we begin with a look at force, motion and work, and examples of simple machines in daily life are given. With this background, we move on to different kinds of simple machines including: Levers, Inclined Planes, Wedges, Screws, Pulleys, and Wheels and Axles. An exploration of some compound machines follows, such as the can opener. Our resource is a real time-saver as all the reading passages, student activities are provided. Presented in s

  16. Oligoribonucleotide (ORN interference-PCR (ORNi-PCR: a simple method for suppressing PCR amplification of specific DNA sequences using ORNs.

    Directory of Open Access Journals (Sweden)

    Naoki Tanigawa

    Full Text Available Polymerase chain reaction (PCR amplification of multiple templates using common primers is used in a wide variety of molecular biological techniques. However, abundant templates sometimes obscure the amplification of minor species containing the same primer sequences. To overcome this challenge, we used oligoribonucleotides (ORNs to inhibit amplification of undesired template sequences without affecting amplification of control sequences lacking complementarity to the ORNs. ORNs were effective at very low concentrations, with IC50 values for ORN-mediated suppression on the order of 10 nM. DNA polymerases that retain 3'-5' exonuclease activity, such as KOD and Pfu polymerases, but not those that retain 5'-3' exonuclease activity, such as Taq polymerase, could be used for ORN-mediated suppression. ORN interference-PCR (ORNi-PCR technology should be a useful tool for both molecular biology research and clinical diagnosis.

  17. A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts.

    Science.gov (United States)

    Sasaki, Tadamasa; Yukawa, Yasushi; Wakasugi, Tatsuya; Yamada, Kyoji; Sugiura, Masahiro

    2006-09-01

    RNA editing is found in various transcripts from land plant chloroplasts. In tobacco chloroplasts, C-to-U conversion occurs at 36 specific sites including two sites identified in this work. Our RNA editing assay system using chloroplast extracts facilitated biochemical analyses of editing reactions but required mRNAs labeled with (32)P at specific sites. Here, we have improved the in vitro system using fluorescence-labeled chain terminators, ddGTP and ddATP, and have measured the editing activity at 19 sites in ndh transcripts. Editing activities varied from site to site. It has been reported that one editing site in ndhA mRNAs is present in spinach but absent in tobacco, but a corresponding editing capacity had been found in vivo in tobacco using biolistic transformation. We confirmed biochemically the existence of this activity in tobacco extracts. Using the non-radioactive assay, we examined sequences essential for editing within a 50-nt mRNA region encompassing an editing site. Editing of the ndhB-2 site requires a short sequence in front of the editing site, while that of the ndhF mRNA requires two separate regions, a sequence surrounding the editing site and a 5' distal sequence. These results suggest that distinct editing mechanisms are present in chloroplasts.

  18. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

    Directory of Open Access Journals (Sweden)

    Brad Thomas Townsley

    2015-05-01

    Full Text Available Next Generation Sequencing (NGS is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE libraries and can easily extend to full transcript coverage shotgun (SHO type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

  19. Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don.

    Science.gov (United States)

    Kumar, Santosh; Shah, Niraj; Garg, Vanika; Bhatia, Sabhyata

    2014-06-01

    Transcriptomic data of C. roseus offering ample sequence resources for providing better insights into gene diversity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful amplification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.

  20. High-speed and high-accuracy DNA sequencing by capillary gel electrophoresis in a simple, low cost instrument. Two-color peak-height encoded sequencing at 40 degrees C.

    Science.gov (United States)

    Lu, H; Arriaga, E; Chen, D Y; Dovichi, N J

    1994-10-07

    A low-cost DNA sequencer was constructed based on a single helium-neon laser. The two-color peak-height encoded sequencing protocol, based on the use of T7 DNA polymerase in a manganese buffer, was used to generate samples. Two termination reactions were performed. In the first, a TAMRA (applied Biosystems)-labeled primer was extended in the presence of ddATP and ddCTP. The amounts of dideoxynucleotides were adjusted to produce a 3:1 peak height ratio. Similarly, a ROX (Applied Biosystems)-labeled primer was extended in the presence of ddGTP and ddTTP; the amounts of dideoxynucleotides was adjusted to produce a 3:1 peak height ratio. The pooled fragments were separated on a 4% T LongRanger gel operated at 39 degrees C. Over 500 bases of sequence were generated in 50 min.

  1. Development of a SCAR marker by inter-simple sequence repeat for diagnosis of dwarf bunt of wheat and detection of Tilletia controversa KüHN.

    Science.gov (United States)

    Gao, L; Chen, W Q; Liu, T G

    2010-05-01

    Dwarf bunt of wheat, caused by Tilletia controversa KüHN: , is a destructive disease on wheat as well as an important internationally quarantined disease in many countries. The primer ISSR818 generated a polymorphic pattern displaying a 867-bp DNA fragment specific for T. controversa. The marker was converted into a sequence characterized amplified region (SCAR), and specific primers (TCKSF3/TCKSR3) designed for use in PCR detection assays; they amplified a unique DNA fragment in all isolates of T. controversa but not in the related pathogens. The detection limit with the primer set (TCKSF3/TCKSR3) was 5 ng of DNA which could be obtained from 5.5 microg of teliospores in a 25-microL PCR reaction mixture.

  2. A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC libraries using High Resolution Melt analysis

    Directory of Open Access Journals (Sweden)

    Caligari Peter DS

    2010-05-01

    Full Text Available Abstract Background The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. Results Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR and High Resolution Melt (HRM analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. Conclusions A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes.

  3. Heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides

    Energy Technology Data Exchange (ETDEWEB)

    Song, Guo-Zhu; Zhang, Mei; Ai, Qing; Yang, Guo-Jian [Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875 (China); Alsaedi, Ahmed; Hobiny, Aatef [NAAM-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia); Deng, Fu-Guo, E-mail: fgdeng@bnu.edu.cn [Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875 (China); NAAM-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia)

    2017-03-15

    We propose a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We show the details by implementing nonlocal entanglement generation, entanglement swapping, and entanglement purification modules with atoms in waveguides, and discuss the feasibility of the repeater with currently achievable technology. In our scheme, the faulty events can be discarded by detecting the polarization of the photons. That is, our protocols are accomplished with a fidelity of 100% in principle, which is advantageous for implementing realistic long-distance quantum communication. Moreover, additional atomic qubits are not required, but only a single-photon medium. Our scheme is scalable and attractive since it can be realized in solid-state quantum systems. With the great progress on controlling atom-waveguide systems, the repeater may be very useful in quantum information processing in the future.

  4. Heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides

    Science.gov (United States)

    Song, Guo-Zhu; Zhang, Mei; Ai, Qing; Yang, Guo-Jian; Alsaedi, Ahmed; Hobiny, Aatef; Deng, Fu-Guo

    2017-03-01

    We propose a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We show the details by implementing nonlocal entanglement generation, entanglement swapping, and entanglement purification modules with atoms in waveguides, and discuss the feasibility of the repeater with currently achievable technology. In our scheme, the faulty events can be discarded by detecting the polarization of the photons. That is, our protocols are accomplished with a fidelity of 100% in principle, which is advantageous for implementing realistic long-distance quantum communication. Moreover, additional atomic qubits are not required, but only a single-photon medium. Our scheme is scalable and attractive since it can be realized in solid-state quantum systems. With the great progress on controlling atom-waveguide systems, the repeater may be very useful in quantum information processing in the future.

  5. (SSR) and inter simple sequence repeat (ISSR)

    African Journals Online (AJOL)

    Cotton is one of the main economic crop plants of Iran cultivated under continuous artificial selection and cultivation which may lead to genetic erosion and possible loss of useful genetic loci resulting in vulnerability to pests and diseases. For this reason increasing and improving the amount of genetic diversity in cotton ...

  6. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Prakash

    alpha-ketoglutaratedecarboxylase, LpqZ, malatedehydrogenase. 289-290. 0.72. +. 7. 4 acyl-CoAsynthase ... proteasome[beta]-typesubunit2, proteasome[alpha]- typesubunit1. 164-165. 0.56. -. 1. 1. 198-199. 0.55 .... PE_PGRS (15840909), cytochrome c oxidase folding protein (15840911), PE_PGRS (15840912), quinone.

  7. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccharum spp.) breeding lines. Kittipat Ukoskit1*, Penjun Thipmongkolcharoen1 and Prasert Chatwachirawong2. 1Department of Biotechnology, Faculty of Science and Technology, ...

  8. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    2006-12-18

    Dec 18, 2006 ... 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 ...

  9. SIMPLE SEQUENCE REPEAT MARKERS ASSOCIATED WITH ...

    African Journals Online (AJOL)

    ACSS

    Transgressive segregation was observed, indicating that both parents carried minor loci or alleles for resistance that differed from each other. SSRs Xtxp25,. Xtxp201, Xtxp302, Xtxp25, Xtxp295 and Xtxp95 were associated, respectively, with anthracnose and TLB resistance, consistent with dominant epistasis gene action.

  10. Investigation of simple sequence repeats (SSR) markerassisted ...

    African Journals Online (AJOL)

    The unweighed pair-group method with arithmetic averages (UPGMA) dendrogram placed Bt- and non-Bt cotton varieties into four major groups. With the exception of 4 accessions (being similar), genetic dissimilarity coefficient among all other genotypes ranged from 0.50 to 0.98 suggesting a wide genetic heterogeneity ...

  11. (SSR) and inter simple sequence repeat (ISSR)

    African Journals Online (AJOL)

    MRT

    2012-07-12

    Jul 12, 2012 ... Key words: Cotton, genetic diversity, ISSR, RAPD. INTRODUCTION. Production of new genetic variants in crop plants is one of the possible sources of obtaining elite genotypes to be. *Corresponding author. E-mail: msheidai@yahoo.com, msheidai@sbu.ac.ir. Tel: +98 21 22431664. Fax: +98 21. 22431664 ...

  12. Abundance, composition and distribution of simple sequence ...

    Indian Academy of Sciences (India)

    Author Affiliations. Malathi Shekar1 Indrani Karunasagar1 Iddya Karunasagar1. Department of Fishery Microbiology, UNESCO Centre for Marine Biotechnology, Karnataka Veterinary, Animal and Fishery Sciences University, College of Fisheries, Mangalore 575 002, India ...

  13. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map

    Energy Technology Data Exchange (ETDEWEB)

    Kelleher, Colin [University of British Columbia, Vancouver; CHIU, Dr. R. [Genome Sciences Centre, Vancouver, BC, Canada; Shin, Dr. H. [Genome Sciences Centre, Vancouver, BC, Canada; Krywinski, Martin [Genome Sciences Centre, Vancouver, BC, Canada; Fjell, Chris [Genome Sciences Centre, Vancouver, BC, Canada; Wilkin, Jennifer [University of British Columbia, Vancouver; Yin, Tongming [ORNL; Difazio, Stephen P. [West Virginia University

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 {+-} 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  14. Probabilistic simple sticker systems

    Science.gov (United States)

    Selvarajoo, Mathuri; Heng, Fong Wan; Sarmin, Nor Haniza; Turaev, Sherzod

    2017-04-01

    A model for DNA computing using the recombination behavior of DNA molecules, known as a sticker system, was introduced by by L. Kari, G. Paun, G. Rozenberg, A. Salomaa, and S. Yu in the paper entitled DNA computing, sticker systems and universality from the journal of Acta Informatica vol. 35, pp. 401-420 in the year 1998. A sticker system uses the Watson-Crick complementary feature of DNA molecules: starting from the incomplete double stranded sequences, and iteratively using sticking operations until a complete double stranded sequence is obtained. It is known that sticker systems with finite sets of axioms and sticker rules generate only regular languages. Hence, different types of restrictions have been considered to increase the computational power of sticker systems. Recently, a variant of restricted sticker systems, called probabilistic sticker systems, has been introduced [4]. In this variant, the probabilities are initially associated with the axioms, and the probability of a generated string is computed by multiplying the probabilities of all occurrences of the initial strings in the computation of the string. Strings for the language are selected according to some probabilistic requirements. In this paper, we study fundamental properties of probabilistic simple sticker systems. We prove that the probabilistic enhancement increases the computational power of simple sticker systems.

  15. Genetic variation in oriental tobacco (Nicotiana tabacum L. by agro-morphological traits and simple sequence repeat markers Variação genética em tabaco oriental (Nicotiana tabacum L. por marcadores agro-morfológicos e traços simples de repetição de sequência

    Directory of Open Access Journals (Sweden)

    Reza Darvishzadeh

    2013-06-01

    Full Text Available The objectives of this study were to assess genetic diversity and determine differences between several oriental tobacco genotypes by examining both agro-morphological traits and molecular markers. Simple lattice design with two replications was used to evaluate 100 oriental tobacco genotypes. Analysis of variance manifested that there is high level of genetic diversity in oriental-type tobaccos based on morphological traits including number of leaf, days to 50% flowering, leaf length, leaf width, leaf fresh weight, leaf dry weight, stem height and stem girth. Classification of genotypes using agro-morphological data by means of un-weighted pair-group method using arithmetic average (UPGMA algorithm based on squared standardized Euclidean distances resulted four distinguishable groups that pursuit own geographical distribution. In the molecular marker investigations, a total of 13 simple sequence repeats (SSR primer pairs were used to determine polymorphism of the test germplasm. Thirty five alleles were scored at 13 SSR loci. The average number of alleles per locus (na and the effective allele number (Ae were 2.69 and 2.34, respectively. By using SSR data, pair wise Jaccard's similarity coefficients were produced. Grouping of genotypes via Jaccard's similarity coefficients and using UPGMA clustering method lead to three groups that had not any accommodated with own origins. Results reveled that there is not completely agreement for classification based on agro-morphological and SSR loci in oriental-type tobaccos. Because of non influence of environmental effects on molecular marker, heterotic groups based on SSR markers could be closer to reality.Os objetivos deste estudo foram avaliar a diversidade genética e determinar as diferenças entre diversos genótipos de tabaco oriental através tratos morfológicos e marcadores moleculares. O delineamento utilizado foi o látice simples com duas repetições e foram avaliados 100 genótipos de

  16. Molecular characterisation and similarity relationships among iranian basil (Ocimum basilicum L. accessions using inter simple sequence repeat markers Caracterização molecular de acessos de Ocimum basilicum L. por meio de marcadores ISSR

    Directory of Open Access Journals (Sweden)

    Mohammad Aghaei

    2012-06-01

    Full Text Available The study of genetic relationships is a prerequisite for plant breeding activities as well as for conservation of genetic resources. In the present study, genetic diversity among 50 Iranian basil (Ocimum basilicum L. accessions was determined using inter simple sequence repeat (ISSR markers. Thirty-eight alleles were generated at 12 ISSR loci. The number of alleles per locus ranged from 1 to 5 with an average of 3.17. The maximum number of alleles was observed at the A7, 818, 825 and 849 loci, and their size ranged from 300 to 2500 bp. A similarity matrix based on Jaccard's coefficient for all 50 basil accessions gave values from 1.00-0.60. The maximum similarity (1.00 was observed between the "Urmia" and "Shahr-e-Rey II" accessions as well as between the "Urmia" and "Qazvin II" accessions. The lowest similarity (0.60 was observed between the "Tuyserkan I" and "Gom II" accessions. The unweighted pair- group method using arithmetique average UPGMA clustering algorithm classified the studied accessions into three distinct groups. All of the basil accessions, with the exception of "Babol III", "Ahvaz II", "Yazd II" and "Ardebil I", were placed in groups I and II. Leaf colour was a specific characteristic that influenced the clustering of Iranian basil accessions. Because of this relationship, the results of the principal coordinate analysis (PCoA approximately corresponded to those obtained through cluster analysis. Our results revealed that the geographical distribution of genotypes could not be used as a basis for crossing parents to obtain high heterosis, and therefore, it must be carried out by genetic studies.O estudo das relações genéticas é um pré-requisito para atividades em reprodução de plantas assim como para conservação de recursos genéticos. Neste trabalho a diversidade genética entre 50 acessos de Manejericão Iraniano (Ocimum basilicum L. foram determinadas usando marcadores de Seqüência Simples Repetida Interna (ISSR

  17. Unique TTC repeat base pair loss mutation in cases of pure neural leprosy: A survival strategy of Mycobacterium leprae?

    Directory of Open Access Journals (Sweden)

    Abhishek De

    2015-01-01

    Full Text Available Background: Genomic reduction helps obligate intracellular microbes to survive difficult host niches. Adaptation of Mycobacterium leprae in cases of pure neural leprosy (PNL in the intracellular niche of peripheral nerves can be associated with some gene loss. Recently, a stable but variable number of tandem repefzats (TTC have been reported in strains of M. leprae. FolP and rpoB genes are the two common mutation sites which deal with the susceptibility of the bacteria to drugs. Aim: We attempted to find if genomic reduction of M. leprae in context of these TTC repeats or mutations in folP1 and rpoB can be the reason for the restriction of M. leprae in the nerves in PNL. Materials and Methods: DNA extracts taken from fine needle aspiration of affected nerves of 24 PNL cases were studied for tandem repeats with 21TTC primer in multiplex-PCR. Mutations were also studied by PCR Amplification of SRDR (Sulphone Resistance Determining Region of the folP1 and multiple primer PCR amplification refractory mutation system (MARS of the rpoB. Results: Of the 24 PNL, only 1 patient showed mutation in the rpoB gene and none in the folp1 gene. Studying the mutation in TTC region of the M. leprae gene we found that all the cases have a loss of a few bases in the sequence. Conclusion: We can conclude that there is consistent loss in the bases in the TTC region in all cases of pure neural Hansen and we postulate that it may be an adaptive response of the bacteria to survive host niche resulting in its restriction to peripheral nerves.

  18. Outcrossing rate in olive assessed by microsatellite and inter simple ...

    African Journals Online (AJOL)

    Olive is known to be an allogamous species. The aim of this study was to estimate the magnitude of cross-pollination rate using microsatellite simple sequence repeats (SSR) and inter simple sequence repeats (ISSR) molecular markers in olive genotypes. The DNA from maternal plants and 23 progenies of two different ...

  19. DNA Sequencing in Undergraduate Laboratory Courses.

    Science.gov (United States)

    Hamilton, Robert G.

    1997-01-01

    Discusses strategies to duplicate current research protocols using biochemical methods of analysis. Describes the use of the Silver Sequence kit that provides a technically simple and relatively inexpensive DNA sequencing exercise. (JRH)

  20. Simple Machine Junk Cars

    Science.gov (United States)

    Herald, Christine

    2010-01-01

    During the month of May, the author's eighth-grade physical science students study the six simple machines through hands-on activities, reading assignments, videos, and notes. At the end of the month, they can easily identify the six types of simple machine: inclined plane, wheel and axle, pulley, screw, wedge, and lever. To conclude this unit,…

  1. A Simple View of Writing in Chinese

    Science.gov (United States)

    Yeung, Pui-sze; Ho, Connie Suk-han; Chan, David Wai-ock; Chung, Kevin Kien-hoa

    2017-01-01

    This study examined the Chinese written composition development of elementary-grade students in relation to the simple view of writing. Measures of nonverbal reasoning ability, component skills of transcription (stroke sequence knowledge, word spelling, and handwriting fluency), oral language (definitional skill, oral narrative skills, and…

  2. Desflurane consumption during automated closed-circuit delivery is higher than when a conventional anesthesia machine is used with a simple vaporizer-O2-N2O fresh gas flow sequence

    Directory of Open Access Journals (Sweden)

    Sosnowski Maurice

    2008-07-01

    Full Text Available Abstract Background The Zeus® (Dräger, Lübeck, Germany, an automated closed-circuit anesthesia machine, uses high fresh gas flows (FGF to wash-in the circuit and the lungs, and intermittently flushes the system to remove unwanted N2. We hypothesized this could increase desflurane consumption to such an extent that agent consumption might become higher than with a conventional anesthesia machine (Anesthesia Delivery Unit [ADU®], GE, Helsinki, Finland used with a previously derived desflurane-O2-N2O administration schedule that allows early FGF reduction. Methods Thirty-four ASA PS I or II patients undergoing plastic, urologic, or gynecologic surgery received desflurane in O2/N2O. In the ADU group (n = 24, an initial 3 min high FGF of O2 and N2O (2 and 4 L.min-1, respectively was used, followed by 0.3 L.min-1 O2 + 0.4 L.min-1 N2O. The desflurane vaporizer setting (FD was 6.5% for the first 15 min, and 5.5% during the next 25 min. In the Zeus group (n = 10, the Zeus® was used in automated closed circuit anesthesia mode with a selected end-expired (FA desflurane target of 4.6%, and O2/N2O as the carrier gases with a target inspired O2% of 30%. Desflurane FA and consumption during the first 40 min were compared using repeated measures one-way ANOVA. Results Age and weight did not differ between the groups (P > 0.05, but patients in the Zeus group were taller (P = 0.04. In the Zeus group, the desflurane FA was lower during the first 3 min (P 0.05, and slightly higher after 4 min (P A between the two groups. Conclusion Agent consumption with an automated closed-circuit anesthesia machine is higher than with a conventional anesthesia machine when the latter is used with a specific vaporizer-FGF sequence. Agent consumption during automated delivery might be further reduced by optimizing the algorithm(s that manages the initial FGF or by tolerating some N2 in the circuit to minimize the need for intermittent flushing.

  3. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  4. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  5. Simple guide to Skype

    CERN Document Server

    Winter, Rick

    2013-01-01

    Simple Guides give you Just the Facts Get up to speed with Skypefast! Simple Guides: get you started quickly. No extra clutter, no extra reading. Learn how to set up Skype, as well as how to add and set up all your friends, family, and other contacts. Find out about all the features of Skype, how to change views, set your status and conduct video and audio only calls. Learn about all the different things you can do to contact your friends and family on Skype for free, and start having fun!

  6. Droids Made Simple

    CERN Document Server

    Mazo, Gary

    2011-01-01

    If you have a Droid series smartphone - Droid, Droid X, Droid 2, or Droid 2 Global - and are eager to get the most out of your device, Droids Made Simple is perfect for you. Authors Martin Trautschold, Gary Mazo and Marziah Karch guide you through all of the features, tips, and tricks using their proven combination of clear instructions and detailed visuals. With hundreds of annotated screenshots and step-by-step directions, Droids Made Simple will transform you into a Droid expert, improving your productivity, and most importantly, helping you take advantage of all of the cool features that c

  7. Excel 2010 Made Simple

    CERN Document Server

    Katz, Abbott

    2011-01-01

    Get the most out of Excel 2010 with Excel 2010 Made Simple - learn the key features, understand what's new, and utilize dozens of time-saving tips and tricks to get your job done. Over 500 screen visuals and clear-cut instructions guide you through the features of Excel 2010, from formulas and charts to navigating around a worksheet and understanding Visual Basic for Applications (VBA) and macros. Excel 2010 Made Simple takes a practical and highly effective approach to using Excel 2010, showing you the best way to complete your most common spreadsheet tasks. You'll learn how to input, format,

  8. A Simple Hydrogen Electrode

    Science.gov (United States)

    Eggen, Per-Odd

    2009-01-01

    This article describes the construction of an inexpensive, robust, and simple hydrogen electrode, as well as the use of this electrode to measure "standard" potentials. In the experiment described here the students can measure the reduction potentials of metal-metal ion pairs directly, without using a secondary reference electrode. Measurements…

  9. (3) Simple processing method

    African Journals Online (AJOL)

    Adeyinka Odunsi

    Simple Processing Method for Recycling Poultry Waste into. Animal Feed Ingredient. *Komolafe, A. A. and Sonaiya, E. B. ... recycled and become consumables to livestock, thus entering the human food chain. Poultry waste is not ... on the concrete roof (20.5 m high) of the Faculty of Agriculture, Obafemi. Awolowo University ...

  10. DNA fingerprinting based on simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    New varieties of sugarcane are protected using morphological descriptors, which have limitations in identifying morphologically similar cultivars. Development of a reliable DNA fingerprint system for identification of new varieties would contribute greatly to the breeding of these species. Microsatellite markers are tools with ...

  11. Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated ...

    African Journals Online (AJOL)

    ONOS

    2010-08-09

    Aug 9, 2010 ... ed through interspecific hybridization of Asian and African rice, formed a cluster with Asian rice. Generally cultivated and wild species clearly observed to have separated groups in both UPGMA and neighbor joining analysis. The two methods showed almost the same tree topology with similar groupings ...

  12. Development of a simple sequence repeat (SSR) marker set to ...

    African Journals Online (AJOL)

    GREGORY

    2010-08-23

    Aug 23, 2010 ... Most of the potato cultivars grown in Turkey are of foreign origin and there are some local landrace varieties. Tuber seeds of most of these ... potato varieties used and only two are of Turkish origin. There are also some landraces ..... 0.171 configurations in 19 Spanish landraces. Relatively, low number of ...

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

    African Journals Online (AJOL)

    home

    2013-10-02

    Oct 2, 2013 ... To provide ready to use markers for back ground selection in marker assisted breeding of rice, we used. GPP 2 as donor parent for xa13, Xa21, Gm4 resistance to bacterial blight, gall midge and NLR 145 as another donor parent for Pi-kh gene resistance to blast and JGL 1798 as recurrent parent was.

  14. Analysis of Tunisian date palm germplasm using simple sequence ...

    African Journals Online (AJOL)

    We used genetic markers generated from selected ISSR primers to assess genetic diversity among a set of Tunisian date palm varieties. Seven primers were used to cluster 12 date palm varieties and 77 polymorphic markers were sufficient to identify all of the varieties. These discrete molecular markers were used to ...

  15. Using inter simple sequence repeat (ISSR) markers to study genetic ...

    African Journals Online (AJOL)

    enoh

    2012-04-10

    Apr 10, 2012 ... During the ISSR screening in this study, good amplification products were obtained from primers based on guanine-adenine (GA), cytosine-adenine. (CA) and guanine-adenine-adenine (GAA) ... This study reports the first application of the ISSR technique in characterization of Algerian pistachio cultivars ...

  16. Identification of informative simple sequence repeat (SSR) markers ...

    African Journals Online (AJOL)

    Phi080) to 0.79 (UMC2359), with a mean PIC of 0.53. The analysis also led to identification of informative SSR markers, namely UMC1862 (bin 1.11), UMC1719 (bin 4.10-4.11), UMC1447 (bin 5.03), UMC2359 (bin 9.07) and UMC1432 (bin 10.02), ...

  17. Random amplified polymorphic DNA (RAPD) and simple sequence ...

    African Journals Online (AJOL)

    To compare these two methods, genetic parameters were computed such as the number of polymorphic bands, average number of alleles per locus, effective number of alleles per locus, expected heterozygosity, effectiveness index of analysis and polymorphism information content (PIC). Better results were provided by ...

  18. Simple sequence repeat (SSR) markers for assessing genetic ...

    African Journals Online (AJOL)

    The highest polymorphic information content (PIC) value (more than 0.60) was observed for eight primers viz., AB 443, RM 3, RM 29, RM 226, RM 228, RM 304, RM 1812 and RM 3873 and average PIC value was 0.444. Cluster analysis using NTSYS generated dendrogram divided all the 56 parental lines into two distinct ...

  19. Application of inter simple sequence repeat (ISSR marker) to detect ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... toxicity in plants is to induce oxidative stress linked to oxidation of proteins and membrane lipids but also to alterations of DNA damage ... abnormalities are obtained in plant or animal systems. (Minissi and Lombi, 1997) and .... It is also used as a vegetable (and not just as a condiment), in the sense that ...

  20. feasibilty of zein proteins, simple sequence repeats and phenotypic

    African Journals Online (AJOL)

    journal

    Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT). 2005. Quality protein maize: Targets poorest in Africa. URL http:/ /www. cimmyt.org Accessed 9 September,. 2010. Coleman, C.E., Clore, A.M., Ranch, .J.P.,. Higgins, R., Lopes, M.A. and Larkins, B.A.. 1997. Expression of a mutant α-zein creates the floury-2 ...

  1. a stable simple sequence repeat marker for resistance to white ...

    African Journals Online (AJOL)

    ACSS

    Received 19 May, 2015; accepted 31 July, 2015). ABSTRACT. White mould, caused by Golovinomyces cichoracearum, is a major fungal disease of tobacco. Breeding for resistance to white mould is slow due to the intensive labour needed in artificial ...

  2. Use of simple sequence repeat (SSR) markers for screening blue ...

    African Journals Online (AJOL)

    African Journal of Biotechnology. Journal Home · ABOUT · Advanced Search · Current Issue · Archives · Journal Home > Vol 14, No 41 (2015) >. Log in or Register to get access to full text downloads.

  3. Chromosomal organization of simple sequence repeats in the ...

    Indian Academy of Sciences (India)

    ... 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 ...

  4. The use of simple sequence repeats markers to study genetic ...

    African Journals Online (AJOL)

    SERVER

    2007-07-18

    Jul 18, 2007 ... ctive management of genetic diversity, germplasm collec- tions need to be .... Studies by other workers have found QTLs on chromosome 2 to have .... 43. Control. E.2.2. B73. USA. 41 pd41. E.2.2. PHB 3253. PIONEER. 4 pa4. E.2.3. OSU 23i. CIMMYT-Ohio State. 7 pa7. E.2.3. TUXPENO SEQUIA. CIMMYT ...

  5. Inter simple sequence repeats (ISSR) and random amplified ...

    African Journals Online (AJOL)

    21 of 30 random amplified polymorphic DNA (RAPD) primers produced 220 reproducible bands with average of 10.47 bands per primer and 80.12% of polymorphism. OPR02 primer showed the highest number of effective allele (Ne), Shannon index (I) and genetic diversity (H). Some of the cultivars had specific bands, ...

  6. Use of simple sequence repeat (SSR) markers for screening blue ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-10-14

    Oct 14, 2015 ... Blue disease of cotton is an economically important disease of the crop first described from the Central. African Republic and spread to other countries. Brazil and other South American countries record crop losses of up to 80% from infection but no cases of the disease have been reported in Tanzania.

  7. Inter simple sequence repeat analysis of genetic diversity of five ...

    African Journals Online (AJOL)

    mallory

    2011-04-29

    Apr 29, 2011 ... Panama. PI209028 Puerto Rico. PI451762. Israel. PI244667 India. PI439378. Jamaica. PI281435 United States. PI640503. Australia. PI215736 Peru ... PI439325. Nicaragua. PI355395 Ecuador. PI566812. Mexico. PI640907 Nigeria. PI631135. Guatemala. PI406847 Honduras. PI631139. Guatemala.

  8. Simple sequence repeat (SSR) markers analysis of genetic diversity ...

    African Journals Online (AJOL)

    The correlation studies showed that seed coat color, anthocyanidin content, total phenol content, melanin content and flavonoid content in seed coat had significant negative correlation with oil content in different environments. The anthocyanidin content, flavonoid content, total phenol content and melanin content had ...

  9. Simple sequence repeat marker development and genetic mapping ...

    Indian Academy of Sciences (India)

    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.

  10. The use of simple sequence repeats markers to study genetic ...

    African Journals Online (AJOL)

    SERVER

    2007-07-18

    Jul 18, 2007 ... Forty-one genotypes comprising of collections from Kenya, International Maize and Wheat. Improvement .... Wheat Improvement Centre (CIMMYT), East African Regional Dis- ease Nursery .... 3.5. 3.5. 2.0. *P=Parents, I=Inbred line, C=Check, GLS= Gray leaf spot, E.T.=Turcicum leaf blight, Rust=Common.

  11. Simple sequence repeat (SSR) markers are effective for identifying ...

    African Journals Online (AJOL)

    The present study characterized and identified pear cultivars growing in the southern region of Minas Gerais State, Brazil, using microsatellite markers. Nineteen (19) pear cultivars were collected from two sites of Southern Minas Gerais State: Ribeirão Vermelho and Lavras. DNA was extracted from newly formed leaves and ...

  12. A Stable Simple Sequence Repeat Marker for Resistance to White ...

    African Journals Online (AJOL)

    White mould, caused by Golovinomyces cichoracearum, is a major fungal disease of tobacco. Breeding for resistance to white mould is slow due to the intensive labour needed in artificial screening and the huge effect of the environment. In order to improve selection efficiency, molecular markers need to be identified to ...

  13. feasibilty of zein proteins, simple sequence repeats and phenotypic

    African Journals Online (AJOL)

    journal

    SSR markers of BC1F2 (a) and BC2F2 (b) progeny on polyacrylamide gel visualised by silver staining. The SSRs are tagged to different chromosomes loci numbered in the top of the panel. Different alleles at the same loci are repre- sented by letters following the chromosome number (e.g. 5d). 1b 1c 1d 3b 3c 5b 5c 7a 7b ...

  14. The use of multiplexed simple sequence repeat (SSR) markers for ...

    African Journals Online (AJOL)

    ... NaCRRI, national crops resources research institute; RAPD, random amplified polymorphic DNA; AFLP, amplified fragment length polymorphisms; RFLP, restriction fragment length polymorphisms; SNP, single nucleotide polymorphisms; BAC, bacterial artificial chromosome; PAC, P1-derived artificial chromosome; PCR, ...

  15. Random amplified polymorphic DNA (RAPD) and simple sequence ...

    African Journals Online (AJOL)

    Administrator

    2011-06-06

    Jun 6, 2011 ... of polymorphic bands, average number of alleles per locus, effective .... Materials for DNA isolation were obtained from a set of 5 to 7 plants ..... Among factors that might have contributed to ... Inheritance of RAPDs in F1 hybrids of corn. ... by using cluster analysis of RAPD molecular marker, phenotype and.

  16. Polymorphism of the simple sequence repeat (AAC)5 in the ...

    Indian Academy of Sciences (India)

    2013-12-04

    Dec 4, 2013 ... Carvalho A., Guedes-Pinto H. and Lima-Brito J. 2011b Intergenic spacer length variants in old Portuguese bread wheat cultivars. J. Genet. 90, 203–208. Castilho A., Vershinin A. and Heslop-Harrison J. S. 2000 Repetitive. DNA and the chromosomes in the genome of oil palm (Elaeis guineensis). Ann. Bot.

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

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    Aug 28, 2012 ... Cambodia, South China and Central Asia. Mungbean is a. *Corresponding author. E-mail: neelu_jain25@yahoo.com. self pollinated diploid plant with 2n = 2x = 22 chromosomes and a genome size of 515 Mb/1C (Parida et al., 1990). Mungbean belongs to the Asian Vigna subgenus Ceratotropis with South ...

  18. Inter simple sequence repeat (ISSR) analysis of Ethiopian white ...

    African Journals Online (AJOL)

    The principal coordinates (PCO) analysis also recovered UPGMA and neighbor joining tree groups, although Amhara region white lupine were intermixed with each other. The genetic diversity among white lupine population considered in the present study indicated that Merawi was the highest (0.223) followed by Addis ...

  19. Development of a simple sequence repeat (SSR) marker set to ...

    African Journals Online (AJOL)

    GREGORY

    2010-08-23

    Aug 23, 2010 ... major potato breeding program, most of the varieties grown are of foreign origin. There are about 80 modern potato varieties used and only two are of Turkish origin. There are also some landraces grown in Turkey. Most of the landraces have not been characterized based on molecular biology techniques ...

  20. Simple Hofmeister series

    NARCIS (Netherlands)

    Lyklema, J.

    2009-01-01

    Hofmeister, or lyotropic, series date back to 1888, when the founder arranged a large number of electrolytes in sequences with respect to their effectiveness salting out egg white. Since then the name has been applied to various phenomena involving ion specificity. In order to isolate effects

  1. Modern mathematics made simple

    CERN Document Server

    Murphy, Patrick

    1982-01-01

    Modern Mathematics: Made Simple presents topics in modern mathematics, from elementary mathematical logic and switching circuits to multibase arithmetic and finite systems. Sets and relations, vectors and matrices, tesselations, and linear programming are also discussed.Comprised of 12 chapters, this book begins with an introduction to sets and basic operations on sets, as well as solving problems with Venn diagrams. The discussion then turns to elementary mathematical logic, with emphasis on inductive and deductive reasoning; conjunctions and disjunctions; compound statements and conditional

  2. The simple complex numbers

    OpenAIRE

    Zalesny, Jaroslaw

    2008-01-01

    A new simple geometrical interpretation of complex numbers is presented. It differs from their usual interpretation as points in the complex plane. From the new point of view the complex numbers are rather operations on vectors than points. Moreover, in this approach the real, imaginary and complex numbers have similar interpretation. They are simply some operations on vectors. The presented interpretation is simpler, more natural, and better adjusted to possible applications in geometry and ...

  3. Information technology made simple

    CERN Document Server

    Carter, Roger

    1991-01-01

    Information Technology: Made Simple covers the full range of information technology topics, including more traditional subjects such as programming languages, data processing, and systems analysis. The book discusses information revolution, including topics about microchips, information processing operations, analog and digital systems, information processing system, and systems analysis. The text also describes computers, computer hardware, microprocessors, and microcomputers. The peripheral devices connected to the central processing unit; the main types of system software; application soft

  4. 7 CRITERIA FOR INTEGER SEQUENCES BEING GRAPHIC

    NARCIS (Netherlands)

    SIERKSMA, G

    Seven criteria for integer sequences being graphic are listed. Being graphic means that there is a simple graph with the given integer sequence as degree sequence. One of the criteria leads to a new and constructive proof of the well-known criterion of Erdos-Gallai.

  5. Adaptation in simple and complex fitness landscapes

    OpenAIRE

    Jain, Kavita; Krug, Joachim

    2005-01-01

    This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different types of mutation-selection dynamics are defined and their relation to problems of statistical physics are outlined. Then the stationary population distribution in simple, single peak fitness landscapes is discussed at length, with particular emphasis on th...

  6. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  8. Simple chain grammars and languages

    NARCIS (Netherlands)

    Nijholt, Antinus

    1979-01-01

    A subclass of the LR(0)-grammars, the class of simple chain grammars is introduced. Although there exist simple chain grammars which are not LL(k) for any k>0, this new class of grammars is very closely related to the LL(1) and simple LL(1) grammars. In fact it can be shown that every simple chain

  9. Data processing made simple

    CERN Document Server

    Wooldridge, Susan

    2013-01-01

    Data Processing: Made Simple, Second Edition presents discussions of a number of trends and developments in the world of commercial data processing. The book covers the rapid growth of micro- and mini-computers for both home and office use; word processing and the 'automated office'; the advent of distributed data processing; and the continued growth of database-oriented systems. The text also discusses modern digital computers; fundamental computer concepts; information and data processing requirements of commercial organizations; and the historical perspective of the computer industry. The

  10. Applied mathematics made simple

    CERN Document Server

    Murphy, Patrick

    1982-01-01

    Applied Mathematics: Made Simple provides an elementary study of the three main branches of classical applied mathematics: statics, hydrostatics, and dynamics. The book begins with discussion of the concepts of mechanics, parallel forces and rigid bodies, kinematics, motion with uniform acceleration in a straight line, and Newton's law of motion. Separate chapters cover vector algebra and coplanar motion, relative motion, projectiles, friction, and rigid bodies in equilibrium under the action of coplanar forces. The final chapters deal with machines and hydrostatics. The standard and conte

  11. Theory of simple liquids

    CERN Document Server

    Hansen, Jean-Pierre

    1986-01-01

    This book gives a comprehensive and up-to-date treatment of the theory of ""simple"" liquids. The new second edition has been rearranged and considerably expanded to give a balanced account both of basic theory and of the advances of the past decade. It presents the main ideas of modern liquid state theory in a way that is both pedagogical and self-contained. The book should be accessible to graduate students and research workers, both experimentalists and theorists, who have a good background in elementary mechanics.Key Features* Compares theoretical deductions with experimental r

  12. Beyond Simple Headquarters Configurations

    DEFF Research Database (Denmark)

    Dellestrand, Henrik; Kappen, Philip; Nell, Phillip Christopher

    .e., an innovation that is important for the firm beyond the divisional boundaries, drives dual headquarters involvement in innovation development. Contrary to expectations, on average, a non-significant effect of cross-divisional embeddedness on dual headquarters involvement is found. Yet, both cross......-divisional importance and embeddedness effects are contingent on the overall complexity of the innovation project as signified by the size of the development network. The results lend support for the notion that parenting in complex structures entails complex headquarters structures and that we need to go beyond simple...

  13. Simple Driving Techniques

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    2002-01-01

    Driving was introduced as a program transformation technique by Valentin Turchin in some papers around 1980. It was intended for the programming language REFAL and used in metasystem transitions based on super compilation. In this paper we present one version of driving for a more conventional lisp......-like language. Our aim is to extract a simple notion of driving and show that even in this tamed form it has much of the power of more general notions of driving. Our driving technique may be used to simplify functional programs which use function composition and will often be able to remove intermediate data...

  14. ASP made simple

    CERN Document Server

    Deane, Sharon

    2003-01-01

    ASP Made Simple provides a brief introduction to ASP for the person who favours self teaching and/or does not have expensive computing facilities to learn on. The book will demonstrate how the principles of ASP can be learned with an ordinary PC running Personal Web Server, MS Access and a general text editor like Notepad.After working through the material readers should be able to:* Write ASP scripts that can display changing information on a web browser* Request records from a remote database or add records to it* Check user names & passwords and take this knowledge forward, either for their

  15. THE SIMPLE SDD

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, A.; Morlat, T.; Felizardo, M.; Collar, J. I.; Puibasset, J.; Waysand, G.; Miley, Harry S.; Ramos, A. R.; Girard, T. A.; Giuliani, F.; Limagne, D.; Marques, J. G.; Martins, R. C.; Oliveira, C.

    2006-09-01

    SIMPLE (superheated instrument for massive particle search) is an experiment(1,2) to search for evidence of spin-dependent dark matter using fluorine-loaded superheated droplet detectors (SDDs). The application of the detector is based on the presence of fluorine, which possesses the highest figure-of-merit for spin-dependent interactions. Furthermore, these devices are virtually insensitive to the majority of backgrounds associated with such searches. For dark matter applications, less than 10 events kg-1 d-1 are expected. The sensitivity to backgrounds is therefore an important issue for detector use. Following the thermal spike model of Seitz(3), there are two thresholds for bubble nucleation: (1) the deposited energy must be larger than the work of formation of a critical nucleus (Ec) and (2) Ec must be deposited over a distance of the order of a critical radius (rc). Both thresholds can be tuned by modifying the operating conditions as to render the SDD insensitive to radiations depositing less than ~200 keV mm-1. Although the SDD can be made insensitive to energetic muons, gamma rays, X rays and electrons with linear energy transfer (LET) below this threshold, response to neutrons and alpha particles remains problematic. These originate from radioactivity in the rock, detector shielding and the detector itself. We describe the detector fabrication and response studies required by the large volume and concentration of the SIMPLE device.

  16. Bernoulli measure of complex admissible kneading sequences

    OpenAIRE

    Bruin, Henk; Schleicher, Dierk

    2012-01-01

    Iterated quadratic polynomials give rise to a rich collection of different dynamical systems that are parametrized by a simple complex parameter $c$. The different dynamical features are encoded by the \\emph{kneading sequence} which is an infinite sequence over $\\{0,\\1\\}$. Not every such sequence actually occurs in complex dynamics. The set of admissible kneading sequences was described by Milnor and Thurston for real quadratic polynomials, and by the authors in the complex case. We prove tha...

  17. A Simple Harmonic Universe

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Peter W.; /Stanford U., ITP; Horn, Bart; Kachru, Shamit; /Stanford U., ITP /SLAC; Rajendran, Surjeet; /Johns Hopkins U. /Stanford U., ITP; Torroba, Gonzalo; /Stanford U., ITP /SLAC

    2011-12-14

    We explore simple but novel bouncing solutions of general relativity that avoid singularities. These solutions require curvature k = +1, and are supported by a negative cosmological term and matter with -1 < w < -1 = 3. In the case of moderate bounces (where the ratio of the maximal scale factor a{sub +} to the minimal scale factor a{sub -} is {Omicron}(1)), the solutions are shown to be classically stable and cycle through an infinite set of bounces. For more extreme cases with large a{sub +} = a{sub -}, the solutions can still oscillate many times before classical instabilities take them out of the regime of validity of our approximations. In this regime, quantum particle production also leads eventually to a departure from the realm of validity of semiclassical general relativity, likely yielding a singular crunch. We briefly discuss possible applications of these models to realistic cosmology.

  18. Simple relation algebras

    CERN Document Server

    Givant, Steven

    2017-01-01

    This monograph details several different methods for constructing simple relation algebras, many of which are new with this book. By drawing these seemingly different methods together, all are shown to be aspects of one general approach, for which several applications are given. These tools for constructing and analyzing relation algebras are of particular interest to mathematicians working in logic, algebraic logic, or universal algebra, but will also appeal to philosophers and theoretical computer scientists working in fields that use mathematics. The book is written with a broad audience in mind and features a careful, pedagogical approach; an appendix contains the requisite background material in relation algebras. Over 400 exercises provide ample opportunities to engage with the material, making this a monograph equally appropriate for use in a special topics course or for independent study. Readers interested in pursuing an extended background study of relation algebras will find a comprehensive treatme...

  19. Molecular genetics made simple

    Directory of Open Access Journals (Sweden)

    Heba Sh. Kassem

    2012-07-01

    Full Text Available Genetics have undoubtedly become an integral part of biomedical science and clinical practice, with important implications in deciphering disease pathogenesis and progression, identifying diagnostic and prognostic markers, as well as designing better targeted treatments. The exponential growth of our understanding of different genetic concepts is paralleled by a growing list of genetic terminology that can easily intimidate the unfamiliar reader. Rendering genetics incomprehensible to the clinician however, defeats the very essence of genetic research: its utilization for combating disease and improving quality of life. Herein we attempt to correct this notion by presenting the basic genetic concepts along with their usefulness in the cardiology clinic. Bringing genetics closer to the clinician will enable its harmonious incorporation into clinical care, thus not only restoring our perception of its simple and elegant nature, but importantly ensuring the maximal benefit for our patients.

  20. SIMPLE LIFE AND RELIGION

    Directory of Open Access Journals (Sweden)

    Ahmet YILDIRIM

    2014-07-01

    Full Text Available Individuals in terms of the economy in which we live is one of the most important phenomenon of the century. This phenomenon present itself as the only determinant of people's lives by entering almost makes itself felt. The mo st obvious objective needs of the economy by triggering motive is to induce people to consume . Consumer culture pervades all aspects of the situation are people . Therefore, these people have the blessing of culture , beauty and value all in the name of w hatever is consumed. This is way out of the siege of moral and religious values we have is to go back again . Referred by local cultural and religious values, based on today increasingly come to the fore and the Muslim way of life appears to be close to th e plain / lean preferred by many people life has been a way of life. Even the simple life , a way of life in the Western world , a conception of life , a philosophy, a movement as it has become widely accepted. Here in determining the Muslim way of life Pr ophet. Prophet (sa lived the kind of life a very important model, sample, and determining which direction is known. Religious values, which is the carrier of the prophets, sent to the society they have always been examples and models. Because every aspect of human life, his life style and the surrounding area has a feature. We also value his life that he has unknowingly and without learning and skills and to understand it is not possible to live our religion . We also our presentation, we mainly of Islam o utlook on life and predicted life - style, including the Prophet of Islam 's (sa simple life to scrutinize and lifestyle issues related to reveal , in short Islam's how life has embraced and the Prophet. Prophet's will try to find answers to questions reg arding how to live.

  1. Entropy Is Simple, Qualitatively

    Science.gov (United States)

    Lambert, Frank L.

    2002-10-01

    Qualitatively, entropy is simple. What it is, why it is useful in understanding the behavior of macro systems or of molecular systems is easy to state: Entropy increase from a macro viewpoint is a measure of the dispersal of energy from localized to spread out at a temperature T. The conventional q in qrev/T is the energy dispersed to or from a substance or a system. On a molecular basis, entropy increase means that a system changes from having fewer accessible microstates to having a larger number of accessible microstates. Fundamentally based on statistical and quantum mechanics, this approach is superior to the non-fundamental "disorder" as a descriptor of entropy change. The foregoing in no way denies the subtlety or the difficulty presented by entropy in thermodynamics—to first-year students or to professionals. However, as an aid to beginners in their quantitative study of thermodynamics, the qualitative conclusions in this article give students the advantage of a clear bird’s-eye view of why entropy increases in a wide variety of basic cases: a substance going from 0 K to T, phase change, gas expansion, mixing of ideal gases or liquids, colligative effects, and the Gibbs equation. See Letter re: this article.

  2. A Simple Accelerometer Calibrator

    Science.gov (United States)

    Salam, R. A.; Islamy, M. R. F.; Munir, M. M.; Latief, H.; Irsyam, M.; Khairurrijal

    2016-08-01

    High possibility of earthquake could lead to the high number of victims caused by it. It also can cause other hazards such as tsunami, landslide, etc. In that case it requires a system that can examine the earthquake occurrence. Some possible system to detect earthquake is by creating a vibration sensor system using accelerometer. However, the output of the system is usually put in the form of acceleration data. Therefore, a calibrator system for accelerometer to sense the vibration is needed. In this study, a simple accelerometer calibrator has been developed using 12 V DC motor, optocoupler, Liquid Crystal Display (LCD) and AVR 328 microcontroller as controller system. The system uses the Pulse Wave Modulation (PWM) form microcontroller to control the motor rotational speed as response to vibration frequency. The frequency of vibration was read by optocoupler and then those data was used as feedback to the system. The results show that the systems could control the rotational speed and the vibration frequencies in accordance with the defined PWM.

  3. Quasispecies made simple.

    Directory of Open Access Journals (Sweden)

    J J Bull

    2005-11-01

    Full Text Available Quasispecies are clouds of genotypes that appear in a population at mutation-selection balance. This concept has recently attracted the attention of virologists, because many RNA viruses appear to generate high levels of genetic variation that may enhance the evolution of drug resistance and immune escape. The literature on these important evolutionary processes is, however, quite challenging. Here we use simple models to link mutation-selection balance theory to the most novel property of quasispecies: the error threshold-a mutation rate below which populations equilibrate in a traditional mutation-selection balance and above which the population experiences an error catastrophe, that is, the loss of the favored genotype through frequent deleterious mutations. These models show that a single fitness landscape may contain multiple, hierarchically organized error thresholds and that an error threshold is affected by the extent of back mutation and redundancy in the genotype-to-phenotype map. Importantly, an error threshold is distinct from an extinction threshold, which is the complete loss of the population through lethal mutations. Based on this framework, we argue that the lethal mutagenesis of a viral infection by mutation-inducing drugs is not a true error catastophe, but is an extinction catastrophe.

  4. Protein sequence analysis using Hewlett-Packard biphasic sequencing cartridges in an applied biosystems 473A protein sequencer.

    Science.gov (United States)

    Tang, S; Mozdzanowski, J; Anumula, K R

    1999-01-01

    Protein sequence analysis using an adsorptive biphasic sequencing cartridge, a set of two coupled columns introduced by Hewlett-Packard for protein sequencing by Edman degradation, in an Applied Biosystems 473A protein sequencer has been demonstrated. Samples containing salts, detergents, excipients, etc. (e.g., formulated protein drugs) can be easily analyzed using the ABI sequencer. Simple modifications to the ABI sequencer to accommodate the cartridge extend its utility in the analysis of difficult samples. The ABI sequencer solvents and reagents were compatible with the HP cartridge for sequencing. Sequence information up to ten residues can be easily generated by this nonoptimized procedure, and it is sufficient for identifying proteins by database search and for preparing a DNA probe for cloning novel proteins.

  5. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  6. Sublocalization of seven human simple sequence repeat polymorphic markers: D5S349, D5S351, and D5S355 to 5q11. 2-q13. 1, D5S350 to 5p13. 1-p14, D5S35s to 5q31. 2-q33. 1, D5S353 to 5q33. 2-qter, and D5S354 to 5q13. 2-q15

    Energy Technology Data Exchange (ETDEWEB)

    Warrington, J.A.; Wasmuth, J.J. (Univ. of California, Irvine (United States))

    1993-01-01

    Seven highly informative human simple sequence repeat polymorphisms that map to human chromosome 5 have been sublocalized using a panel of somatic cell hybrids that retain naturally occurring deletions (4, 7). Simple sequence repeats are useful in the construction of high-resolution maps of the human genome because they are highly polymorphic and easily typed by the polymerase chain reaction (2, 9, 10, 11). The presence or absence of each of the seven simple sequence repeats, D5S349, D5S350, D5S351, D5S352, D5S353, D5S354, and D5S355, in a panel of somatic cell hybrids was determined using the polymerase chain reaction. The sequence of the PCR primer sets was previously reported by Hudson et al. Each PCR was carried out in a total volume of 25 PI using 0.2 pg DNA in 67 mM Tris-HCI (pH 8.3),6.7 mM MgCl[sub 2], 16.6 mM ammonium sulfate, 10 mM [beta]-mercaptoethanol, 1.25 mM each dNTP, 25 pmol each primer, and I unit of Thermos aquaticus DNA polymerase. The initial denaturation was at 94[degrees]R C for 1.5 min and the annealing temperatures ranged from 57 to 67[degrees]R C. Figure 1 depicts the chromosome 5 natural deletion mapping panel and the location of the markers. D5S350 was present in all hybrid cell lines except HHW1124 and HHW764 (SRO p13.1-p14). D5S349, D5S351, and D5S355 were absent in HHW1064 and HHW1124 and present in all other cell lines (SROq11.2-q13.1).D5S354 was absent in HHW1124 and present in all other cell lines (SRO q13.2-q15). D5S352 was present in all cell lines (SRO q31.2-q33.1), and D5S353 was present in all cell lines except HHW1138 (SRO q33.2-qter). 11 refs., 1 fig.

  7. Una historia muy simple

    Directory of Open Access Journals (Sweden)

    Miha Mazzini

    2009-12-01

    Full Text Available Voy a contarles una historia muy simple. Probablemente no les parecerá nada espe- cial y no quiero robarles tiempo, así que voy a tratar de hacerlo lo más rápido posible. Me inscribí en psicología porque eso hizo mi mejor amiga. Éramos compañeras desde jardín de infantes y siempre la seguí en todo. En tercer año de facultad conoció a su novio y continuó sus estudios en otro país; por primera vez no podía seguirla. Cuando rendí todos los exámenes, el profesor me preguntó si estaba interesada en hacer mi tesis sobre el perfil psicológico de los participantes de reality shows. Accedí para no tener que pensar en otro tema, aunque no veía mucho la televisión porque me pasaba las noches entre los libros de estudio. Enseguida me di cuenta de que, evidentemente, el profesor había firmado un contrato con la emisora: a él lo empleaban y y yo era la que iba a tener que trabajar, pero no me importaba. La tesis de licenciatura no es más que eso y hay que hacerla. Yo evaluaba los candidatos y elegía a los participantes que vivirían juntos duran- te algunos meses. Como hacían el programa con una licencia extranjera y ya sabían qué le interesaba a la audiencia, yo tenía preparados los rasgos de los perfiles psicológicos que en ese aislamiento colectivo no resultan bien. Tuve que elegir gente variada, pero dentro de la media; nunca nada verdaderamente especial. Cuando me gradué, tuve las noches libres: de pronto tenía mucho más tiempo y podía haber visto el programa, pero ya había terminado. Pero oí que había sido todo un éxito y que sobre todo a los chicos les había encantado el reality y los participantes elegidos.

  8. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_se...quence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  9. Monitoring method call sequences using annotations

    NARCIS (Netherlands)

    B. Nobakht (Behrooz); F.S. de Boer (Frank); M.M. Bonsangue (Marcello); C.P.T. de Gouw (Stijn); M.M. Jaghouri (MohammadMahdi)

    2014-01-01

    htmlabstractIn this paper we introduce JMSeq, a Java-based tool for monitoring sequences of method calls. JMSeq provides a simple but expressive language to specify the observables of a Java program in terms of sequences of possibly nested method calls. Similar to many monitoring-oriented

  10. a simple a simple excitation control excitation control excitation

    African Journals Online (AJOL)

    eobe

    synchronous generator from no-load to full load while maintaining the rated terminal voltage on the stator terminals. The d-q rotor reference frame equations were used for the calculations and it is shown that values of the field voltages determined follow a simple quadratic relationship that offer a very simple control scheme, ...

  11. Simple Rules for Detecting Depression

    NARCIS (Netherlands)

    Jenny, M.A.; Pachur, T.; Williams, S.L.; Becker, E.S.; Margraf, J.

    2013-01-01

    Depressive disorders are major public health issues worldwide. We tested the capacity of a simple lexicographic and noncompensatory fast and frugal tree (FFT) and a simple compensatory unit-weight model to detect depressed mood relative to a complex compensatory logistic regression and a naïve

  12. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  13. Digital event recorder capable of simple computations and with ...

    African Journals Online (AJOL)

    An event recorder which can summate and display stored data is described. This instrument can be used to record behavioural events or sequences in the laboratory or the field and produces a punched tape record which may be read by a computer, without need for an interface. Its ability to perform simple calculations for ...

  14. A Practical Workshop for Generating Simple DNA Fingerprints of Plants

    Science.gov (United States)

    Rouziere, A.-S.; Redman, J. E.

    2011-01-01

    Gel electrophoresis DNA fingerprints offer a graphical and visually appealing illumination of the similarities and differences between DNA sequences of different species and individuals. A polymerase chain reaction (PCR) and restriction digest protocol was designed to give high-school students the opportunity to generate simple fingerprints of…

  15. Molecular characterization of ten mango cultivars using simple ...

    African Journals Online (AJOL)

    DEAN

    2013-11-20

    Nov 20, 2013 ... Molecular characterization of ten mango cultivars using simple sequences repeat (SSR) markers. M. Kumar1*, V. Ponnuswami1, P. Nagarajan2, P. Jeyakumar3 and N. Senthil2. 1Horticultural College and Research Institute, Periyakulam, Tamil Nadu, 625604, India. 2Centre for Plant Molecular Biology, ...

  16. Foreshocks and Aftershocks in Simple Earthquake Models

    Science.gov (United States)

    Tiampo, K. F.; Klein, W.; Dominguez, R.; Kazemian, J.; González, P. J.

    2014-12-01

    Natural earthquake fault systems are highly heterogeneous in space; inhomogeneities occur because the earth is made of a variety of materials of different strengths and dissipate stress differently. Because the spatial arrangement of these materials is dependent on the geologic history, the distribution of these various materials can be quite complex and occur over a wide range of length scales. Despite their inhomogeneous nature, real faults are often modeled as spatially homogeneous systems. Here we present a simple earthquake fault model based on the Olami-Feder-Christensen (OFC) and Rundle-Jackson-Brown (RJB) cellular automata models with long-range interactions that incorporates a fixed percentage of stronger sites, or 'asperity cells', into the lattice. These asperity cells are significantly stronger than the surrounding lattice sites but eventually rupture when the applied stress reaches their higher threshold stress. The introduction of these spatial heterogeneities results in temporal clustering in the model that mimics those seen in natural fault systems. We observe sequences of activity that start with a gradually accelerating number of larger events (foreshocks) prior to a mainshock that is followed by a tail of decreasing activity (aftershocks). These recurrent large events occur at regular intervals, as is often observed in historic seismicity, and the time between events and their magnitude are a function of the stress dissipation parameter. The relative length of the foreshock to aftershock sequence depends on the amount of stress dissipation in the system, resulting in relatively long aftershock sequences when the stress dissipation is large versus long foreshock sequences when the stress dissipation is weak. This work provides further evidence that the spatial and temporal patterns observed in natural seismicity are strongly influenced by the underlying physical properties and are not solely the result of a simple cascade mechanism. We find that

  17. Simple ocean carbon cycle models

    Energy Technology Data Exchange (ETDEWEB)

    Caldeira, K. [Lawrence Livermore National Lab., CA (United States); Hoffert, M.I. [New York Univ., NY (United States). Dept. of Earth System Sciences; Siegenthaler, U. [Bern Univ. (Switzerland). Inst. fuer Physik

    1994-02-01

    Simple ocean carbon cycle models can be used to calculate the rate at which the oceans are likely to absorb CO{sub 2} from the atmosphere. For problems involving steady-state ocean circulation, well calibrated ocean models produce results that are very similar to results obtained using general circulation models. Hence, simple ocean carbon cycle models may be appropriate for use in studies in which the time or expense of running large scale general circulation models would be prohibitive. Simple ocean models have the advantage of being based on a small number of explicit assumptions. The simplicity of these ocean models facilitates the understanding of model results.

  18. Chermak-Delgado Simple Groups

    OpenAIRE

    McCulloch, Ryan

    2015-01-01

    This paper provides the first steps in classifying the finite solvable groups having Property A, which is a property involving abelian normal subgroups. We see that this classification is reduced to classifying the solvable Chermak-Delgado simple groups, which the author defines. The author completes a classification of Chermak-Delgado simple groups under certain restrictions on the primes involved in the group order.

  19. SWORDS: A statistical tool for analysing large DNA sequences

    Indian Academy of Sciences (India)

    In this article, we present some simple yet effective statistical techniques for analysing and comparing large DNA sequences. These techniques are based on frequency distributions of DNA words in a large sequence, and have been packaged into a software called SWORDS. Using sequences available in public domain ...

  20. Simulations Using Random-Generated DNA and RNA Sequences

    Science.gov (United States)

    Bryce, C. F. A.

    1977-01-01

    Using a very simple computer program written in BASIC, a very large number of random-generated DNA or RNA sequences are obtained. Students use these sequences to predict complementary sequences and translational products, evaluate base compositions, determine frequencies of particular triplet codons, and suggest possible secondary structures.…

  1. Sequencer table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available name: rpd_sequencer.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_sequencer.zip File...size: 23 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/rpd_sequencer#en Data acquisition

  2. Simple machines made simple a teacher resource manual

    CERN Document Server

    Andre, Ralph E St

    1993-01-01

    This book allows you to present scientific principles and simple mechanics through hands-on cooperative learning activities. Using inexpensive materials (e.g., tape, paper clips), students build simple machines-such as levers, pulleys, spring scales, gears, wheels and axles, windmills, and wedges-that demonstrate how things work. Activities have easy-to-locate materials lists, time requirements, and step-by-step directions (usually illustrated) on presentation. Ideas for bulletin boards, learning centers, and computer-assisted instruction are an added bonus.

  3. Construction of simple pathways and simple cycles in ecosystems.

    Science.gov (United States)

    Kincaid, D T; Pilette, R

    1992-06-01

    We present software tools for overcoming the problem of combinatorics in the enumeration of simple pathways and simple cycles in a first flow-through analysis of carbon transfer in large ecosystems. Rather than search through the very large number of potential routes in a reasonably sized ecosystem for the relatively small number of actual routes, our main algorithm performs an efficient rule-based construction of the actual routes. The enumeration of the unique pathways becomes tractable in terms of CPU time, which increases linearly with ecosystem size and connectedness. Networks of up to 80 entities can be evaluated using our software.

  4. Centralizers in simple locally finite groups

    Directory of Open Access Journals (Sweden)

    Mahmut Kuzucuoğlu

    2013-03-01

    Full Text Available This is a survey article on centralizers of finitesubgroups in locally finite, simple groups or LFS-groups as wewill call them. We mention some of the open problems aboutcentralizers of subgroups in LFS-groups and applications of theknown information about the centralizers of subgroups to thestructure of the locally finite group. We also prove thefollowing: Let $G$ be a countably infinite non-linear LFS-groupwith a Kegel sequence $mathcal{K}={(G_i,N_i | iinmathbf{N} }$. If there exists an upper bound for ${ |N_i| |iin mathbf{N} }$, then for any finite semisimplesubgroup $F$ in $G$ the subgroup $C_G(F$ has elements oforder $p_i$ for infinitely many distinct prime $p_i$. Inparticular $C_G(F$ is an infinite group. This answers Hartley'squestion provided that there exists a bound on ${ |N_i| | iin mathbf{N}$.

  5. Simple arithmetic: not so simple for highly math anxious individuals.

    Science.gov (United States)

    Chang, Hyesang; Sprute, Lisa; Maloney, Erin A; Beilock, Sian L; Berman, Marc G

    2017-12-01

    Fluency with simple arithmetic, typically achieved in early elementary school, is thought to be one of the building blocks of mathematical competence. Behavioral studies with adults indicate that math anxiety (feelings of tension or apprehension about math) is associated with poor performance on cognitively demanding math problems. However, it remains unclear whether there are fundamental differences in how high and low math anxious individuals approach overlearned simple arithmetic problems that are less reliant on cognitive control. The current study used functional magnetic resonance imaging to examine the neural correlates of simple arithmetic performance across high and low math anxious individuals. We implemented a partial least squares analysis, a data-driven, multivariate analysis method to measure distributed patterns of whole-brain activity associated with performance. Despite overall high simple arithmetic performance across high and low math anxious individuals, performance was differentially dependent on the fronto-parietal attentional network as a function of math anxiety. Specifically, low-compared to high-math anxious individuals perform better when they activate this network less-a potential indication of more automatic problem-solving. These findings suggest that low and high math anxious individuals approach even the most fundamental math problems differently. © The Author (2017). Published by Oxford University Press.

  6. Practical Session: Simple Linear Regression

    Science.gov (United States)

    Clausel, M.; Grégoire, G.

    2014-12-01

    Two exercises are proposed to illustrate the simple linear regression. The first one is based on the famous Galton's data set on heredity. We use the lm R command and get coefficients estimates, standard error of the error, R2, residuals …In the second example, devoted to data related to the vapor tension of mercury, we fit a simple linear regression, predict values, and anticipate on multiple linear regression. This pratical session is an excerpt from practical exercises proposed by A. Dalalyan at EPNC (see Exercises 1 and 2 of http://certis.enpc.fr/~dalalyan/Download/TP_ENPC_4.pdf).

  7. Canonical fitness model for simple scale-free graphs

    OpenAIRE

    Flegel, F.; Sokolov, I. M.

    2012-01-01

    We consider a fitness model assumed to generate simple graphs with power-law heavy-tailed degree sequence: P(k) \\propto k^{-1-\\alpha} with 0 < \\alpha < 1, in which the corresponding distributions do not posses a mean. We discuss the situations in which the model is used to produce a multigraph and examine what happens if the multiple edges are merged to a single one and thus a simple graph is built. We give the relation between the (normalized) fitness parameter r and the expected degree \

  8. Simple Combinatorial Optimisation Cost Games

    NARCIS (Netherlands)

    van Velzen, S.

    2005-01-01

    In this paper we introduce the class of simple combinatorial optimisation cost games, which are games associated to {0, 1}-matrices.A coalitional value of a combinatorial optimisation game is determined by solving an integer program associated with this matrix and the characteristic vector of the

  9. A Simple Plant Growth Analysis.

    Science.gov (United States)

    Oxlade, E.

    1985-01-01

    Describes the analysis of dandelion peduncle growth based on peduncle length, epidermal cell dimensions, and fresh/dry mass. Methods are simple and require no special apparatus or materials. Suggests that limited practical work in this area may contribute to students' lack of knowledge on plant growth. (Author/DH)

  10. Simple stålrammebygninger

    DEFF Research Database (Denmark)

    Ellum, J.C.

    Anvisningen gennemgår dimensioneringen og bringer detaljerede konstruktionstegninger til simple stålrammebygninger, dvs. lukkede, fritliggende bygninger i én etage, hvor tagkonstruktionen ud over egenlast kun er påvirket af naturlaster, dvs. sne og vind. Dimensioneringen sker ved at udfylde et...

  11. Determining Salinity by Simple Means.

    Science.gov (United States)

    Schlenker, Richard M.

    This paper describes the construction and use of a simple salinometer. The salinometer is composed, mainly, of a milliammeter and a battery and uses the measurement of current flow to determine the salinity of water. A complete list of materials is given, as are details of construction and operation of the equipment. The use of the salinometer in…

  12. Simple stålrammebygninger

    DEFF Research Database (Denmark)

    Ellum, J.C.

    Anvisningen gennemgår dimensioneringen og bringer detaljerede konstruktionstegninger til simple stålrammebygninger, dvs. lukkede, fritliggende bygninger i én etage, hvor tagkonstruktionen ud over egenlast kun er påvirket af naturlaster, dvs. sne og vind. Dimensioneringen sker ved at udfylde et di...

  13. Simple models with ALICE fluxes

    CERN Document Server

    Striet, J

    2000-01-01

    We introduce two simple models which feature an Alice electrodynamics phase. In a well defined sense the Alice flux solutions we obtain in these models obey first order equations similar to those of the Nielsen-Olesen fluxtube in the abelian higgs model in the Bogomol'nyi limit. Some numerical solutions are presented as well.

  14. Solving Simple Kinetics without Integrals

    Science.gov (United States)

    de la Pen~a, Lisandro Herna´ndez

    2016-01-01

    The solution of simple kinetic equations is analyzed without referencing any topic from differential equations or integral calculus. Guided by the physical meaning of the rate equation, a systematic procedure is used to generate an approximate solution that converges uniformly to the exact solution in the case of zero, first, and second order…

  15. Simple Indolizidine and Quinolizidine Alkaloids.

    Science.gov (United States)

    Michael, Joseph P

    2016-01-01

    This review of simple indolizidine and quinolizidine alkaloids (i.e., those in which the parent bicyclic systems are in general not embedded in polycyclic arrays) is an update of the previous coverage in Volume 55 of this series (2001). The present survey covers the literature from mid-1999 to the end of 2013; and in addition to aspects of the isolation, characterization, and biological activity of the alkaloids, much emphasis is placed on their total synthesis. A brief introduction to the topic is followed by an overview of relevant alkaloids from fungal and microbial sources, among them slaframine, cyclizidine, Steptomyces metabolites, and the pantocins. The important iminosugar alkaloids lentiginosine, steviamine, swainsonine, castanospermine, and related hydroxyindolizidines are dealt with in the subsequent section. The fourth and fifth sections cover metabolites from terrestrial plants. Pertinent plant alkaloids bearing alkyl, functionalized alkyl or alkenyl substituents include dendroprimine, anibamine, simple alkaloids belonging to the genera Prosopis, Elaeocarpus, Lycopodium, and Poranthera, and bicyclic alkaloids of the lupin family. Plant alkaloids bearing aryl or heteroaryl substituents include ipalbidine and analogs, secophenanthroindolizidine and secophenanthroquinolizidine alkaloids (among them septicine, julandine, and analogs), ficuseptine, lasubines, and other simple quinolizidines of the Lythraceae, the simple furyl-substituted Nuphar alkaloids, and a mixed quinolizidine-quinazoline alkaloid. The penultimate section of the review deals with the sizable group of simple indolizidine and quinolizidine alkaloids isolated from, or detected in, ants, mites, and terrestrial amphibians, and includes an overview of the "dietary hypothesis" for the origin of the amphibian metabolites. The final section surveys relevant alkaloids from marine sources, and includes clathryimines and analogs, stellettamides, the clavepictines and pictamine, and bis

  16. Simple Electromagnetic Analysis in Cryptography

    Directory of Open Access Journals (Sweden)

    Zdenek Martinasek

    2012-07-01

    Full Text Available The article describes the main principle and methods of simple electromagnetic analysis and thus provides an overview of simple electromagnetic analysis.The introductions chapters describe specific SPA attack used visual inspection of EM traces, template based attack and collision attack.After reading the article, the reader is sufficiently informed of any context of SEMA.Another aim of the article is the practical realization of SEMA which is focused on AES implementation.The visual inspection of EM trace of AES is performed step by step and the result is the determination of secret key Hamming weight.On the resulting EM trace, the Hamming weight of the secret key 1 to 8 was clearly visible.This method allows reduction from the number of possible keys for following brute force attack.

  17. Simple techniques can increase motivation

    Energy Technology Data Exchange (ETDEWEB)

    Smith, E.A.

    1982-12-01

    Productivity depends upon strong motivation. This article describes how the symptoms of weak motivation can be detected among engineers and other employees and what to do about it. Fortunately, most people want to be productive and respond to simple motivation building techniques. These techniques include establishing twoway communication between supervisor and subordinate, delegating authority on the basis of responsibility, effective organization of time, and the use of positive reinforcement (or rewards) and, when conditions merit it, negative reinforcement (or sanctions).

  18. A simple electron plasma wave

    Energy Technology Data Exchange (ETDEWEB)

    Brodin, G., E-mail: gert.brodin@physics.umu.se [Department of Physics, Umeå University, SE-901 87 Umeå (Sweden); Stenflo, L. [Department of Physics, Linköping University, SE-581 83 Linköping (Sweden)

    2017-03-18

    Considering a class of solutions where the density perturbations are functions of time, but not of space, we derive a new exact large amplitude wave solution for a cold uniform electron plasma. This result illustrates that most simple analytical solutions can appear even if the density perturbations are large. - Highlights: • The influence of large amplitude electromagnetic waves on electrostatic oscillations is found. • A generalized Mathieu equation is derived. • Anharmonic wave profiles are computed numerically.

  19. Instant simple botting with PHP

    CERN Document Server

    Anderson, Shay Michael

    2013-01-01

    do for you, and then get to work with the most important features and tasks. This book is a hands-on Starter guide that takes the reader from initialization to the coding and implementation of bot apps.Instant Simple Botting with PHP targets programmers of all levels who are familiar with common PHP functions and syntax, and who want to learn about bots and how to design and develop bots using objects.

  20. SIMPLE Dark Matter Search Results

    CERN Document Server

    Girard, T A; Morlat, T; Costa, M F; Collar, J I; Limagne, D; Waysand, G; Puibasset, J; Miley, H S; Auguste, M; Boyer, D; Cavaillou, A; Marques, J G; Oliveira, C; Felizardo, M; Fernandes, A C; Ramos, A R; Martins, R C; Girard, TA

    2005-01-01

    We report an improved SIMPLE experiment comprising four superheated droplet detectors with a total exposure of 0.42 kgd. The result yields ~ factor 10 improvement in the previously-reported results, and -- despite the low exposure -- is seen to provide restrictions on the allowed phase space of spin-dependent coupling strengths almost equivalent to those from the significantly larger exposure NAIADCDMS/ZEPLIN searches.

  1. Simple and Realistic Data Generation

    DEFF Research Database (Denmark)

    Pedersen, Kenneth Houkjær; Torp, Kristian; Wind, Rico

    2006-01-01

    This paper presents a generic, DBMS independent, and highly extensible relational data generation tool. The tool can efficiently generate realistic test data for OLTP, OLAP, and data streaming applications. The tool uses a graph model to direct the data generation. This model makes it very simple...... to generate data even for large database schemas with complex inter- and intra table relationships. The model also makes it possible to generate data with very accurate characteristics....

  2. Classification of simple current invariants

    CERN Document Server

    Gato-Rivera, Beatriz

    1992-01-01

    We summarize recent work on the classification of modular invariant partition functions that can be obtained with simple currents in theories with a center (Z_p)^k with p prime. New empirical results for other centers are also presented. Our observation that the total number of invariants is monodromy-independent for (Z_p)^k appears to be true in general as well. (Talk presented in the parallel session on string theory of the Lepton-Photon/EPS Conference, Geneva, 1991.)

  3. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  4. Simple waves in Hertzian chains.

    Science.gov (United States)

    McDonald, B Edward; Calvo, David

    2012-06-01

    The discrete system of equations for a chain consisting of a large number of spheres interacting via the Hertz force of index 3/2 in strain is examined in the very long wavelength limit, yielding an effective medium description. The resulting continuum second-order equation of motion possesses a subset of simple waves obeying a first-order equation of reduced index 5/4. These simple waves appear not to have examined before. For a given initial strain, the simple wave solution prescribes initial sphere centroid velocities. Together the initial strain and velocities are used in the second-order discrete system. Results for shock wave development compare very well between the second-order discrete system (minus physically valid oscillations) and the reduced first-order equation. A second-order simulation of colliding waves examines the ability of waves to pass through each other, with a phase advance accruing during the collision process. An arbitrary initial condition is shown to evolve toward a universal similarity solution proportional to (x/t)(4). A closed-form solution is given including the complete history of the waveform, shock location, and amplitude.

  5. High dimensional Bernstein-von Mises: simple examples

    OpenAIRE

    Johnstone, Iain M.

    2010-01-01

    In Gaussian sequence models with Gaussian priors, we develop some simple examples to illustrate three perspectives on matching of posterior and frequentist probabilities when the dimension p increases with sample size n: (i) convergence of joint posterior distributions, (ii) behavior of a non-linear functional: squared error loss, and (iii) estimation of linear functionals. The three settings are progressively less demanding in terms of conditions needed for validity of the Bernstein-von Mise...

  6. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_se...quence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  7. The sequence of sequencers: The history of sequencing DNA

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  8. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  9. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  10. Sequence crystallization during isotherm evaporation of southern ...

    African Journals Online (AJOL)

    Sequence crystallization during isotherm evaporation of southern Algeria chott Baghdad natural brine. M Zatout, M Hacini, A.H. Hamzaoui, A M'nif. Abstract. Southern Algerian's natural brine sampled from chott Baghdad may be a source of mineral salts with a high economic value. These salts are recoverable by simple ...

  11. Hurdles in Acquiring the Number Word Sequence

    Science.gov (United States)

    Gould, Peter

    2016-01-01

    Learning the sequence of number words in English up to 30 is not a simple process. In NSW government schools taking part in "Early Action for Success," over 800 students in each of the first 3 years of school were assessed every 5 weeks over the school year to determine the highest correct oral count they could produce. Rather than…

  12. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    T.N. Jennings; B.J. Knaus; T.D. Mullins; S.M. Haig; R.C. Cronn

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of...

  13. Bladder Cancer: A Simple Model Becomes Complex

    Science.gov (United States)

    Pierro, Giovanni Battista Di; Gulia, Caterina; Cristini, Cristiano; Fraietta, Giorgio; Marini, Lorenzo; Grande, Pietro; Gentile, Vincenzo; Piergentili, Roberto

    2012-01-01

    Bladder cancer is one of the most frequent malignancies in developed countries and it is also characterized by a high number of recurrences. Despite this, several authors in the past reported that only two altered molecular pathways may genetically explain all cases of bladder cancer: one involving the FGFR3 gene, and the other involving the TP53 gene. Mutations in any of these two genes are usually predictive of the malignancy final outcome. This cancer may also be further classified as low-grade tumors, which is always papillary and in most cases superficial, and high-grade tumors, not necessarily papillary and often invasive. This simple way of considering this pathology has strongly changed in the last few years, with the development of genome-wide studies on expression profiling and the discovery of small non-coding RNA affecting gene expression. An easy search in the OMIM (On-line Mendelian Inheritance in Man) database using “bladder cancer” as a query reveals that genes in some way connected to this pathology are approximately 150, and some authors report that altered gene expression (up- or down-regulation) in this disease may involve up to 500 coding sequences for low-grade tumors and up to 2300 for high-grade tumors. In many clinical cases, mutations inside the coding sequences of the above mentioned two genes were not found, but their expression changed; this indicates that also epigenetic modifications may play an important role in its development. Indeed, several reports were published about genome-wide methylation in these neoplastic tissues, and an increasing number of small non-coding RNA are either up- or down-regulated in bladder cancer, indicating that impaired gene expression may also pass through these metabolic pathways. Taken together, these data reveal that bladder cancer is far to be considered a simple model of malignancy. In the present review, we summarize recent progress in the genome-wide analysis of bladder cancer, and analyse non

  14. Sequencing and analysis of a genomic fragment provide an insight into the Dunaliella viridis genomic sequence.

    Science.gov (United States)

    Sun, Xiao-Ming; Tang, Yuan-Ping; Meng, Xiang-Zong; Zhang, Wen-Wen; Li, Shan; Deng, Zhi-Rui; Xu, Zheng-Kai; Song, Ren-Tao

    2006-11-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)(n) type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  15. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. What Is a Simple Liquid?

    Directory of Open Access Journals (Sweden)

    Trond S. Ingebrigtsen

    2012-03-01

    Full Text Available This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS. This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r^{-n} pair potentials with n=18,6,4, Lennard-Jones (LJ models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture, the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be

  17. What Is a Simple Liquid?

    Science.gov (United States)

    Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2012-01-01

    This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials) and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS). This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r-n pair potentials with n=18,6,4), Lennard-Jones (LJ) models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture), the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be characterized in three quite

  18. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  19. Computer electronics made simple computerbooks

    CERN Document Server

    Bourdillon, J F B

    1975-01-01

    Computer Electronics: Made Simple Computerbooks presents the basics of computer electronics and explains how a microprocessor works. Various types of PROMs, static RAMs, dynamic RAMs, floppy disks, and hard disks are considered, along with microprocessor support devices made by Intel, Motorola and Zilog. Bit slice logic and some AMD bit slice products are also described. Comprised of 14 chapters, this book begins with an introduction to the fundamentals of hardware design, followed by a discussion on the basic building blocks of hardware (NAND, NOR, AND, OR, NOT, XOR); tools and equipment that

  20. Nonlinear Pendulum: A Simple Generalization

    OpenAIRE

    Neto, J. P. Juchem

    2010-01-01

    In this work we solve the nonlinear second order differential equation of the simple pendulum with a general initial angular displacement ($\\theta(0)=\\theta_0$) and velocity ($\\dot{\\theta}(0)=\\phi_0$), obtaining a closed-form solution in terms of the Jacobi elliptic function $\\text{sn}(u,k)$, and of the the incomplete elliptical integral of the first kind $F(\\varphi,k)$. Such a problem can be used to introduce concepts like elliptical integrals and functions to advanced undergraduate students...

  1. Simple Simulations of DNA Condensation

    Energy Technology Data Exchange (ETDEWEB)

    STEVENS,MARK J.

    2000-07-12

    Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed. All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions. No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described. Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored Coulombic structure is a charge ordered state. Condensation is a generic phenomena and occurs for a variety of polyelectrolyte parameters. Toroids and rods are the condensate structures. Toroids form preferentially when the molecular stiffness is sufficiently strong.

  2. Systems analysis made simple computerbooks

    CERN Document Server

    Antill, Lyn

    1980-01-01

    Systems Analysis: Made Simple Computerbooks introduces the essential elements of information systems analysis and design and teaches basic technical skills required for the tasks involved. The book covers the aspects to the design of an information system; information systems and the organization, including the types of information processing activity and computer-based information systems; the role of the systems analyst; and the human activity system. The text also discusses information modeling, socio-technical design, man-machine interface, and the database design. Software specification

  3. Simple laws of urban growth

    CERN Document Server

    Masucci, Paolo; Batty, Michael

    2012-01-01

    By analysing the evolution of the street network of Greater London from the late 1700s to the present, we are able to shed light on the inner mechanisms that lie behind the growth of a city. First we define an object called a city as a spatial discontinuous phenomena, from clustering the density of street intersections. Second, we find that the city growth mechanisms can be described by two logistic laws, hence can be determined by a simple model of urban network growth in the presence of competition for limited space.

  4. Windows Phone 7 Made Simple

    CERN Document Server

    Trautschold, Martin

    2011-01-01

    With Windows Phone 7, Microsoft has created a completely new smartphone operating system that focuses on allowing users to be productive with their smartphone in new ways, while offering seamless integration and use of Microsoft Office Mobile as well as other productivity apps available in the Microsoft App Store. Windows Phone 7 Made Simple offers a clear, visual, step-by-step approach to using your Windows Phone 7 smartphone, no matter what the manufacturer. Author Jon Westfall is an expert in mobile devices, recognized by Microsoft as a "Most Valuable Professional" with experience

  5. Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

    Science.gov (United States)

    Craig S Echt; Surya Saha; Dennis L Deemer; C Dana Nelson

    2011-01-01

    Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant...

  6. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  7. Squid – a simple bioinformatics grid

    Directory of Open Access Journals (Sweden)

    de Miranda Antonio B

    2005-08-01

    Full Text Available Abstract Background BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. Results Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. Conclusion Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example.

  8. Simple spectrophotometric determination of monopersulfate.

    Science.gov (United States)

    Wacławek, S; Grübel, K; Černík, M

    2015-10-05

    A simple, sensitive and accurate spectrophotometric method has been developed and validated for the determination of monopersulfate (MPS) which is an active part of potassium monopersulfate triple salt that has the commercial name - Oxone. This work proposes a spectrophotometric determination of monopersulfate based on modification of the iodometric titration method. The analysis of absorption spectra was made for the concentration range from 1.35 to 13.01 ppm of MPS (with a detection and quantification limit of 0.41 and 1.35 ppm, respectively) and different pH values. The influence of several anions on the measurement was also investigated. Furthermore, the absorbance of iron and cobalt (often used as free radical initiators) proved to have no effect on the measurement of MPS concentrations. On the basis of the conducted studies, we propose 395 nm as an optimal wavelength for the determination of MPS concentrations. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Methadone radioimmunoassay: two simple methods

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, K.; Smith, R.N. (Metropolitan Police Forensic Science Laboratory, London (UK))

    1983-09-01

    Two simple and economical radioimmunoassays for methadone in blood or urine are described. Haemolysis, decomposition, common anticoagulants and sodium fluoride do not affect the results. One assay used commercially-available (1-/sup 3/H)(-)-methadone hydrobromide as the label, while the other uses a radioiodinated conjugate of 4-dimethylamino-2,2-diphenylpentanoic acid and L-tyrosine methyl ester. A commercially-available antiserum is used in both assays. Normethadone and ..cap alpha..-methadol cross-react to a small extent with the antiserum while methadone metabolites, dextropropoxyphene, dipipanone and phenadoxone have negligible cross-reactivities. The 'cut-offs' of the two assays as described are 30 and 33 ng ml/sup -1/ for blood, and 24 and 21 ng ml/sup -1/ for urine. The assay using the radioiodinated conjugate can be made more sensitive if required by increasing the specific activity of the label.

  10. iPad Made Simple

    CERN Document Server

    Trautschold, Martin; Learning, MSL Made Simple

    2010-01-01

    The new iPad is sleek, powerful, and most importantly, it's much more than just a big iPhone. Your iPad is can be used for reading, surfing the web, emailing, watching TV/Movies, getting work done, and much more. And with the upcoming wave of iPad apps, the possibilities are endless. iPad X Made Simple clarifies all of the key features on the iPad, introduces what's new, and also reveals dozens of time-saving shortcuts and techniques. The book has over 1,000 screen shots that are carefully annotated with step-by-step instructions. * Clear instructions on how to set up and use the iPad * Illust

  11. Simple lattice model of macroevolution

    Science.gov (United States)

    Borkowski, Wojciech

    2009-04-01

    In future astrobiology, like in modern astrophysics, the numerical simulations can be a very important tool for proving theories. In this paper, I propose a simple lattice model of a multi-species ecosystem suitable for the study of emergent properties of macroevolution. Unlike the majority of ecological models, the number of species is not fixed - they emerge by "mutation" of existing species, then survive or go extinct depending on the balance between local ecological interactions. The Monte-Carlo numerical simulations show that this model is able to qualitatively reproduce phenomena that have been empirically observed, like the dependence between size of the isolated area and the number of species inhabiting there, primary production and species-diversity. The model allows also studying the causes of mass extinctions and more generally, repeatability, and the role of pure chance in macroevolution.

  12. Optimal decision fusion for verification of face sequences

    NARCIS (Netherlands)

    Tao, Q.; Veldhuis, Raymond N.J.; Veldhuis, R.N.J.; Cronie, H.S.

    2007-01-01

    Face sequence contains more information of the user than a single face image. In this paper, optimal decision fusion is proposed to verify the face sequences, based on the original verification system for a single face image. We show by experiments that optimal decision fusion is a simple but

  13. accessions with sequence-related amplified polymorphism (SRAP)

    African Journals Online (AJOL)

    Sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR), two advanced molecular markers for genetic research in grass and forage, were used to analyze the genetic diversity among 44 accessions of cocksfoot collected from seven countries and regions. 21 SRAP primer combinations ...

  14. Computation Sequences: A Way to Characterize Classes of Attribute Grammars

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis

    1983-01-01

    A computation sequence for a derivation tree specifies a way of walking through the tree evaluating all the attributes of all nodes. By requiring that each derivation tree has a computation sequence with a certain property, it is possible to give simple characterizations of well-known subclasses ...

  15. Gene mining a marama bean expressed sequence tags (ESTs ...

    African Journals Online (AJOL)

    The authors reported the identification of genes associated with embryonic development and microsatellite sequences. The future direction will entail characterization of these genes using gene over-expression and mutant assays. Key words: Namibia, simple sequence repeats (SSR), data mining, homology searches, ...

  16. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki

    2015-09-01

    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  17. A Simple Demonstration Model of Osmosis

    Science.gov (United States)

    Morse, Joseph G.

    1999-01-01

    A simple device constructed from a wire screen, a large beaker, beans, and oats is described. It provides a simple and effective visual model of the phenomenon of osmosis and, by extension, the origin of other colligative properties of solutions.

  18. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

    2014-01-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...

  19. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.

    Science.gov (United States)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta; Mikkelsen, Martin; Johansen, Peter; Børsting, Claus; Morling, Niels

    2014-08-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.

  20. Simple substrates for complex cognition

    Directory of Open Access Journals (Sweden)

    Peter Dayan

    2008-12-01

    Full Text Available Complex cognitive tasks present a range of computational and algorithmic challenges for neural accounts of both learning and inference. In particular, it is extremely hard to solve them using the sort of simple policies that have been extensively studied as solutions to elementary Markov decision problems. There has thus been recent interest in architectures for the instantiation and even learning of policies that are formally more complicated than these, involving operations such as gated working memory. However, the focus of these ideas and methods has largely been on what might best be considered as automatized, routine or, in the sense of animal conditioning, habitual, performance. Thus, they have yet to provide a route towards understanding the workings of rule-based control, which is critical for cognitively sophisticated competence. Here, we review a recent suggestion for a uniform architecture for habitual and rule-based execution, discuss some of the habitual mechanisms that underpin the use of rules, and consider a statistical relationship between rules and habits.

  1. Semiregular factorization of simple graphs

    Directory of Open Access Journals (Sweden)

    Anthony J. Hilton

    2004-11-01

    Full Text Available A graph G is a (d, d + s-graph if the degree of each vertex of G lies in the interval [d, d + s]. A (d, d + 1-graph is said to be semiregular. An (r, r + 1 -factorization of a graph is a decomposition of the graph into edgedisjoint (r, r + 1-factors.We discuss here the state of knowledge about (r, r + 1-factorizations of d -regular graphs and of (d, d + 1-graphs.For r, s ≥ 0, let φ(r, s be the least integer such that, if d ≥ φ(r, s and G is any simple [d, d + s]-graph, then G has an (r, r + 1-factorization.Akiyama and Kano (when r is even and Cai (when r is odd showed that φ(r, s exists for all r, s. We show that, for s ≥ 2, φ(r, s = r(r + s + 1 + 1. Earlier φ(r, 0 was determined by Egawa and Era, and φ(r, 1 was determined by Hilton.

  2. Simple Quantum Dynamics with Thermalization.

    Science.gov (United States)

    Jansen, Thomas L C

    2018-01-11

    In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.

  3. Simple model for molecular scattering

    Science.gov (United States)

    Mehta, Nirav; Ticknor, Christopher; Hazzard, Kaden

    2017-04-01

    The collisions of ultracold molecules are qualitatively different from the collisions of ultracold atoms due to the high density of bimolecular resonances near the collision energy. We present results from a simple N-channel scattering model with square-well channel potentials and constant channel couplings (inside the well) designed to reproduce essential features of chaotic molecular scattering. The potential depths and channel splittings are tuned to reproduce the appropriate density of states for the short-range bimolecular collision complex (BCC), which affords a direct comparison of the resulting level-spacing distribution to that expected from random matrix theory (RMT), namely the so-called Wigner surmise. The density of states also sets the scale for the rate of dissociation from the BCC to free molecules, as approximated by transition state theory (TST). Our model affords a semi-analytic solution for the scattering amplitude in the open channel, and a determinantal equation for the eigenenergies of the short-ranged BCC. It is likely the simplest finite-ranged scattering model that can be compared to expectations from the approximations of RMT, and TST. The validity of these approximations has implications for the many-channel Hubbard model recently developed. This research was funded in part by the National Science Foundation under Grant No. NSF PHY-1125915.

  4. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  5. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  6. Colligative properties of simple solutions.

    Science.gov (United States)

    Andrews, F C

    1976-11-05

    Vapor pressure lowering, osmotic pressure, boiling point elevation, and freezing point depression are all related quantitatively to the decrease in micro(1)(soln) upon the addition of solute in forming a solution. In any equilibrium system, regardless of whether it is in a gravitational field or whether it contains walls, semipermeable membranes, phase transitions, or solutes, all equilibria are maintained locally, in the small region of the equilibrium, by the equality of micro(1)(soln). If there are several subsystems in a gravitational field, at any fixed height, microi will have the same value in each subsystem into which substance i can get, and microi + M(i)gh is constant throughout the entire system. In a solution, there is no mechanism by which solvent and solute molecules could sustain different pressures. Both the solvent and solute are always under identical pressures in a region of solution, namely, the pressure of the solution in that region. Since nature does not know which component we call the solvent and which the solute, equations should be symmetric in the two (acknowledging that the nonvolatile component, if any, is commonly chosen to be solute). Simple molecular pictures illustrate what is happening to cause pressure (positive or negative) in liquids, vapor pressure of liquids, and the various colligative properties of solutions. The only effect of solute involved in these properties is that it dilutes the solvent, with the resulting increase in S and decrease in micro(1)(soln). Water can be driven passively up a tree to enormous heights by the difference between its chemical potential in the roots and the ambient air. There is nothing mysterious about the molecular bases for any of these phenomena. Biologists can use the well-understood pictures of these phenomena with confidence to study what is happening in the complicated living systems they consider.

  7. MPRINT: VAX printing made simple

    Energy Technology Data Exchange (ETDEWEB)

    Worlton, T.

    1994-08-01

    Users with stand-alone personal computers and personal printers usually find printing simple, but on a VAX computer or VAX cluster there may be many printers of different types located in different areas. The print queues set up for these printers may require different form qualifiers and may not all be able to print all documents. This article describes the basic steps a VAX system manager should take in setting up and managing print queues on a VAX and tells how to access these queues from a VAX, Unix, Macintosh, or DOS Computer. It gives a basic overview, but includes several helpful items that are obscure or completely undocumented. Following this overview, there is a description of a Fortran program, MPRINT, written to simplify printing for users. The MPRINT program simplifies the choice of printers and print forms for users of VAX print queues by allowing them to select from a one line per queue menu. The menu includes queue descriptions and only lists printers which can correctly print the specified file. MPRINT selects the correct form to use based on file type and maximum record length of the file. MPRINT may be useful at your site, and provides examples of a number of system services. MPRINT includes routines to do a user open of a file and get information from the File and Record Access Blocks (FAB and RAB), and a routine to obtain information about print queues. There are also routines to parse a file name, detab a character buffer, and trim trailing nulls and blanks from a character string.

  8. The LHC Sequencer

    CERN Document Server

    Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris

    2011-01-01

    The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.

  9. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  10. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

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

  11. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  12. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  13. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    Science.gov (United States)

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  14. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    The behavior of wowen prepreg fabric during automated draping sequences is investigated. A drape tool under development with an arrangement of grippers facilitates the placement of a woven prepreg fabric in a mold. It is essential that the draped configuration is free from wrinkles and other...... framework shows a good potential for obtaining a better understanding of the drape process and guide the development of the drape tool. However, results obtained from using the framework on a simple test case indicate that the generation of draping sequences is non-trivial....

  15. Simple singularities and N = 2 supersymmetric Yang-Mills theory

    CERN Document Server

    Klemm, A D; Theisen, Stefan J; Yankielowicz, Shimon; Klemm, A; Lerche, W; Theisen, S

    1995-01-01

    We present a first step towards generalizing the work of Seiberg and Witten on N=2 supersymmetric Yang-Mills theory to arbitrary gauge groups. Specifically, we propose a particular sequence of hyperelliptic genus n-1 Riemann surfaces to underly the quantum moduli space of SU(n) N=2 supersymmetric gauge theory. These curves have an obvious generalization to arbitrary simply laced gauge groups, which involves the A-D-E type simple singularities. To support our proposal, we argue that the monodromy in the semiclassical regime is correctly reproduced. We also give some remarks on a possible relation to string theory.

  16. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

    OpenAIRE

    Ebhardt, H. Alexander; Tsang, Herbert H.; Dai, Denny C.; Liu, Yifeng; Bostan, Babak; Fahlman, Richard P.

    2009-01-01

    Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous...

  17. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  18. HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes.

    Science.gov (United States)

    Sherman, Westley Arthur; Kuchibhatla, Durga Bhavani; Limviphuvadh, Vachiranee; Maurer-Stroh, Sebastian; Eisenhaber, Birgit; Eisenhaber, Frank

    2015-10-01

    Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .

  19. Spatial and Temporal Clustering in a Simple Earthquake Asperity Model

    Science.gov (United States)

    Tiampo, K. F.; Kazemian, J.; Dominguez, R.; Klein, W.

    2016-12-01

    Natural earthquake fault systems are highly heterogeneous in space, the result of inhomogeneities that are a function of the variety of materials of different strengths. However, despite their inhomogeneous nature, real faults are often modeled as spatially homogeneous systems. Here we present a simple earthquake fault model based on the Olami-Feder-Christensen (OFC) and Rundle-Jackson-Brown (RJB) cellular automata models with long-range interactions that incorporates asperities, or stronger sites, into the lattice (Rundle and Jackson, 1977; Olami et al., 1992). These asperity cells are significantly stronger than the surrounding lattice sites but eventually rupture when the applied stress reaches their higher threshold stress. The introduction of these spatial heterogeneities results in spatial and temporal clustering in the model similar to that seen in natural fault systems. We observe sequences of activity that begin with a gradually accelerating number of larger events, or foreshocks, prior to a large event, followed by a tail of decreasing activity, or aftershocks. These recurrent large events occur at regular intervals and the characteristic time between events and their magnitude are a function of the stress dissipation parameter. The relative length of the foreshock to aftershock sequence depends on the amount of stress dissipation in the system. This work provides further evidence that the spatial and temporal patterns observed in natural seismicity are strongly influenced by the underlying physical properties and are not solely the result of a simple cascade mechanism. We find that the scaling depends not only on the amount of damage, but also on the spatial distribution of that damage (Dominguez et al., 2011; Kazemian et al., 2014). Here we compare the modeled sequences to those of natural earthquake sequences from California and around the world in order to investigate the interplay between cascade dynamics and spatial structure.

  20. On the solution, the critical exponents and the transition equation of the simple cubic three-dimensional Ising model

    NARCIS (Netherlands)

    Hoede, C.; Zandvliet, Henricus J.W.

    In a recent paper Hoede and Zandvliet introduced the concept of gauging on an equation. This enables the simulation of more complex Ising models by the simple quadratic model. The possibility of simulating the simple cubic model was defended by calculating a sequence of approximations to the

  1. How Does Sequence Structure Affect the Judgment of Time? Exploring a Weighted Sum of Segments Model

    Science.gov (United States)

    Matthews, William J.

    2013-01-01

    This paper examines the judgment of segmented temporal intervals, using short tone sequences as a convenient test case. In four experiments, we investigate how the relative lengths, arrangement, and pitches of the tones in a sequence affect judgments of sequence duration, and ask whether the data can be described by a simple weighted sum of…

  2. Double sequence core theorems

    Directory of Open Access Journals (Sweden)

    Richard F. Patterson

    1999-01-01

    Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.

  3. Efficient probability sequence

    OpenAIRE

    Regnier, Eva

    2014-01-01

    A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficient forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and ...

  4. Efficient probability sequences

    OpenAIRE

    Regnier, Eva

    2014-01-01

    DRMI working paper A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficiency forecasting systems, including memorylessness and increasing discrimination. These res...

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

    Directory of Open Access Journals (Sweden)

    Miri eMichaeli

    2012-12-01

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

  6. The Fluid Foil: The Seventh Simple Machine

    Science.gov (United States)

    Mitts, Charles R.

    2012-01-01

    A simple machine does one of two things: create a mechanical advantage (lever) or change the direction of an applied force (pulley). Fluid foils are unique among simple machines because they not only change the direction of an applied force (wheel and axle); they convert fluid energy into mechanical energy (wind and Kaplan turbines) or vice versa,…

  7. Simple utility functions with Giffen demand

    DEFF Research Database (Denmark)

    Sørensen, Peter Norman

    2007-01-01

    Simple utility functions with the Giffen property are presented: locally, the demand curve for a good is upward sloping. The utility functions represent continuous, monotone, convex preferences......Simple utility functions with the Giffen property are presented: locally, the demand curve for a good is upward sloping. The utility functions represent continuous, monotone, convex preferences...

  8. Sunspots and Their Simple Harmonic Motion

    Science.gov (United States)

    Ribeiro, C. I.

    2013-01-01

    In this paper an example of a simple harmonic motion, the apparent motion of sunspots due to the Sun's rotation, is described, which can be used to teach this subject to high-school students. Using real images of the Sun, students can calculate the star's rotation period with the simple harmonic motion mathematical expression.

  9. Simple Numerical Analysis of Longboard Speedometer Data

    Science.gov (United States)

    Hare, Jonathan

    2013-01-01

    Simple numerical data analysis is described, using a standard spreadsheet program, to determine distance, velocity (speed) and acceleration from voltage data generated by a skateboard/longboard speedometer (Hare 2012 "Phys. Educ." 47 409-17). This simple analysis is an introduction to data processing including scaling data as well as…

  10. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin sequence (or syndrome) is a condition in which an infant has a smaller than normal lower jaw, a tongue ... The exact causes of Pierre Robin sequence are unknown. It may be ... jaw develops slowly before birth, but may grow faster during ...

  11. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  12. sequences in Chickpea

    African Journals Online (AJOL)

    Milena

    Author(s) retain the copyright of this article http://www.academicjournals.org/AJB. African Journal of Biotechnology. Full Length Research Paper. Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite. (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes. Himanshu ...

  13. Sequences, Series, and Mathematica.

    Science.gov (United States)

    Mathews, John H.

    1992-01-01

    Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of sequences and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about sequences. (MDH)

  14. Modeling How, When, and What Is Learned in a Simple Fault-Finding Task

    Science.gov (United States)

    Ritter, Frank E.; Bibby, Peter A.

    2008-01-01

    We have developed a process model that learns in multiple ways while finding faults in a simple control panel device. The model predicts human participants' learning through its own learning. The model's performance was systematically compared to human learning data, including the time course and specific sequence of learned behaviors. These…

  15. Nanotechnology and Nanopore Sequencing.

    Science.gov (United States)

    Abedini-Nassab, Roozbeh

    2017-01-01

    DNA sequencing is one of the crucially important tasks in the fields of genetics and cellular biology, which is benefiting from nanotechnology. DNA carries genetic information and sequencing it in a quick way helps researchers in achieving essential goals, including personalized medicine. Solid state nanopores potentially can offer more durability, in sequencing biomolecules, over the proteinbased nanopores. In recent years, various ideas are introduced towards the goal of fast and low cost sequencing. In this review article recent advances presented in journal articles as well as patents in this field, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  16. SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

    Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

  17. Simple bone cysts of two brothers

    Energy Technology Data Exchange (ETDEWEB)

    An, Seo Young; An, Chang Hyeon; Choi, Karp Shik [Department of Oral and Maxillofacial Radiology, School of Dentistry, Kyungpook National University, Daegu (Korea, Republic of)

    2008-09-15

    17-year-old and 14-year-old brothers were referred for evaluation of the cystic lesions on the mandibular anterior area with no symptoms. Neither their mother nor the brothers could recall any past trauma to those areas. Panoramic and intraoral radiographs revealed moderately defined cystic lesions on their mandibular anterior areas. Biopsies on both lesions revealed simple bone cysts. Hereditary cause or familial history of simple bone cysts could not be found in literature review. This case may have been a coincidence. However, further investigation is needed to find the cause of simple bone cysts occurring in patients those are closely related.

  18. Simple-cell-like receptive fields maximize temporal coherence in natural video.

    Science.gov (United States)

    Hurri, Jarmo; Hyvärinen, Aapo

    2003-03-01

    Recently, statistical models of natural images have shown the emergence of several properties of the visual cortex. Most models have considered the nongaussian properties of static image patches, leading to sparse coding or independent component analysis. Here we consider the basic time dependencies of image sequences instead of their nongaussianity. We show that simple-cell-type receptive fields emerge when temporal response strength correlation is maximized for natural image sequences. Thus, temporal response strength correlation, which is a nonlinear measure of temporal coherence, provides an alternative to sparseness in modeling simple-cell receptive field properties. Our results also suggest an interpretation of simple cells in terms of invariant coding principles, which have previously been used to explain complex-cell receptive fields.

  19. BLAST Ring Image Generator (BRIG: simple prokaryote genome comparisons

    Directory of Open Access Journals (Sweden)

    Beatson Scott A

    2011-08-01

    Full Text Available Abstract Background Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. Results BLAST Ring Image Generator (BRIG can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons

  20. Empirical insights into the stochasticity of small RNA sequencing

    Science.gov (United States)

    Qin, Li-Xuan; Tuschl, Thomas; Singer, Samuel

    2016-04-01

    The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic nature of exponential PCR amplification. We validated our findings with two independent datasets, one for microRNA sequencing and another for RNA sequencing. Motivated by the gamma distributed stochasticity, we provided a simple method for the analysis of RNA sequencing data and showed its superiority to three existing methods for differential expression analysis using three data examples of technical replicate data and biological replicate data.

  1. Selecting soybean resistant to the cyst nematode Heterodera glycines using simple sequence repeat (microssatellite) markers.

    Science.gov (United States)

    Espindola, S M C G; Hamawaki, O T; Oliveira, A P; Hamawaki, C D L; Hamawaki, R L; Takahashi, L M

    2016-03-11

    The soybean cyst nematode (SCN) is a major cause of soybean yield reduction. The objective of this study was to evaluate the efficiency of marker-assisted selection to identify genotypes resistant to SCN race 3 infection, using Sat_168 and Sat-141 resistance quantitative trait loci. The experiment was carried out under greenhouse conditions, using soybean populations originated from crosses between susceptible and resistant parent stock: CD-201 (susceptible) and Foster IAC (resistant), Conquista (susceptible) and S83-30 (resistant), La-Suprema (susceptible) and S57-11 (resistant), and Parecis (susceptible) and S65-50 (resistant). Plants were inoculated with SCN and evaluated according to the female index (FI), those with FI < 10% were classified as resistant to nematode infection. Plants were genotyped for SCN resistance using microsatellite markers Sat-141 and Sat_168. Marker selection efficiency was analyzed by a contingency table, taking into account genotypic versus phenotypic evaluations for each line. These markers were shown to be useful tool for selection of SCN race 3.

  2. Inter-simple sequence repeat (ISSR) markers in the evaluation of ...

    African Journals Online (AJOL)

    shawkat

    2013-02-13

    Feb 13, 2013 ... conclusion, the results show that ISSR markers detected a considerable genetic diversity in the studied pepper hybrids, which could be used in conservation of genetic resources of new Egyptian hybrids and crop breeding through marker assisted selection (MAS). REFERENCES. Ahmed SM (2012).

  3. Molecular diversity of Cuban cassava (Manihot esculenta Crantz cultivars assessed by simple sequences repeats (SSR

    Directory of Open Access Journals (Sweden)

    Beovides, Y.

    2015-01-01

    Full Text Available A total of 36 microsatellites (SSR markers were used to analyze the genetic diversity of 163 accessions of cultivated cassava (Manihot esculenta Crantz, 94 accessions of them from the Cuban Cassava Germplasm Collection and 69 genotypes from different countries and conserved at the International Center for Tropical Agriculture (Colombia. This study was carried out to determine genetic diversity within and between all accessions to promote their better use and conservation strategies. Thirty-four of those markers were used for the genetic diversity study based on their higher polymorphism. The Cuban cultivars showed the highest average allele number per loci with 5.8 and 100% of the loci were polymorphic, as well as those from Guatemala. The average proportion of individual heterozygocity observed (HO was high (0.5918 ± 0.0351, while the highest HO rates were observed in groups of genotypes from Cuba (0.6016 and Tanzania (0.6459. The total heterozygocity (HT was high (0.6538 ± 0.1770, but only 7.4% (GST = 0.0740 ± 0.0377 was due to differences between the five countries studied. Genetic differentiation coefficients (estimated by F-statistics were low to moderate (FST > 0.04 and 17 unique alleles with low frequency were found in Cuban cultivars. The results provide the first molecular characterization of Cuban cassava genotypes and showed a wide diversity among landraces from Cuba. Application of this valuable information can be used for genetic diversity conservation and genotype identification studies for the genetic breeding program of cassava.

  4. Image-model coupling: a simple information theoretic perspective for image sequences

    Directory of Open Access Journals (Sweden)

    N. D. Smith

    2009-03-01

    Full Text Available Images are widely used to visualise physical processes. Models may be developed which attempt to replicate those processes and their effects. The technique of coupling model output to images, which is here called "image-model coupling", may be used to help understand the underlying physical processes, and better understand the limitations of the models. An information theoretic framework is presented for image-model coupling in the context of communication along a discrete channel. The physical process may be regarded as a transmitter of images and the model as part of a receiver which decodes or recognises those images. Image-model coupling may therefore be interpreted as image recognition. Of interest are physical processes which exhibit "memory". The response of such a system is not only dependent on the current values of driver variables, but also on the recent history of drivers and/or system description. Examples of such systems in geophysics include the ionosphere and Earth's climate. The discrete channel model is used to help derive expressions for matching images and model output, and help analyse the coupling.

  5. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

    Science.gov (United States)

    Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

    2015-01-01

    Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations. PMID:26381889

  6. Molecular Characterization and Genetic Structure in Avocado (Persea americana Mill.) Using Simple Sequence Repeat (SSR) Markers

    Science.gov (United States)

    Avocado (Persea americana Mill.) is an economically important tropical fruit native to Mesoamerica. It belongs to the Lauraceae family and is subdivided in three horticultural races (Guatemalan, Mexican, and West Indian) based primarily on ecological adaptation, botanical and physiological traits. T...

  7. Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis.

    Directory of Open Access Journals (Sweden)

    Harsh Kumar Dikshit

    Full Text Available Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei's genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard's structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.

  8. Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers.

    Science.gov (United States)

    Xue, Huiling; Xiao, Yao; Jin, Yanling; Li, Xinbo; Fang, Yang; Zhao, Hai; Zhao, Yun; Guan, Jiafa

    2012-01-01

    Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.

  9. Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats

    Science.gov (United States)

    2009-01-01

    Based on nine microsatellite loci, the aim of this study was to appraise the genetic diversity of 42 cassava (Manihot esculenta) landraces from selected regions in Brazil, and examine how this variety is distributed according to origin in several municipalities in the states of Minas Gerais, São Paulo, Mato Grosso do Sul, Amazonas and Mato Grosso. High diversity values were found among the five above-mentioned regions, with 3.3 alleles per locus on an average, a high percentage of polymorphic loci varying from 88.8% to 100%, an average of 0.265 for observed heterozygosity and 0.570 for gene diversity. Most genetic diversity was concentrated within the regions themselves (HS = 0.52). Cluster analysis and principal component based scatter plotting showed greater similarity among landraces from São Paulo, Mato Grosso do Sul and Amazonas, whereas those from Minas Gerais were clustered into a sub-group within this group. The plants from Mato Grosso, mostly collected in the municipality of General Carneiro, provided the highest differentiation. The migration of human populations is one among the possible reasons for this closer resemblance or greater disparity among plants from the various regions. PMID:21637653

  10. Image-model coupling: a simple information theoretic perspective for image sequences

    Science.gov (United States)

    Smith, N. D.; Mitchell, C. N.; Budd, C. J.

    2009-03-01

    Images are widely used to visualise physical processes. Models may be developed which attempt to replicate those processes and their effects. The technique of coupling model output to images, which is here called "image-model coupling", may be used to help understand the underlying physical processes, and better understand the limitations of the models. An information theoretic framework is presented for image-model coupling in the context of communication along a discrete channel. The physical process may be regarded as a transmitter of images and the model as part of a receiver which decodes or recognises those images. Image-model coupling may therefore be interpreted as image recognition. Of interest are physical processes which exhibit "memory". The response of such a system is not only dependent on the current values of driver variables, but also on the recent history of drivers and/or system description. Examples of such systems in geophysics include the ionosphere and Earth's climate. The discrete channel model is used to help derive expressions for matching images and model output, and help analyse the coupling.

  11. Assessing the genetic relationships of Curcuma alismatifolia varieties using simple sequence repeat markers.

    Science.gov (United States)

    Taheri, S; Abdullah, T L; Abdullah, N A P; Ahmad, Z; Karimi, E; Shabanimofrad, M R

    2014-09-05

    The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (SSRs) to elucidate genetic variation and relationships between five varieties of Curcuma (Curcuma alismatifolia) cultivated in Malaysia. Of the primers tested, 8 (of 17) SSR primers were selected for their reproducibility and high rates of polymorphism. The number of presumed alleles revealed by the SSR analysis ranged from two to six alleles, with a mean value of 3.25 alleles per locus. The values of HO and HE ranged from 0 to 0.8 (mean value of 0.2) and 0.1837 to 0.7755 (mean value of 0.5102), respectively. Eight SSR primers yielded 26 total amplified fragments and revealed high rates of polymorphism among the varieties studied. The polymorphic information content varied from 0.26 to 0.73. Dice's similarity coefficient was calculated for all pairwise comparisons and used to construct an unweighted pair group method with arithmetic average (UPGMA) dendrogram. Similarity coefficient values from 0.2105 to 0.6667 (with an average of 0.4386) were found among the five varieties examined. A cluster analysis of data using a UPGMA algorithm divided the five varieties/hybrids into 2 groups.

  12. Analyzing clonal fidelity of micropropagated Psidium guajava L. plants using simple sequence repeat markers

    Science.gov (United States)

    Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planti...

  13. Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences

    Science.gov (United States)

    Britten, Roy J.

    1998-01-01

    The terminal regions (last 20 kb) of Saccharomyces cerevisiae chromosomes universally contain blocks of precise sequence similarity to other chromosome terminal regions. The left and right terminal regions are distinct in the sense that the sequence similarities between them are reverse complements. Direct sequence similarity occurs between the left terminal regions and also between the right terminal regions, but not between any left ends and right ends. With minor exceptions the relationships range from 80% to 100% match within blocks. The regions of similarity are composites of familiar and unfamiliar repeated sequences as well as what could be considered “single-copy” (or better “two-copy”) sequences. All terminal regions were compared with all other chromosomes, forward and reverse complement, and 768 comparisons are diagrammed. It appears there has been an extensive history of sequence exchange or copying between terminal regions. The subtelomeric sequences fall into two classes. Seventeen of the chromosome ends terminate with the Y′ repeat, while 15 end with the 800-nt “X2” repeats just adjacent to the telomerase simple repeats. The just-subterminal repeats are very similar to each other except that chromosome 1 right end is more divergent. PMID:9600891

  14. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  15. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  16. Evolution of DNA sequencing.

    Science.gov (United States)

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  17. Thirty Simple Ideas for Interactive Whiteboards

    Science.gov (United States)

    Adams, Caralee

    2011-01-01

    This article presents thirty simple ideas for interactive whiteboards and how IWB can make one's teaching life easier. These teaching ideas for the interactive whiteboard can be used by teachers every day. Tips for classroom management are also presented.

  18. A Simple Preparation Method for Diphosphoimidazole

    DEFF Research Database (Denmark)

    Rosenberg, T.

    1964-01-01

    A simple method for the preparation of diphosphoimidazole is presented that involves direct phosphorylation of imidazole by phosphorus oxychloride in alkaline aqueous solution. Details are given on the use of diphosphoimidazole in preparing sodium phosphoramidate and certain phosphorylated amino...

  19. Technical note: simple vibroacoustic foetal stimulator.

    Science.gov (United States)

    Stojanović, D; Frković, A; Filiplić-Stojanović, H; Kirincić, N

    2001-01-01

    To build and test a simple vibroacoustic foetal stimulator. A vibroacoustic foetal stimulator was constructed and subjected to bench testing. Clinical trial was carried out in comparison to an electro laynx. Screening specificity of 98% and 100% sensitivity was achieved, with no decrease in specificity due to user's maladjustments. The device was characterized by simple use, maintenance and disinfection. The device is a good screening instrument for foetal health in prenatal care, despite its simplicity and low price.

  20. Simple trophic modules for complex food webs

    OpenAIRE

    Bascompte, Jordi; Carlos J. Melián

    2005-01-01

    There are two common approaches to food webs. On the one hand, empirical studies have described aggregate statistical measures of many-species food webs. On the other hand, theoretical studies have explored the dynamic properties of simple tri-trophic food chains (i.e., trophic modules). The question remains to what extent results based on simple modules are relevant for whole food webs. Here we bridge between these two independent research agendas by exploring the relative fr...

  1. Modeling of prepregs during automated draping sequences

    Science.gov (United States)

    Krogh, Christian; Glud, Jens A.; Jakobsen, Johnny

    2017-10-01

    The behavior of wowen prepreg fabric during automated draping sequences is investigated. A drape tool under development with an arrangement of grippers facilitates the placement of a woven prepreg fabric in a mold. It is essential that the draped configuration is free from wrinkles and other defects. The present study aims at setting up a virtual draping framework capable of modeling the draping process from the initial flat fabric to the final double curved shape and aims at assisting the development of an automated drape tool. The virtual draping framework consists of a kinematic mapping algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping sequence. The model is based on a transient finite element analysis with the material's constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping framework shows a good potential for obtaining a better understanding of the drape process and guide the development of the drape tool. However, results obtained from using the framework on a simple test case indicate that the generation of draping sequences is non-trivial.

  2. Delayed Sequence Intubation

    DEFF Research Database (Denmark)

    Weingart, Scott D; Trueger, N Seth; Wong, Nelson

    2015-01-01

    , patients were paralyzed and intubated. The primary outcome of this study was the difference in oxygen saturations after maximal attempts at preoxygenation before delayed sequence intubation compared with saturations just before intubation. Predetermined secondary outcomes and complications were also...... assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...... intubation to 98.8% afterward, with an increase of 8.9% (95% confidence interval 6.4% to 10.9%). Thirty-two patients were in a predetermined group with high potential for critical desaturation (pre-delayed sequence intubation saturations ≤93%). All of these patients increased their saturations post...

  3. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  4. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    comparative genomics studies. Conclusion This simple, inexpensive method now allows immediate access to plastid sequence, increasing experimental throughput and serving generally as a universal platform for plastid genome characterization. The method applies well to whole genome studies and speeds assessment of variability across species, making it a useful tool in plastid structural genomics.

  5. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  6. What's Decidable About Sequences?

    OpenAIRE

    Furia, Carlo A.

    2010-01-01

    We present a first-order theory of sequences with integer elements, Presburger arithmetic, and regular constraints, which can model significant properties of data structures such as arrays and lists. We give a decision procedure for the quantifier-free fragment, based on an encoding into the first-order theory of concatenation; the procedure has PSPACE complexity. The quantifier-free fragment of the theory of sequences can express properties such as sortedness and injectivity, as well as Bool...

  7. Simple virtual reality display of fetal volume ultrasound.

    Science.gov (United States)

    Tutschek, B

    2008-12-01

    Three-dimensional (3D) ultrasound volume acquisition, analysis and display of fetal structures have enhanced their visualization and greatly improved the general understanding of their anatomy and pathology. The dynamic display of volume data generally depends on proprietary software, usually supplied with the ultrasound system, and on the operator's ability to maneuver the dataset digitally. We have used relatively simple tools and an established storage, display and manipulation format to generate non-linear virtual reality object movies of prenatal images (including moving sequences and 3D-rendered views) that can be navigated easily and interactively on any current computer. This approach permits a viewing or learning experience that is superior to watching a linear movie passively. (c) 2008 ISUOG.

  8. Regular Simple Queues of Protein Contact Maps.

    Science.gov (United States)

    Guo, Qiang-Hui; Sun, Lisa Hui; Wang, Jian

    2017-01-01

    A protein fold can be viewed as a self-avoiding walk in certain lattice model, and its contact map is a graph that represents the patterns of contacts in the fold. Goldman, Istrail, and Papadimitriou showed that a contact map in the 2D square lattice can be decomposed into at most two stacks and one queue. In the terminology of combinatorics, stacks and queues are noncrossing and nonnesting partitions, respectively. In this paper, we are concerned with 2-regular and 3-regular simple queues, for which the degree of each vertex is at most one and the arc lengths are at least 2 and 3, respectively. We show that 2-regular simple queues are in one-to-one correspondence with hill-free Motzkin paths, which have been enumerated by Barcucci, Pergola, Pinzani, and Rinaldi by using the Enumerating Combinatorial Objects method. We derive a recurrence relation for the generating function of Motzkin paths with [Formula: see text] peaks at level i, which reduces to the generating function for hill-free Motzkin paths. Moreover, we show that 3-regular simple queues are in one-to-one correspondence with Motzkin paths avoiding certain patterns. Then we obtain a formula for the generating function of 3-regular simple queues. Asymptotic formulas for 2-regular and 3-regular simple queues are derived based on the generating functions.

  9. The Design of SimpleITK

    Directory of Open Access Journals (Sweden)

    Bradley Christopher Lowekamp

    2013-12-01

    Full Text Available SimpleITK is a new interface to the Insight Segmentation andRegistration Toolkit (ITK designed to facilitate rapid prototyping, educationand scientific activities, via high level programminglanguages. ITK is a templated C++ library of image processingalgorithms and frameworks for biomedical and other applications, andit was designed to be generic, flexible and extensible. Initially, ITKprovided a direct wrapping interface to languages such as Python andTcl through the WrapITK system. Unlike WrapITK, which exposed ITK'scomplex templated interface, SimpleITK was designed to provide an easyto use and simplified interface to ITK's algorithms. It includesprocedural methods, hides ITK's demand driven pipeline, and provides atemplate-less layer. Also SimpleITK provides practical conveniencessuch as binary distribution packages and overloaded operators. Ouruser-friendly design goals dictated a departure from the directinterface wrapping approach of WrapITK, towards a new facadeclass structure that only exposes the required functionality, hidingITK's extensive template use. Internally SimpleITK utilizes a manualdescription of each filter with code-generation and advanced C++meta-programming to provide the higher-level interface, bringing thecapabilities of ITK to a wider audience. SimpleITK is licensed asopen source software under the Apache License Version 2.0 and more informationabout downloading it can be found at http://www.simpleitk.org.

  10. Cognitive processing in new and practiced discrete keying sequences

    Directory of Open Access Journals (Sweden)

    Willem B Verwey

    2010-07-01

    Full Text Available This study addresses the role of cognitive control in the initiation and execution of familiar and unfamiliar movement sequences. To become familiar with two movement sequences participants first practiced two discrete key press sequences by responding to two fixed series of 6 key specific stimuli. In the ensuing test phase they executed these two familiar and also two unfamiliar keying sequences while there was a two-third chance a tone was presented together with one randomly selected key specific stimulus in each sequence. In the counting condition of the test phase participants counted the low pitched (i.e., target tones. By and large the results support the dual processor model in which the prime role of the cognitive processor shifts from executing to initiating sequences while the gradual development of motor chunks allows a motor processor to execute the sequences. Yet, the results extend this simple model by suggesting that with little practice sequence execution is based also on some non-cognitive (perhaps associative learning mechanism and, for some participants, on the use of explicit sequence knowledge. Also, after extensive practice the cognitive processor appears to still contribute to slower responses. The occurrence of long interkey intervals was replicated suggesting that fixed 6-key sequences include several motor chunks. Yet, no indication was found that the cognitive processor is responsible for concatenating these chunks.

  11. TOPPE: A framework for rapid prototyping of MR pulse sequences.

    Science.gov (United States)

    Nielsen, Jon-Fredrik; Noll, Douglas C

    2017-11-02

    To introduce a framework for rapid prototyping of MR pulse sequences. We propose a simple file format, called "TOPPE", for specifying all details of an MR imaging experiment, such as gradient and radiofrequency waveforms and the complete scan loop. In addition, we provide a TOPPE file "interpreter" for GE scanners, which is a binary executable that loads TOPPE files and executes the sequence on the scanner. We also provide MATLAB scripts for reading and writing TOPPE files and previewing the sequence prior to hardware execution. With this setup, the task of the pulse sequence programmer is reduced to creating TOPPE files, eliminating the need for hardware-specific programming. No sequence-specific compilation is necessary; the interpreter only needs to be compiled once (for every scanner software upgrade). We demonstrate TOPPE in three different applications: k-space mapping, non-Cartesian PRESTO whole-brain dynamic imaging, and myelin mapping in the brain using inhomogeneous magnetization transfer. We successfully implemented and executed the three example sequences. By simply changing the various TOPPE sequence files, a single binary executable (interpreter) was used to execute several different sequences. The TOPPE file format is a complete specification of an MR imaging experiment, based on arbitrary sequences of a (typically small) number of unique modules. Along with the GE interpreter, TOPPE comprises a modular and flexible platform for rapid prototyping of new pulse sequences. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  12. SVA: software for annotating and visualizing sequenced human genomes.

    Science.gov (United States)

    Ge, Dongliang; Ruzzo, Elizabeth K; Shianna, Kevin V; He, Min; Pelak, Kimberly; Heinzen, Erin L; Need, Anna C; Cirulli, Elizabeth T; Maia, Jessica M; Dickson, Samuel P; Zhu, Mingfu; Singh, Abanish; Allen, Andrew S; Goldstein, David B

    2011-07-15

    Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Freely available on the web at http://www.svaproject.org.

  13. Burstiness parameter for finite event sequences

    CERN Document Server

    Kim, Eun-Kyeong

    2016-01-01

    Characterizing inhomogeneous temporal patterns in natural and social phenomena is important to understand underlying mechanisms behind such complex systems, hence even to predict and control them. Temporal inhomogeneities in event sequences have been described in terms of bursts that are rapidly occurring events in short time periods alternating with long inactive periods. The bursts can be quantified by a simple measure, called burstiness parameter, which was introduced by Goh and Barab\\'asi [EPL \\textbf{81}, 48002 (2008)]. The burstiness parameter has been widely used due to its simplicity, which however turns out to be strongly biased when the number of events in the time series is not large enough. As the finite size effects on burstiness parameter have been largely ignored, we analytically investigate the finite size effects of the burstiness parameter. Then we suggest an alternative definition of burstiness parameter that is unbiased and yet simple. Using our alternative burstiness parameter, one can di...

  14. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

    National Research Council Canada - National Science Library

    Cox, Murray P; Peterson, Daniel A; Biggs, Patrick J

    2010-01-01

    .... However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data...

  15. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences

    National Research Council Canada - National Science Library

    Campanella, James J; Bitincka, Ledion; Smalley, John

    2003-01-01

    .... We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data...

  16. Steinitz theorems for simple orthogonal polyhedra

    Directory of Open Access Journals (Sweden)

    David Eppstein

    2014-09-01

    Full Text Available We define a simple orthogonal polyhedron to be a three-dimensional polyhedron with the topology of a sphere in which three mutually-perpendicular edges meet at each vertex.By analogy to Steinitz's theorem characterizing the graphs of convex polyhedra, we find graph-theoretic characterizations of three classes of simple orthogonal polyhedra: corner polyhedra, which can be drawn by isometric projection in the plane with only one hidden vertex, xyz polyhedra, in which each axis-parallel line through a vertex contains exactly one other vertex, and arbitrary simple orthogonal polyhedra. In particular, the graphs of xyz polyhedra are exactly the bipartite cubic polyhedral graphs, and every bipartite cubic polyhedral graph with a 4-connected dual graph is the graph of a corner polyhedron. Based on our characterizations we find efficient algorithms for constructing orthogonal polyhedra from their graphs.

  17. Maximal temperature in a simple thermodynamical system

    Science.gov (United States)

    Dai, De-Chang; Stojkovic, Dejan

    2016-06-01

    Temperature in a simple thermodynamical system is not limited from above. It is also widely believed that it does not make sense talking about temperatures higher than the Planck temperature in the absence of the full theory of quantum gravity. Here, we demonstrate that there exist a maximal achievable temperature in a system where particles obey the laws of quantum mechanics and classical gravity before we reach the realm of quantum gravity. Namely, if two particles with a given center of mass energy come at the distance shorter than the Schwarzschild diameter apart, according to classical gravity they will form a black hole. It is possible to calculate that a simple thermodynamical system will be dominated by black holes at a critical temperature which is about three times lower than the Planck temperature. That represents the maximal achievable temperature in a simple thermodynamical system.

  18. Simple microfluidic stagnation point flow geometries.

    Science.gov (United States)

    Dockx, Greet; Verwijlen, Tom; Sempels, Wouter; Nagel, Mathias; Moldenaers, Paula; Hofkens, Johan; Vermant, Jan

    2016-07-01

    A geometrically simple flow cell is proposed to generate different types of stagnation flows, using a separation flow and small variations of the geometric parameters. Flows with high local deformation rates can be changed from purely rotational, over simple shear flow, to extensional flow in a region surrounding a stagnation point. Computational fluid dynamic calculations are used to analyse how variations of the geometrical parameters affect the flow field. These numerical calculations are compared to the experimentally obtained streamlines of different designs, which have been determined by high speed confocal microscopy. As the flow type is dictated predominantly by the geometrical parameters, such simple separating flow devices may alleviate the requirements for flow control, while offering good stability for a wide variety of flow types.

  19. Vortex breakdown in simple pipe bends

    Science.gov (United States)

    Ault, Jesse; Shin, Sangwoo; Stone, Howard

    2016-11-01

    Pipe bends and elbows are one of the most common fluid mechanics elements that exists. However, despite their ubiquity and the extensive amount of research related to these common, simple geometries, unexpected complexities still remain. We show that for a range of geometries and flow conditions, these simple flows experience unexpected fluid dynamical bifurcations resembling the bubble-type vortex breakdown phenomenon. Specifically, we show with simulations and experiments that recirculation zones develop within the bends under certain conditions. As a consequence, fluid and particles can remain trapped within these structures for unexpectedly-long time scales. We also present simple techniques to mitigate this recirculation effect which can potentially have impact across industries ranging from biomedical and chemical processing to food and health sciences.

  20. Simple shearing interferometer suitable for vibration measurements

    Science.gov (United States)

    Mihaylova, Emilia M.; Whelan, Maurice P.; Toal, Vincent

    2004-06-01

    Recently there has been an increasing interest in the application of shearography for modal analysis of vibrating objects. New interferometric systems, which are simple and flexible are of interest for engineering and industrial applications. An electronic speckle pattern shearing interferometer (ESPSI) with a very simple shearing device is used for study of vibrations. The shearing device consists of two partially reflective glass plates. The reflection coefficients of the coatings are 0.3 and 0.7 respectively. The distance between the two glass plates controls the size of the shear. The versatility of this simple shearing interferometer is shown. It is demonstrated that the ESPSI system can be used for vibration measurements and phase-shifting implemented for fringe analysis. The results obtained are promising for future applications of the system for modal analysis.

  1. A simple probabilistic model of multibody interactions in proteins.

    Science.gov (United States)

    Johansson, Kristoffer Enøe; Hamelryck, Thomas

    2013-08-01

    Protein structure prediction methods typically use statistical potentials, which rely on statistics derived from a database of know protein structures. In the vast majority of cases, these potentials involve pairwise distances or contacts between amino acids or atoms. Although some potentials beyond pairwise interactions have been described, the formulation of a general multibody potential is seen as intractable due to the perceived limited amount of data. In this article, we show that it is possible to formulate a probabilistic model of higher order interactions in proteins, without arbitrarily limiting the number of contacts. The success of this approach is based on replacing a naive table-based approach with a simple hierarchical model involving suitable probability distributions and conditional independence assumptions. The model captures the joint probability distribution of an amino acid and its neighbors, local structure and solvent exposure. We show that this model can be used to approximate the conditional probability distribution of an amino acid sequence given a structure using a pseudo-likelihood approach. We verify the model by decoy recognition and site-specific amino acid predictions. Our coarse-grained model is compared to state-of-art methods that use full atomic detail. This article illustrates how the use of simple probabilistic models can lead to new opportunities in the treatment of nonlocal interactions in knowledge-based protein structure prediction and design. Copyright © 2013 Wiley Periodicals, Inc., a Wiley company.

  2. Simple methods for the 3' biotinylation of RNA.

    Science.gov (United States)

    Moritz, Bodo; Wahle, Elmar

    2014-03-01

    Biotinylation of RNA allows its tight coupling to streptavidin and is thus useful for many types of experiments, e.g., pull-downs. Here we describe three simple techniques for biotinylating the 3' ends of RNA molecules generated by chemical or enzymatic synthesis. First, extension with either the Schizosaccharomyces pombe noncanonical poly(A) polymerase Cid1 or Escherichia coli poly(A) polymerase and N6-biotin-ATP is simple, efficient, and generally applicable independently of the 3'-end sequences of the RNA molecule to be labeled. However, depending on the enzyme and the reaction conditions, several or many biotinylated nucleotides are incorporated. Second, conditions are reported under which splint-dependent ligation by T4 DNA ligase can be used to join biotinylated and, presumably, other chemically modified DNA oligonucleotides to RNA 3' ends even if these are heterogeneous as is typical for products of enzymatic synthesis. Third, we describe the use of 29 DNA polymerase for a template-directed fill-in reaction that uses biotin-dUTP and, thanks to the enzyme's proofreading activity, can cope with more extended 3' heterogeneities.

  3. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  4. Pressure Sequence - A Novel Method of Protecting Smart Cards

    NARCIS (Netherlands)

    Hartel, Pieter H.; Henderson, N.J.; Domingo-Ferrer, J; Chan, D.; Watson, A.

    If someone knocks on your door, the chances are that you can tell by the sound who it is. This simple idea is the basis of our pressure sequence method, which records the signal arising from a user tapping on a smart card. We have built a prototype, piezoelectric, screen printed pressure sensor on a

  5. Kangaroo – A pattern-matching program for biological sequences

    Directory of Open Access Journals (Sweden)

    Betel Doron

    2002-07-01

    Full Text Available Abstract Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats.

  6. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  7. TRSkit: A Simple Digital Library Toolkit

    Science.gov (United States)

    Nelson, Michael L.; Esler, Sandra L.

    1997-01-01

    This paper introduces TRSkit, a simple and effective toolkit for building digital libraries on the World Wide Web. The toolkit was developed for the creation of the Langley Technical Report Server and the NASA Technical Report Server, but is applicable to most simple distribution paradigms. TRSkit contains a handful of freely available software components designed to be run under the UNIX operating system and served via the World Wide Web. The intended customer is the person that must continuously and synchronously distribute anywhere from 100 - 100,000's of information units and does not have extensive resources to devote to the problem.

  8. Uso del simulador SimpleReuse

    OpenAIRE

    Álvarez Martínez, Carlos; Valero Cortés, Mateo

    2005-01-01

    Este report explica el funcionamiento del simulador SimpleReuse (una evolución de SimpleScalar y Wattch) para su uso en simulación de reuso de instrucciones o regiones. Este simulador realiza medidas de tiempo, instrucciones y consumo de potencia de códigos Alpha ejecutados en máquinas de muy distinta complejidad. El simulador no se encuentra disponible en la Web en este momento debido a que está en constante mejora, pero si hay alguien interesado en su uso puede pedirlo directamente a través...

  9. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system.

    Science.gov (United States)

    Schloss, Patrick D; Jenior, Matthew L; Koumpouras, Charles C; Westcott, Sarah L; Highlander, Sarah K

    2016-01-01

    Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina's MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3-V5, V1-V3, V1-V5, V1-V6, and V1-V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1-V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina's MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.

  10. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

    Directory of Open Access Journals (Sweden)

    Patrick D. Schloss

    2016-03-01

    Full Text Available Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina’s MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3–V5, V1–V3, V1–V5, V1–V6, and V1–V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1–V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina’s MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.

  11. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  12. Enzymatic sequencing of partially acetylated chitosan oligomers.

    Science.gov (United States)

    Hamer, Stefanie Nicole; Moerschbacher, Bruno Maria; Kolkenbrock, Stephan

    2014-06-17

    Chitosan oligosaccharides have diverse biological activities with potentially valuable applications, for example, in the fields of medicine and agriculture. These functionalities are thought to depend on their degree of polymerization and acetylation, and possibly on specific patterns of acetylation. Chitosan oligomers with fully defined architecture are difficult to produce, and their complete analysis is demanding. Analysis is typically done using MS or NMR, requiring access to expensive infrastructure, and yielding unequivocal results only in the case of rather small oligomers. We here describe a simple and cost-efficient method for the sequencing of μg amounts of chitosan oligosaccharides which is based on the sequential action of two recombinant glycosidases, namely an exo-β-N-acetylhexosaminidase (GlcNAcase) from Bacillus subtilis 168 and an exo-β-d-glucosaminidase (GlcNase) from Thermococcus kodakarensis KOD1. Starting from the non-reducing end, GlcNAcase and GlcNase specifically remove N-acetyl glucosamine (A) and glucosamine (D) units, respectively. By the sequential addition and removal of these enzymes in an alternating way followed by analysis of the products using high-performance thin-layer chromatography, the sequence of chitosan oligosaccharides can be revealed. Importantly, both enzymes work under identical conditions so that no buffer exchange is required between steps, and the enzyme can be removed conveniently using simple ultra-filtration devices. As proof-of-principle, the method was used to sequence the product of enzymatic deacetylation of chitin pentamer using a recombinant chitin deacetylase from Vibrio cholerae which specifically removes the acetyl group from the second unit next to the non-reducing end of the substrate, yielding mono-deacetylated pentamer with the sequence ADAAA. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Sequence-Dependent Persistence Lengths of DNA.

    Science.gov (United States)

    Mitchell, Jonathan S; Glowacki, Jaroslaw; Grandchamp, Alexandre E; Manning, Robert S; Maddocks, John H

    2017-04-11

    A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of l F = 53.5 nm in the sense of Flory, and of l p = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe the agreement to be good given that the cgDNA model is itself parametrized from molecular dynamics simulations of short fragments of length 10-20 bp, with no explicit fit to persistence length. Our Monte Carlo simulations further predict that there can be substantial dependence of persistence lengths on the specific sequence [Formula: see text] of a fragment. We propose, and confirm the numerical accuracy of, a simple factorization that separates the part of the apparent tangent-tangent correlation decay [Formula: see text] attributable to intrinsic shape, from a part [Formula: see text] attributable purely to stiffness, i.e., a sequence-dependent version of what has been called sequence-averaged dynamic persistence length l̅ d (=58.8 nm within the cgDNA model). For ensembles of both random and λ-phage fragments, the apparent persistence length [Formula: see text] has a standard deviation of 4 nm over sequence, whereas our dynamic persistence length [Formula: see text] has a standard deviation of only 1 nm. However, there are notable dynamic persistence length outliers, including poly(A) (exceptionally straight and stiff), poly(TA) (tightly coiled and exceptionally soft), and phased A-tract sequence motifs (exceptionally bent and stiff). The results of our numerical simulations agree reasonably well with both molecular dynamics simulation and diverse experimental data including minicircle cyclization rates and stereo cryo-electron microscopy images.

  14. Accident sequence precursor analysis level 2/3 model development

    Energy Technology Data Exchange (ETDEWEB)

    Lui, C.H. [Nuclear Regulatory Commission, Washington, DC (United States); Galyean, W.J.; Brownson, D.A. [Idaho National Engineering Lab., Idaho Falls, ID (United States)] [and others

    1997-02-01

    The US Nuclear Regulatory Commission`s Accident Sequence Precursor (ASP) program currently uses simple Level 1 models to assess the conditional core damage probability for operational events occurring in commercial nuclear power plants (NPP). Since not all accident sequences leading to core damage will result in the same radiological consequences, it is necessary to develop simple Level 2/3 models that can be used to analyze the response of the NPP containment structure in the context of a core damage accident, estimate the magnitude of the resulting radioactive releases to the environment, and calculate the consequences associated with these releases. The simple Level 2/3 model development work was initiated in 1995, and several prototype models have been completed. Once developed, these simple Level 2/3 models are linked to the simple Level 1 models to provide risk perspectives for operational events. This paper describes the methods implemented for the development of these simple Level 2/3 ASP models, and the linkage process to the existing Level 1 models.

  15. Statistical and linguistic features of DNA sequences

    Science.gov (United States)

    Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

  16. A Simple Sketch Symbolizing Self-Reliance

    Centers for Disease Control (CDC) Podcasts

    2017-02-16

    EID Managing Editor, Byron Breedlove, reads his cover art story, A Simple Sketch Symbolizing Self-Reliance.  Created: 2/16/2017 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 2/16/2017.

  17. Simple Obstacle Avoidance Algorithm for Rehabilitation Robots

    NARCIS (Netherlands)

    Stuyt, Floran H.A.; Römer, GertWillem R.B.E.; Stuyt, Harry .J.A.

    2007-01-01

    The efficiency of a rehabilitation robot is improved by offering record-and-replay to operate the robot. While automatically moving to a stored target (replay) collisions of the robot with obstacles in its work space must be avoided. A simple, though effective, generic and deterministic algorithm

  18. Energy: Simple Experiments for Young Scientists.

    Science.gov (United States)

    White, Larry

    This book contains simple experiments through which students can learn about the properties of energy. These experiments include making a kitchen "volcano," a soda-pop "cannon," and a puffed-rice "scooter." Topics include: energy and work, fossil fuels, solar energy, kinetic energy, potential energy, mechanical energy, heat energy, sound energy,…

  19. Simple suture and anchor in rabbit hips

    Science.gov (United States)

    Garcia Filho, Fernando Cal; Guarniero, Roberto; de Godoy Júnior, Rui Maciel; Pereira, César Augusto Martins; Matos, Marcos Almeida; Garcia, Lucas Cortizo

    2012-01-01

    Objective Using biomechanical studies, this research aims to compare hip capsulorrhaphy in rabbits, carried out with two different techniques: capsulorrhaphy with simple sutures and with anchors. Method Thirteen New Zealand Albino (Oryctolaguscuniculus) male rabbits, twenty-six hip joints, were used. First, a pilot project was performed with three rabbits (six hip joints). This experiment consisted of ten rabbits divided into two groups: group 1 underwent capsulorrhaphy on both right and left hips with simple suture using polyglycolic acid absorbable thread, and group 2 underwent capsulorrhaphy with titanium anchors. After a four-week postoperative period, the animals were euthanized and the hip joints were frozen. On the same day of the biomechanical studies, after the hip joints were previously unfrozen, the following parameters were evaluated: rigidity, maximum force, maximum deformity and energy. Results There was no relevant statistical difference in rigidity, maximum force, maximum deformity and energy between the simple suture and anchor groups. Conclusion Through biomechanical analyses, using parameters of rigidity, maximum force, maximum deformity and energy, it has been shown that capsulorrhaphy with simple suture and with anchors has similar results in rabbit hip joints. Level of Evidence II, Prospective Comparative Study. PMID:24453618

  20. A Simple Homemade Polarised Sunglasses Test Card

    Science.gov (United States)

    Bamdad, Farzad

    2016-01-01

    In this article construction of a simple and inexpensive test card which can be used to demonstrate the polarisation ability of sunglasses is described. The card was fabricated simply by using a piece of polariser sheet with one to three layers of cellophane tape fixed on it.

  1. Building systems from simple hyperbolic ones

    NARCIS (Netherlands)

    Zwart, Heiko J.; Le Gorrec, Y.; Maschke, B.

    In this article we introduce a technique that derives from the existence and uniqueness of solutions to a simple hyperbolic partial differential equation (p.d.e.) the existence and uniqueness of solutions to hyperbolic and parabolic p.d.e.’s. Among others, we show that starting with an impedance

  2. A Simple Classroom Demonstration of Natural Convection

    Science.gov (United States)

    Wheeler, Dean R.

    2005-01-01

    This article explains a simple way to demonstrate natural convection, such as from a lit candle, in the classroom using an overhead projector. The demonstration is based on the principle of schlieren imaging, commonly used to visualize variations in density for gas flows.

  3. Tour of a Simple Trigonometry Problem

    Science.gov (United States)

    Poon, Kin-Keung

    2012-01-01

    This article focuses on a simple trigonometric problem that generates a strange phenomenon when different methods are applied to tackling it. A series of problem-solving activities are discussed, so that students can be alerted that the precision of diagrams is important when solving geometric problems. In addition, the problem-solving plan was…

  4. A simple design rule for overlap joints

    NARCIS (Netherlands)

    Straalen, IJ.J. van

    2004-01-01

    For toughened and flexible adhesives it is found that a simple prediction model for overlap joints can be used to calculate the ultimate strength for the static load case. The absolute maximum strength for a lap joint is when the whole of the adhesive layer is at the shear yield strength. An

  5. Strong Bisimilarity of Simple Process Algebras

    DEFF Research Database (Denmark)

    Srba, Jirí

    2003-01-01

    We study bisimilarity and regularity problems of simple process algebras. In particular, we show PSPACE-hardness of the following problems: (i) strong bisimilarity of Basic Parallel Processes (BPP), (ii) strong bisimilarity of Basic Process Algebra (BPA), (iii) strong regularity of BPP, and (iv) ...

  6. Correcting the SIMPLE Model of Free Recall

    Science.gov (United States)

    Lee, Michael D.; Pooley, James P.

    2013-01-01

    The scale-invariant memory, perception, and learning (SIMPLE) model developed by Brown, Neath, and Chater (2007) formalizes the theoretical idea that scale invariance is an important organizing principle across numerous cognitive domains and has made an influential contribution to the literature dealing with modeling human memory. In the context…

  7. Modelling of the simple pendulum Experiment

    Directory of Open Access Journals (Sweden)

    Palka L.

    2016-01-01

    Full Text Available Abstract - work focuses on the design of the simulation embedded in remote experiment “Simple pendulum” built on the Internet School Experimental System (ISES. This platform is intended for wide educational purposes at schools and universities in order to provide the suitable measuring environment for students using conventional computing resources Informatics.

  8. A simple method for complex eigenvalues

    Energy Technology Data Exchange (ETDEWEB)

    Killingbeck, John P [Mathematics Department, University of Hull, Hull HU6 7RX (United Kingdom); Grosjean, Alain [Laboratoire d' Astrophysique de l' Observatoire de Besancon, CNRS, UMR 6091, 41 bis Avenue de l' Observatoire, BP1615, 25010 Besancon Cedex (France); Jolicard, Georges [Laboratoire d' Astrophysique de l' Observatoire de Besancon, CNRS, UMR 6091, 41 bis Avenue de l' Observatoire, BP1615, 25010 Besancon Cedex (France)

    2004-11-05

    A simple iterative method is described for finding the eigenvalues of a general square complex matrix. Several numerical examples involving complex symmetric matrices are treated. In particular, it is found that a naive matrix calculation without complex rotation produces resonant state energies in accord with those given by the recently introduced naive complex hypervirial perturbation theory. (letter to the editor)

  9. SLURM: Simple Linux Utility for Resource Management

    Energy Technology Data Exchange (ETDEWEB)

    Jette, M; Grondona, M

    2002-12-19

    Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

  10. Studying the Greenhouse Effect: A Simple Demonstration.

    Science.gov (United States)

    Papageorgiou, G.; Ouzounis, K.

    2000-01-01

    Studies the parameters involved in a presentation of the greenhouse effect and describes a simple demonstration of this effect. Required equipment includes a 100-120 watt lamp, a 250mL beaker, and a thermometer capable of recording 0-750 degrees Celsius together with a small amount of chloroform. (Author/SAH)

  11. Simple Calculation Programs for Biology Other Methods

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Simple Calculation Programs for Biology Other Methods. Hemolytic potency of drugs. Raghava et al., (1994) Biotechniques 17: 1148. FPMAP: methods for classification and identification of microorganisms 16SrRNA. graphical display of restriction and fragment map of ...

  12. Simple classical approach to spin resonance phenomena

    DEFF Research Database (Denmark)

    Gordon, R A

    1977-01-01

    A simple classical method of describing spin resonance in terms of the average power absorbed by a spin system is discussed. The method has several advantages over more conventional treatments, and a number of important spin resonance phenomena, not normally considered at the introductory level...

  13. Geometric classification of simple graph algebras

    DEFF Research Database (Denmark)

    Sørensen, Adam Peder Wie

    2013-01-01

    Inspired by Franks’ classification of irreducible shifts of finite type, we provide a short list of allowed moves on graphs that preserve the stable isomorphism class of the associated C ∗ -algebras. We show that if two graphs have stably isomorphic and simple unital algebras then we can use...

  14. Figuring the Acceleration of the Simple Pendulum

    Science.gov (United States)

    Lieberherr, Martin

    2011-01-01

    The centripetal acceleration has been known since Huygens' (1659) and Newton's (1684) time. The physics to calculate the acceleration of a simple pendulum has been around for more than 300 years, and a fairly complete treatise has been given by C. Schwarz in this journal. But sentences like "the acceleration is always directed towards the…

  15. Simple Analysis of Historical Lime Mortars

    Science.gov (United States)

    Pires, Joa~o

    2015-01-01

    A laboratory experiment is described in which a simple characterization of a historical lime mortar is made by the determination of its approximate composition by a gravimetric method. Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) are also used for the qualitative characterization of the lime mortar components. These…

  16. Simple Activity Demonstrates Wind Energy Principles

    Science.gov (United States)

    Roman, Harry T.

    2012-01-01

    Wind energy is an exciting and clean energy option often described as the fastest-growing energy system on the planet. With some simple materials, teachers can easily demonstrate its key principles in their classroom. (Contains 1 figure and 2 tables.)

  17. Lumbar Puncture for First Simple Febrile Seizure

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2009-01-01

    Full Text Available Compliance with American Academy of Pediatrics consensus statement recommendations regarding lumbar puncture for infants 6-18 months of age with a first simple febrile seizure was investigated by a retrospective review of 704 infants evaluated in the pediatric emergency medicine division at Children’s Hospital Boston, MA, Oct 1995-Oct 2006.

  18. Simple wave interaction of an elastic string

    NARCIS (Netherlands)

    Broer, L.J.F.; van Groesen, Embrecht W.C.

    1977-01-01

    The equations for the two-dimensional motion of a completely flexible elastic string can be derived from a Lagrangian. The equations of motion possess four characteristic velocities, to which the following four simple wave solutions correspond: leftward and rightward propagating longitudinal and

  19. Question Answering for Dutch : Simple does it

    NARCIS (Netherlands)

    Hoekstra, A.H.; Hiemstra, Djoerd; van der Vet, P.E.; Huibers, Theo W.C.; Schobbens, Pierre-Yves; Vanhoof, Wim; Schwanen, Gabriel

    2006-01-01

    When people pose questions in natural language to search for information on the web, the role of question answering (QA) systems becomes important. In this paper the QAsystem simpleQA, capable of answering Dutch questions on which the answer is a person or a location, is described. The system's

  20. Knowledge acquisition for a simple expert controller

    Science.gov (United States)

    Bieker, B.

    1987-01-01

    A method is presented for process control which has the properties of being incremental, cyclic and top-down. It is described on the basis of the development of an expert controller for a simple, but nonlinear control route. A quality comparison between expert controller and process operator shows the ability of the method for knowledge acquisition.

  1. A Simple Decoder for Topological Codes

    Directory of Open Access Journals (Sweden)

    James Wootton

    2015-04-01

    Full Text Available Here we study an efficient algorithm for decoding topological codes. It is a simple form of HDRG decoder, which could be straightforwardly generalized to complex decoding problems. Specific results are obtained for the planar code with both i.i.d. and spatially correlated errors. The method is shown to compare well with existing ones, despite its simplicity.

  2. Simple Calculation Programs for Biology Immunological Methods

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Simple Calculation Programs for Biology Immunological Methods. Computation of Ab/Ag Concentration from EISA data. Graphical Method; Raghava et al., 1992, J. Immuno. Methods 153: 263. Determination of affinity of Monoclonal Antibody. Using non-competitive ...

  3. Simple concurrent garbage collection almost without synchronization

    NARCIS (Netherlands)

    Hesselink, Wim H.; Lali, M.I.

    We present two simple mark and sweep algorithms, A and B, for concurrent garbage collection by a single collector running concurrently with a number of mutators that concurrently modify shared data. Both algorithms are based on the ideas of Ben-Ari's classical algorithm for on-the-fly garbage

  4. Simple tertiary phosphines to hexaphosphane ligands: Syntheses ...

    Indian Academy of Sciences (India)

    Abstract. Designing efficient phosphorus-based ligands to make catalysts for homogeneous catalysis has been a great challenge for chemists. Despite a plethora of phosphorus ligands ranging from simple tertiary phosphines to polyphosphines are known, the enthusiasm to generate new ones is mainly due to the demand.

  5. Simple algebraic data types for C

    NARCIS (Netherlands)

    Hartel, Pieter H.; Muller, Henk L.

    Adt is a simple tool in the spirit of Lex and Yacc that makes monomorphic algebraic data types, polymorphic built-in types like the list and an efficient form of pattern matching available in C programs. C programs built with ADTs typically use NULL pointers only to indicate don't care values, and

  6. Nature versus Nurture: The Simple Contrast

    Science.gov (United States)

    Davidoff, Jules; Goldstein, Julie; Roberson, Debi

    2009-01-01

    We respond to the commentary of Franklin, Wright, and Davies ("Journal of Experimental Child Psychology, 102", 239-245 [2009]) by returning to the simple contrast between nature and nurture. We find no evidence from the toddler data that makes us revise our ideas that color categories are learned and never innate. (Contains 1 figure.)

  7. Simulated Holograms: A Simple Introduction to Holography.

    Science.gov (United States)

    Dittmann, H.; Schneider, W. B.

    1992-01-01

    Describes a project that uses a computer and a dot matrix printer to simulate the holographic recording process of simple object structures. The process' four steps are (1) superposition of waves; (2) representing the superposition of a plane reference wave on the monitor screen; (3) photographic reduction of the images; and (4) reconstruction of…

  8. Simple Approach to Superamphiphobic Overhanging Silicon Nanostructures

    DEFF Research Database (Denmark)

    Kumar, Rajendra; Mogensen, Klaus Bo; Bøggild, Peter

    2010-01-01

    with contact angles up to 152 degrees and roll-off angle down to 8 degrees. Such nonlithographic nanoscale overhanging Structures can also be added to silicon nanograss by deposition of a thin SiO2 layer, which equips the silicon rods with 100-300 nm sized overhanging Structures. This is a simple, fast...

  9. Simple Demonstration of the Seebeck Effect

    Science.gov (United States)

    Molki, Arman

    2010-01-01

    In this article we propose a simple and low-cost experimental set-up through which science educators can demonstrate the Seebeck effect using a thermocouple and an instrumentation amplifier. The experiment can be set up and conducted during a 1-hour laboratory session. (Contains 3 tables and 3 figures.)

  10. A SIMPLE SPECTROPHOTOMETRIC DETERMINATION OF TRACE ...

    African Journals Online (AJOL)

    a

    ABSTRACT. A simple and sensitive spectrophotometric method has been developed for the determination of trace amounts of vanadium using thionin as a chromogenic reagent. The proposed method is based on the reaction of vanadium(V) with potassium iodide in acid medium to liberate iodine, which bleaches the violet ...

  11. Simple Numerical Model of Laminated Glass Beams

    Directory of Open Access Journals (Sweden)

    A. Zemanová

    2008-01-01

    Full Text Available This paper presents a simple Finite Element model aimed at efficient simulation of layered glass units. The approach is based on considering the independent kinematics of each layer, tied together via Lagrange multipliers. Validation and verification of the resulting model against independent data demonstrate its accuracy, showing its potential for generalization towards more complex problems. 

  12. Jacks--A Study of Simple Machines.

    Science.gov (United States)

    Parsons, Ralph

    This vocational physics individualized student instructional module on jacks (simple machines used to lift heavy objects) contains student prerequisites and objectives, an introduction, and sections on the ratchet bumper jack, the hydraulic jack, the screw jack, and load limitations. Designed with a laboratory orientation, each section consists of…

  13. Microwave Radiometer Linearity Measured by Simple Means

    DEFF Research Database (Denmark)

    Skou, Niels

    2002-01-01

    Modern spaceborne radiometer systems feature an almost perfect on-board calibration, hence the primary calibration task to be carried out before launch is a check of radiometer linearity. This paper describes two ways of measuring linearity of microwave radiometers only requiring relatively simple...

  14. Building Simple Hidden Markov Models. Classroom Notes

    Science.gov (United States)

    Ching, Wai-Ki; Ng, Michael K.

    2004-01-01

    Hidden Markov models (HMMs) are widely used in bioinformatics, speech recognition and many other areas. This note presents HMMs via the framework of classical Markov chain models. A simple example is given to illustrate the model. An estimation method for the transition probabilities of the hidden states is also discussed.

  15. Special Relativity as a Simple Geometry Problem

    Science.gov (United States)

    de Abreu, Rodrigo; Guerra, Vasco

    2009-01-01

    The null result of the Michelson-Morley experiment and the constancy of the one-way speed of light in the "rest system" are used to formulate a simple problem, to be solved by elementary geometry techniques using a pair of compasses and non-graduated rulers. The solution consists of a drawing allowing a direct visualization of all the fundamental…

  16. Linear Deterministic Accumulator Models of Simple Choice

    Directory of Open Access Journals (Sweden)

    Andrew eHeathcote

    2012-08-01

    Full Text Available We examine theories of simple choice as a race among evidence accumulation processes. We focus on the class of deterministic race models, which assume that the effects of fluctuations in the parameters of the accumulation processes between choice trials (between-choice noise dominate the effects of fluctuations occurring while making a choice (within-choice noise in behavioural data (i.e., response times and choices. The latter deterministic approximation, when combined with the assumption that accumulation is linear, leads to a class of models that can be readily applied to simple-choice behaviour because they are computationally tractable. We develop a new and mathematically simple exemplar within the class of linear deterministic models, the Lognormal Race (LNR. We then examine how the LNR, and another widely applied linear deterministic model, Brown and Heathcote’s (2008 LBA, account for a range of benchmark simple-choice effects in lexical-decision task data reported by Wagenmakers, Ratcliff, Gomez and McKoon (2008.

  17. A Simple Technique for High Resistance Measurement

    Science.gov (United States)

    Aguilar, Horacio Munguia; Landin, Ramon Ochoa

    2012-01-01

    A simple electronic system for the measurement of high values of resistance is shown. This system allows the measurement of resistance in the range of a few megohm up to 10[superscript 9] [omega]. We have used this system for the evaluation of CdS thin film resistance, but other practical uses in the basic physics laboratory are presented.…

  18. An auditory display tool for DNA sequence analysis.

    Science.gov (United States)

    Temple, Mark D

    2017-04-24

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code. Lastly nucleotide pairs can be parsed as two separate frames or codons can be parsed as three reading frames giving rise to multiple streams of audio. The most informative sonification algorithm reads the DNA sequence as codons in three reading frames to produce three concurrent streams of audio in an auditory display. This approach is advantageous since start and stop codons in either frame have a direct affect to start or stop the audio in that frame, leaving the other frames unaffected. Using these methods, DNA sequences such as open reading frames or repetitive DNA sequences can be distinguished from one another. These sonification tools are available through a webpage interface in which an input DNA sequence can be processed in real time to produce an auditory display playable directly within the browser. The potential of this approach as an analytical tool is discussed with reference to auditory displays derived from test sequences including simple nucleotide sequences, repetitive DNA sequences and coding or non-coding genes. This study presents a proof-of-concept that some properties of a DNA sequence can be identified through sonification alone and argues for their inclusion within the toolkit of DNA sequence browsers as an adjunct to existing visual and analytical tools.

  19. Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors.

    Science.gov (United States)

    MacLeod, Iona M; Larkin, Denis M; Lewin, Harris A; Hayes, Ben J; Goddard, Mike E

    2013-09-01

    Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant challenges to fully utilize such large data sets and to ensure that sequencing errors do not introduce bias into the inferred demography. Using whole-genome sequence data from two Holstein cattle, we demonstrate a new method to correct for bias caused by hidden errors and then infer stepwise changes in ancestral demography up to present. There was a strong upward bias in estimates of recent effective population size (Ne) if the correction method was not applied to the data, both for our method and the Li and Durbin (Inference of human population history from individual whole-genome sequences. Nature 475:493-496) pairwise sequentially Markovian coalescent method. To infer demography, we use an analytical predictor of multiloci linkage disequilibrium (LD) based on a simple coalescent model that allows for changes in Ne. The LD statistic summarizes the distribution of runs of homozygosity for any given demography. We infer a best fit demography as one that predicts a match with the observed distribution of runs of homozygosity in the corrected sequence data. We use multiloci LD because it potentially holds more information about ancestral demography than pairwise LD. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago, possibly related to the divergence of African and European Bos taurus cattle. This is followed by a further reduction coinciding with the period of cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. Our approach can be applied to whole-genome sequence from any diploid species and can be scaled up to use sequence from multiple individuals.

  20. Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

    Science.gov (United States)

    MacLeod, Iona M.; Larkin, Denis M.; Lewin, Harris A.; Hayes, Ben J.; Goddard, Mike E.

    2013-01-01

    Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant challenges to fully utilize such large data sets and to ensure that sequencing errors do not introduce bias into the inferred demography. Using whole-genome sequence data from two Holstein cattle, we demonstrate a new method to correct for bias caused by hidden errors and then infer stepwise changes in ancestral demography up to present. There was a strong upward bias in estimates of recent effective population size (Ne) if the correction method was not applied to the data, both for our method and the Li and Durbin (Inference of human population history from individual whole-genome sequences. Nature 475:493–496) pairwise sequentially Markovian coalescent method. To infer demography, we use an analytical predictor of multiloci linkage disequilibrium (LD) based on a simple coalescent model that allows for changes in Ne. The LD statistic summarizes the distribution of runs of homozygosity for any given demography. We infer a best fit demography as one that predicts a match with the observed distribution of runs of homozygosity in the corrected sequence data. We use multiloci LD because it potentially holds more information about ancestral demography than pairwise LD. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago, possibly related to the divergence of African and European Bos taurus cattle. This is followed by a further reduction coinciding with the period of cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. Our approach can be applied to whole-genome sequence from any diploid species and can be scaled up to use sequence from multiple individuals. PMID:23842528

  1. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  2. Sequence Classification: 893720 [

    Lifescience Database Archive (English)

    Full Text Available ial ribosomal protein of the large subunit; MRP51 exhibits genetic interactions with mutations in the COX2 and COX3 mRNA 5'-untransla...ted leader sequences; Mrp51p || http://www.ncbi.nlm.nih.gov/protein/6325139 ...

  3. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...

  4. The Compliment Sequence.

    Science.gov (United States)

    Sims, Anntarie L.

    1989-01-01

    Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)

  5. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  6. absolutely regular random sequences

    Directory of Open Access Journals (Sweden)

    Michel Harel

    1996-01-01

    Full Text Available In this paper, the central limit theorems for the density estimator and for the integrated square error are proved for the case when the underlying sequence of random variables is nonstationary. Applications to Markov processes and ARMA processes are provided.

  7. Draft sequences of the radish (Raphanus sativus L.) genome.

    Science.gov (United States)

    Kitashiba, Hiroyasu; Li, Feng; Hirakawa, Hideki; Kawanabe, Takahiro; Zou, Zhongwei; Hasegawa, Yoichi; Tonosaki, Kaoru; Shirasawa, Sachiko; Fukushima, Aki; Yokoi, Shuji; Takahata, Yoshihito; Kakizaki, Tomohiro; Ishida, Masahiko; Okamoto, Shunsuke; Sakamoto, Koji; Shirasawa, Kenta; Tabata, Satoshi; Nishio, Takeshi

    2014-10-01

    Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥ 300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  8. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  9. Swaps in protein sequences.

    Science.gov (United States)

    Fliess, Amit; Motro, Benny; Unger, Ron

    2002-08-01

    An important question in protein evolution is to what extent proteins may have undergone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolution of proteins, and has practical implications for using swaps as a design tool in protein engineering. In order to analyze the question systematically, we conducted a large scale survey of possible swaps and permutations among all pairs of protein from the Swissport database. A swap is defined as a specific kind of sequence mutation between two proteins in which two fragments that appear in both sequences have different relative order in the two sequences. For example, aXbYc and dYeXf are defined as a swap, where X and Y represent sequence fragments that switched their order. Identifying such swaps is difficult using standard sequence comparison packages. One of the main problems in the analysis stems from the fact that many sequences contain repeats, which may be identified as false-positive swaps. We have used two different approaches to detect pairs of proteins with swaps. The first approach is based on the predefined list of domains in Pfam. We identified all the proteins that share at least two domains and analyzed their relative order, looking for pairs in which the order of these domains was switched. We designed an algorithm to distinguish between real swaps and duplications. In the second approach, we used Blast to detect pairs of proteins that share several fragments. Then, we used an automatic procedure to select pairs that are likely to contain swaps. Those pairs were analyzed visually, using a graphical tool, to eliminate duplications. Combining these approaches, about 140 different cases of swaps in the Swissprot database were found (after eliminating

  10. Learning predictive statistics from temporal sequences: Dynamics and strategies

    Science.gov (United States)

    Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E.; Kourtzi, Zoe

    2017-01-01

    Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics—that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments. PMID:28973111

  11. Learning predictive statistics from temporal sequences: Dynamics and strategies.

    Science.gov (United States)

    Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

    2017-10-01

    Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

  12. Estimation of the simple correlation coefficient.

    Science.gov (United States)

    Shieh, Gwowen

    2010-11-01

    This article investigates some unfamiliar properties of the Pearson product-moment correlation coefficient for the estimation of simple correlation coefficient. Although Pearson's r is biased, except for limited situations, and the minimum variance unbiased estimator has been proposed in the literature, researchers routinely employ the sample correlation coefficient in their practical applications, because of its simplicity and popularity. In order to support such practice, this study examines the mean squared errors of r and several prominent formulas. The results reveal specific situations in which the sample correlation coefficient performs better than the unbiased and nearly unbiased estimators, facilitating recommendation of r as an effect size index for the strength of linear association between two variables. In addition, related issues of estimating the squared simple correlation coefficient are also considered.

  13. Simple educational tool for digital speckle shearography

    Science.gov (United States)

    Schirripa Spagnolo, Giuseppe; Martocchia, Andrea; Papalillo, Donato; Cozzella, Lorenzo

    2012-07-01

    In this study, an educational tool has been prepared for obtaining short-term and more economic training on digital speckle shearography (DSS). Shearography non-destructive testing (NDT) has gained wide acceptance over the last decade, providing a number of important and exciting inspection solutions in aerospace, electronics and medical device manufacturing. For exploring these motivations, it is important to develop didactic tools to understand the potential of digital shearography through training and didactic courses in the field of NDT. In this paper we describe a simple tool for making one familiar with the potential of DSS in the area of education and training. The system is realized with a simple and economic optical setup and a virtual instrument based on the LabVIEW™ and DAQ.

  14. Assessment of daylight quality in simple rooms

    DEFF Research Database (Denmark)

    Johnsen, Kjeld; Dubois, Marie-Claude; Sørensen, Karl Grau

    The present report documents the results of a study on daylight conditions in simple rooms of residential buildings. The overall objective of the study was to develop a basis for a method for the assessment of daylight quality in a room with simple geometry and window configurations. As a tool...... for the analyses the Radiance Lighting Simulation System was used. A large number of simulations were performed for 3 rooms (window configurations) under overcast, intermediate, and 40-50 sunny sky conditions for each window (7 months, three orientations and for every other hour with direct sun penetration through......-to-horizontal illuminance ratio as well as scale of shadow gave valuable information allowing a detailed description of the three-dimensional geometry of daylight in the space. It should be mentioned however, that there is no universal definition of light quality. The approach of this study was to analyse differences...

  15. Is the world simple or complicated

    CERN Document Server

    Barrow, John D

    1998-01-01

    Stop some particle physicists in the street and they will soon be trying to persuade you that the world is altogether simple and symmetrical. But stop a biologist, an economist, or a social scientist and they will tell you quite the opposite: the world is a higgledy-piggledy collection of complexities that owes little to symmetry and displays precious little simplicity. So who is right : is the world really complicated or is it simple ? We shall look at the reasoning that leads to these different conclusions, show why we got different answers to our question, and look at some of the recent developments that have taken place in the study of systems from sand-piles to music on the border between order and chaos. We shall also look at some of the connections between our aesthetic sensibilities and the structure of scientific theories.

  16. A simple solution of the proton crisis

    CERN Document Server

    Pankovic, Vladan

    2014-01-01

    In this work we suggest a simple theoretical model of the proton able to effectively solve proton spin crisis. Within domain of applicability of this simple model proton consists only of two u quarks and one d quarks (two of which have spin opposite to proton and one identical to proton) and one neutral vector phi meson (with spin two times larger than proton spin and directed identically to proton spin). This model is in full agreement not only with existing DIS experiments, but also with spin and electric charge conservation as well as in a satisfactory agreement with rest mass-energy conservation (since phi meson mass is close to proton rest mass). Our model opens an interesting possibility of the solution of the quarks and leptons families problem (proton is not an absolutely non-strange particle, but only a particle with almost totally effectively hidden strange).

  17. Complex Systems Built by Simple Elements

    Directory of Open Access Journals (Sweden)

    Petró Gábor

    2007-02-01

    Full Text Available There are a lot of systems, which behave complexly, around us. We cannot predict their behaviour. Unpredictability is almost a character of complexity but how can we tackle the phenomenon of it. The formal mathematical descriptions of them are more and more complex and only several times solvable. Is the making a system of non-linear equations the only way to handle and descript systems like them? Using simple elements we can build models which show complex behaviour. Simple rule-systems can be a model of a complex system. For example algorithms can be appropriate for this task. We can implement these models for the language of computers, as well, and running simulations. Can we observe or perceive emergent characters? What is the measure of emergent phenomena? These are the questions to which I am searching the answers. The algorithms can give us a better way to understand the complex world.

  18. Simple spherical ablative-implosion model

    Energy Technology Data Exchange (ETDEWEB)

    Mayer, F.J.; Steele, J.T.; Larsen, J.T.

    1980-06-23

    A simple model of the ablative implosion of a high-aspect-ratio (shell radius to shell thickness ratio) spherical shell is described. The model is similar in spirit to Rosenbluth's snowplow model. The scaling of the implosion time was determined in terms of the ablation pressure and the shell parameters such as diameter, wall thickness, and shell density, and compared these to complete hydrodynamic code calculations. The energy transfer efficiency from ablation pressure to shell implosion kinetic energy was examined and found to be very efficient. It may be possible to attach a simple heat-transport calculation to our implosion model to describe the laser-driven ablation-implosion process. The model may be useful for determining other energy driven (e.g., ion beam) implosion scaling.

  19. Multiphase flow in geometrically simple fracture intersections

    Science.gov (United States)

    Basagaoglu, H.; Meakin, P.; Green, C.T.; Mathew, M.; ,

    2006-01-01

    A two-dimensional lattice Boltzmann (LB) model with fluid-fluid and solid-fluid interaction potentials was used to study gravity-driven flow in geometrically simple fracture intersections. Simulated scenarios included fluid dripping from a fracture aperture, two-phase flow through intersecting fractures and thin-film flow on smooth and undulating solid surfaces. Qualitative comparisons with recently published experimental findings indicate that for these scenarios the LB model captured the underlying physics reasonably well.

  20. Entropy estimates for simple random fields

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Justesen, Jørn

    1995-01-01

    We consider the problem of determining the maximum entropy of a discrete random field on a lattice subject to certain local constraints on symbol configurations. The results are expected to be of interest in the analysis of digitized images and two dimensional codes. We shall present some examples...... of binary and ternary fields with simple constraints. Exact results on the entropies are known only in a few cases, but we shall present close bounds and estimates that are computationally efficient...