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Sample records for character est sequencing

  1. EST2Prot: Mapping EST sequences to proteins

    Directory of Open Access Journals (Sweden)

    Lin David M

    2006-03-01

    Full Text Available Abstract Background EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since they cannot be mapped to known genes. Consequently, new discoveries are possibly overlooked. Results We describe a system (EST2Prot that uses multiple elements to map EST sequences to their corresponding protein products. EST2Prot uses UniGene clusters, substring analysis, information about protein coding regions in existing DNA sequences and protein database searches to detect protein products related to a query EST sequence. Gene Ontology terms, Swiss-Prot keywords, and protein similarity data are used to map the ESTs to functional descriptors. Conclusion EST2Prot extends and significantly enriches the popular UniGene mapping by utilizing multiple relations between known biological entities. It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.

  2. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  3. Novel expressed sequence tag- simple sequence repeats (EST ...

    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 ...

  4. AcEST(EST sequences of Adiantum capillus-veneris and their annotation) - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AcEST AcEST(EST sequences of Adiantum capillus-veneris and their annotation) Data detail Dat...a name AcEST(EST sequences of Adiantum capillus-veneris and their annotation) DOI 10.18908/lsdba.nbdc00839-0...01 Description of data contents EST sequence of Adiantum capillus-veneris and its annotation (clone ID, libr...le search URL http://togodb.biosciencedbc.jp/togodb/view/archive_acest#en Data acquisition method Capillary ...ainst UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases) Number of data entries Adiantum capillus-veneris

  5. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs).

    Science.gov (United States)

    Liang, Chun; Wang, Gang; Liu, Lin; Ji, Guoli; Fang, Lin; Liu, Yuansheng; Carter, Kikia; Webb, Jason S; Dean, Jeffrey F D

    2007-05-29

    With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST) sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences. ConiferEST is an integrated system for data reprocessing, visualization and mining of conifer ESTs. In its current release, Build 1.0, it houses 172,229 loblolly pine EST sequence reads, which were obtained from reprocessing raw DNA sequencer traces using our software--WebTraceMiner. The trace files were downloaded from NCBI Trace Archive. ConiferEST provides biologists unique, easy-to-use data visualization and mining tools for a variety of putative sequence features including cloning vector segments, adapter sequences, restriction endonuclease recognition sites, polyA and polyT runs, and their corresponding Phred quality values. Based on these putative features, verified sequence features such as 3' and/or 5' termini of cDNA inserts in either sense or non-sense strand have been identified in-silico. Interestingly, only 30.03% of the designated 3' ESTs were found to have an authenticated 5' terminus in the non-sense strand (i.e., polyT tails), while fewer than 5.34% of the designated 5' ESTs had a verified 5' terminus in the sense strand. Such previously ignored features provide valuable insight for data quality control and validation of error-prone ESTs, as well as the ability to identify novel functional motifs embedded in large EST datasets. We found that "double-termini adapters" were effective indicators of potential EST chimeras. For all sequences with in-silico verified termini/terminus, we used InterProScan to assign protein domain signatures, results of which are available for in-depth exploration using our biologist

  6. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Carter Kikia

    2007-05-01

    Full Text Available Abstract Background With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences. Description ConiferEST is an integrated system for data reprocessing, visualization and mining of conifer ESTs. In its current release, Build 1.0, it houses 172,229 loblolly pine EST sequence reads, which were obtained from reprocessing raw DNA sequencer traces using our software – WebTraceMiner. The trace files were downloaded from NCBI Trace Archive. ConiferEST provides biologists unique, easy-to-use data visualization and mining tools for a variety of putative sequence features including cloning vector segments, adapter sequences, restriction endonuclease recognition sites, polyA and polyT runs, and their corresponding Phred quality values. Based on these putative features, verified sequence features such as 3' and/or 5' termini of cDNA inserts in either sense or non-sense strand have been identified in-silico. Interestingly, only 30.03% of the designated 3' ESTs were found to have an authenticated 5' terminus in the non-sense strand (i.e., polyT tails, while fewer than 5.34% of the designated 5' ESTs had a verified 5' terminus in the sense strand. Such previously ignored features provide valuable insight for data quality control and validation of error-prone ESTs, as well as the ability to identify novel functional motifs embedded in large EST datasets. We found that "double-termini adapters" were effective indicators of potential EST chimeras. For all sequences with in-silico verified termini/terminus, we used InterProScan to assign protein domain signatures, results of which are available

  7. Linear discriminant analysis of character sequences using occurrences of words

    KAUST Repository

    Dutta, Subhajit; Chaudhuri, Probal; Ghosh, Anil

    2014-01-01

    Classification of character sequences, where the characters come from a finite set, arises in disciplines such as molecular biology and computer science. For discriminant analysis of such character sequences, the Bayes classifier based on Markov models turns out to have class boundaries defined by linear functions of occurrences of words in the sequences. It is shown that for such classifiers based on Markov models with unknown orders, if the orders are estimated from the data using cross-validation, the resulting classifier has Bayes risk consistency under suitable conditions. Even when Markov models are not valid for the data, we develop methods for constructing classifiers based on linear functions of occurrences of words, where the word length is chosen by cross-validation. Such linear classifiers are constructed using ideas of support vector machines, regression depth, and distance weighted discrimination. We show that classifiers with linear class boundaries have certain optimal properties in terms of their asymptotic misclassification probabilities. The performance of these classifiers is demonstrated in various simulated and benchmark data sets.

  8. Linear discriminant analysis of character sequences using occurrences of words

    KAUST Repository

    Dutta, Subhajit

    2014-02-01

    Classification of character sequences, where the characters come from a finite set, arises in disciplines such as molecular biology and computer science. For discriminant analysis of such character sequences, the Bayes classifier based on Markov models turns out to have class boundaries defined by linear functions of occurrences of words in the sequences. It is shown that for such classifiers based on Markov models with unknown orders, if the orders are estimated from the data using cross-validation, the resulting classifier has Bayes risk consistency under suitable conditions. Even when Markov models are not valid for the data, we develop methods for constructing classifiers based on linear functions of occurrences of words, where the word length is chosen by cross-validation. Such linear classifiers are constructed using ideas of support vector machines, regression depth, and distance weighted discrimination. We show that classifiers with linear class boundaries have certain optimal properties in terms of their asymptotic misclassification probabilities. The performance of these classifiers is demonstrated in various simulated and benchmark data sets.

  9. Rapid in silico cloning of genes using expressed sequence tags (ESTs).

    Science.gov (United States)

    Gill, R W; Sanseau, P

    2000-01-01

    Expressed sequence tags (ESTs) are short single-pass DNA sequences obtained from either end of cDNA clones. These ESTs are derived from a vast number of cDNA libraries obtained from different species. Human ESTs are the bulk of the data and have been widely used to identify new members of gene families, as markers on the human chromosomes, to discover polymorphism sites and to compare expression patterns in different tissues or pathologies states. Information strategies have been devised to query EST databases. Since most of the analysis is performed with a computer, the term "in silico" strategy has been coined. In this chapter we will review the current status of EST databases, the pros and cons of EST-type data and describe possible strategies to retrieve meaningful information.

  10. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

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    Strassmann Joan E

    2004-03-01

    Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

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

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    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.

  12. galaxieEST: addressing EST identity through automated phylogenetic analysis.

    Science.gov (United States)

    Nilsson, R Henrik; Rajashekar, Balaji; Larsson, Karl-Henrik; Ursing, Björn M

    2004-07-05

    Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and

  13. Large-scale Identification of Expressed Sequence Tags (ESTs from Nicotianatabacum by Normalized cDNA Library Sequencing

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    Alvarez S Perez

    2014-12-01

    Full Text Available An expressed sequence tags (EST resource for tobacco plants (Nicotianatabacum was established using high-throughput sequencing of randomly selected clones from one cDNA library representing a range of plant organs (leaf, stem, root and root base. Over 5000 ESTs were generated from the 3’ ends of 8000 clones, analyzed by BLAST searches and categorized functionally. All annotated ESTs were classified into 18 functional categories, unique transcripts involved in energy were the largest group accounting for 831 (32.32% of the annotated ESTs. After excluding 2450 non-significant tentative unique transcripts (TUTs, 100 unique sequences (1.67% of total TUTs were identified from the N. tabacum database. In the array result two genes strongly related to the tobacco mosaic virus (TMV were obtained, one basic form of pathogenesis-related protein 1 precursor (TBT012G08 and ubiquitin (TBT087G01. Both of them were found in the variety Hongda, some other important genes were classified into two groups, one of these implicated in plant development like those genes related to a photosynthetic process (chlorophyll a-b binding protein, photosystem I, ferredoxin I and III, ATP synthase and a further group including genes related to plant stress response (ubiquitin, ubiquitin-like protein SMT3, glycine-rich RNA binding protein, histones and methallothionein. The interesting finding in this study is that two of these genes have never been reported before in N. tabacum (ubiquitin-like protein SMT3 and methallothionein. The array results were confirmed using quantitative PCR.

  14. An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

    Science.gov (United States)

    Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

    2004-01-01

    Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

  15. GarlicESTdb: an online database and mining tool for garlic EST sequences

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    Choi Sang-Haeng

    2009-05-01

    Full Text Available Abstract Background Allium sativum., commonly known as garlic, is a species in the onion genus (Allium, which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. Description GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition software technology (JSP/EJB/JavaServlet for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation

  16. GarlicESTdb: an online database and mining tool for garlic EST sequences.

    Science.gov (United States)

    Kim, Dae-Won; Jung, Tae-Sung; Nam, Seong-Hyeuk; Kwon, Hyuk-Ryul; Kim, Aeri; Chae, Sung-Hwa; Choi, Sang-Haeng; Kim, Dong-Wook; Kim, Ryong Nam; Park, Hong-Seog

    2009-05-18

    Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The Garlic

  17. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.

    Science.gov (United States)

    Asamizu, Erika; Nakamura, Yasukazu; Sato, Shusei; Tabata, Satoshi

    2004-02-01

    To perform a comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 74472 3'-end expressed sequence tags (EST) were generated from cDNA libraries produced from six different organs. Clustering of sequences was performed with an identity criterion of 95% for 50 bases, and a total of 20457 non-redundant sequences, 8503 contigs and 11954 singletons were generated. EST sequence coverage was analyzed by using the annotated L. japonicus genomic sequence and 1093 of the 1889 predicted protein-encoding genes (57.9%) were hit by the EST sequence(s). Gene content was compared to several plant species. Among the 8503 contigs, 471 were identified as sequences conserved only in leguminous species and these included several disease resistance-related genes. This suggested that in legumes, these genes may have evolved specifically to resist pathogen attack. The rate of gene sequence divergence was assessed by comparing similarity level and functional category based on the Gene Ontology (GO) annotation of Arabidopsis genes. This revealed that genes encoding ribosomal proteins, as well as those related to translation, photosynthesis, and cellular structure were more abundantly represented in the highly conserved class, and that genes encoding transcription factors and receptor protein kinases were abundantly represented in the less conserved class. To make the sequence information and the cDNA clones available to the research community, a Web database with useful services was created at http://www.kazusa.or.jp/en/plant/lotus/EST/.

  18. Preparing and Analyzing Expressed Sequence Tags (ESTs Library for the Mammary Tissue of Local Turkish Kivircik Sheep

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    Nehir Ozdemir Ozgenturk

    2017-01-01

    Full Text Available Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST sequences were assembled with the CAP3 software. Putative functions of all unique sequences and statistical analysis were determined by Geneious software. Total 422 ESTs have over 80% similarity to known sequences of other organisms in NCBI classified by Panther database for the Gene Ontology (GO category. By comparing gene expression profiles, we observed some putative genes that may be relative to reproductive performance or play important roles in milk synthesis and secretion. A total of 2414 ESTs have been deposited to the NCBI GenBank database (GW996847–GW999260. EST data in this study have provided a new source of information to functional genome studies of sheep.

  19. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis

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    Qian Ding

    2015-01-01

    Full Text Available Simple sequence repeats (SSRs are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%, amplicons were successfully generated with high quality. Seventeen (89.5% showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

  20. Generation and Analysis of Expressed Sequence Tags (ESTs from Halophyte Atriplex canescens to Explore Salt-Responsive Related Genes

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    Jingtao Li

    2014-06-01

    Full Text Available Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs were also identified contributing to the study of A. canescens resources.

  1. [EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

    Science.gov (United States)

    Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

    2017-09-01

    Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

  2. Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

    KAUST Repository

    Brenner, Sydney

    2012-10-08

    Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the \\'oligo-capping\\' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5\\'-ESTs and 41,317 3\\'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for

  3. Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

    KAUST Repository

    Brenner, Sydney; Kodzius, Rimantas; Tan, Yue Ying; Tay, Alice; Tay, Boon-Hui; Venkatesh, Byrappa

    2012-01-01

    Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole

  4. Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

    Science.gov (United States)

    Li, Li; Brunk, Brian P.; Kissinger, Jessica C.; Pape, Deana; Tang, Keliang; Cole, Robert H.; Martin, John; Wylie, Todd; Dante, Mike; Fogarty, Steven J.; Howe, Daniel K.; Liberator, Paul; Diaz, Carmen; Anderson, Jennifer; White, Michael; Jerome, Maria E.; Johnson, Emily A.; Radke, Jay A.; Stoeckert, Christian J.; Waterston, Robert H.; Clifton, Sandra W.; Roos, David S.; Sibley, L. David

    2003-01-01

    Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%–20% represent putative homologs with a conservative cutoff of p neurona: , , , , , , , , , , , , , –, –, –, –, –. Eimeria tenella: –, –, –, –, –, –, –, –, – , –, –, –, –, –, –, –, –, –, –, –. Neospora caninum: –, –, , – , –, –.] PMID:12618375

  5. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Directory of Open Access Journals (Sweden)

    Marais Gabriel AB

    2011-07-01

    Full Text Available Abstract Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO terms, and thousands of single-nucleotide polymorphisms (SNPs were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49% that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to

  6. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Science.gov (United States)

    2011-01-01

    Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a

  7. Development of EST-derived markers in Dendrobium from EST of related taxa

    OpenAIRE

    Narisa Juejun; Chataporn Chunwongse; Julapark Chunwongse

    2013-01-01

    Public databases are useful for molecular marker development. The major aim of this study was to develop expressedsequence tag (EST)-derived markers in Dendrobium from available ESTs of Phalaenopsis and Dendrobium. A total of 6063sequences were screened for simple sequence repeats (SSRs) and introns. Primers flanking these regions were generated andtested on genomic DNAs of Phalaenopsis and Dendrobium. Twenty-three percent of amplifiable Phalaenopsis EST-derivedmarkers were cross-genera trans...

  8. Analysis of a normalised expressed sequence tag (EST) library from a key pollinator, the bumblebee Bombus terrestris.

    Science.gov (United States)

    Sadd, Ben M; Kube, Michael; Klages, Sven; Reinhardt, Richard; Schmid-Hempel, Paul

    2010-02-15

    The bumblebee, Bombus terrestris (Order Hymenoptera), is of widespread importance. This species is extensively used for commercial pollination in Europe, and along with other Bombus spp. is a key member of natural pollinator assemblages. Furthermore, the species is studied in a wide variety of biological fields. The objective of this project was to create a B. terrestris EST resource that will prove to be valuable in obtaining a deeper understanding of this significant social insect. A normalised cDNA library was constructed from the thorax and abdomen of B. terrestris workers in order to enhance the discovery of rare genes. A total of 29'428 ESTs were sequenced. Subsequent clustering resulted in 13'333 unique sequences. Of these, 58.8 percent had significant similarities to known proteins, with 54.5 percent having a "best-hit" to existing Hymenoptera sequences. Comparisons with the honeybee and other insects allowed the identification of potential candidates for gene loss, pseudogene evolution, and possible incomplete annotation in the honeybee genome. Further, given the focus of much basic research and the perceived threat of disease to natural and commercial populations, the immune system of bumblebees is a particularly relevant component. Although the library is derived from unchallenged bees, we still uncover transcription of a number of immune genes spanning the principally described insect immune pathways. Additionally, the EST library provides a resource for the discovery of genetic markers that can be used in population level studies. Indeed, initial screens identified 589 simple sequence repeats and 854 potential single nucleotide polymorphisms. The resource that these B. terrestris ESTs represent is valuable for ongoing work. The ESTs provide direct evidence of transcriptionally active regions, but they will also facilitate further functional genomics, gene discovery and future genome annotation. These are important aspects in obtaining a greater

  9. Salmon louse (Lepeophtheirus salmonis transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis

    Directory of Open Access Journals (Sweden)

    Jonassen Inge

    2008-03-01

    Full Text Available Abstract Background Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proportion of novel transcripts. In order to link unknown transcripts to biological functions we have combined EST sequencing and microarray analysis to characterize female salmon louse transcriptomes during post molting maturation and egg production. Results EST sequence analysis shows that 43% of the ESTs have no significant hits in GenBank. Sequenced ESTs assembled into 556 contigs and 1614 singletons and whenever homologous genes were identified no clear correlation with homologous genes from any specific animal group was evident. Sequence comparison of 27 L. salmonis proteins with homologous proteins in humans, zebrafish, insects and crustaceans revealed an almost identical sequence identity with all species. Microarray analysis of maturing female adult salmon lice revealed two major transcription patterns; up-regulation during the final molting followed by down regulation and female specific up regulation during post molting growth and egg production. For a third minor group of ESTs transcription decreased during molting from pre-adult II to immature adults. Genes regulated during molting typically gave hits with cuticula proteins whilst transcripts up regulated during post molting growth were female specific, including two vitellogenins. Conclusion The copepod L.salmonis contains high a level of novel genes. Among analyzed L.salmonis proteins, sequence identities with homologous proteins in crustaceans are no higher than to homologous proteins in humans. Three distinct processes, molting, post molting growth and egg production correlate with transcriptional regulation of three groups of transcripts; two including genes related to growth, one including genes related to egg production. The function of the regulated

  10. Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers.

    Science.gov (United States)

    Chen, Honglin; Wang, Lixia; Wang, Suhua; Liu, Chunji; Blair, Matthew Wohlgemuth; Cheng, Xuzhen

    2015-01-01

    Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

  11. PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill).

    Science.gov (United States)

    Chaudhary, Sakshi; Mishra, Bharat Kumar; Vivek, Thiruvettai; Magadum, Santoshkumar; Yasin, Jeshima Khan

    2016-01-01

    Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

  12. Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project

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    Heinz Ruth A

    2003-09-01

    Full Text Available Abstract Background Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of small scale cDNA sequencing projects aimed to the specific identification of useful genes for breeding purposes. The objective of this work is to evaluate alternative strategies to high-throughput sequencing projects for the identification of novel genes differentially expressed in sunflower as a source of organ-specific genetic markers that can be functionally associated to important traits. Results Differential organ-specific ESTs were generated from leaf, stem, root and flower bud at two developmental stages (R1 and R4. The use of different sources of RNA as tester and driver cDNA for the construction of differential libraries was evaluated as a tool for detection of rare or low abundant transcripts. Organ-specificity ranged from 75 to 100% of non-redundant sequences in the different cDNA libraries. Sequence redundancy varied according to the target and driver cDNA used in each case. The R4 flower cDNA library was the less redundant library with 62% of unique sequences. Out of a total of 919 sequences that were edited and annotated, 318 were non-redundant sequences. Comparison against sequences in public databases showed that 60% of non-redundant sequences showed significant similarity to known sequences. The number of predicted novel genes varied among the different cDNA libraries, ranging from 56% in the R4 flower to 16 % in the R1 flower bud library. Comparison with sunflower ESTs on public databases showed that 197 of non-redundant sequences (60% did not exhibit significant similarity to previously reported sunflower ESTs. This approach helped to successfully isolate a significant number of new reported sequences

  13. Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

    Science.gov (United States)

    García, Miguel A; Costea, Mihai; Kuzmina, Maria; Stefanović, Saša

    2014-04-01

    The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.

  14. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies. PMID:26960153

  15. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers.

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies.

  16. Generation and analysis of large-scale expressed sequence tags (ESTs from a full-length enriched cDNA library of porcine backfat tissue

    Directory of Open Access Journals (Sweden)

    Lee Hae-Young

    2006-02-01

    Full Text Available Abstract Background Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and microarray analysis is a useful approach to reduce the overall effort needed to identify genes associated with quantitative traits of interest. Results We constructed a full-length enriched cDNA library from porcine backfat tissue. The estimated average size of the cDNA inserts was 1.7 kb, and the cDNA fullness ratio was 70%. In total, we deposited 16,110 high-quality sequences in the dbEST division of GenBank (accession numbers: DT319652-DT335761. For all the expressed sequence tags (ESTs, approximately 10.9 Mb of porcine sequence were generated with an average length of 674 bp per EST (range: 200–952 bp. Clustering and assembly of these ESTs resulted in a total of 5,008 unique sequences with 1,776 contigs (35.46% and 3,232 singleton (65.54% ESTs. From a total of 5,008 unique sequences, 3,154 (62.98% were similar to other sequences, and 1,854 (37.02% were identified as having no hit or low identity (Sus scrofa. Gene ontology (GO annotation of unique sequences showed that approximately 31.7, 32.3, and 30.8% were assigned molecular function, biological process, and cellular component GO terms, respectively. A total of 1,854 putative novel transcripts resulted after comparison and filtering with the TIGR SsGI; these included a large percentage of singletons (80.64% and a small proportion of contigs (13.36%. Conclusion The sequence data generated in this study will provide valuable information for studying expression profiles using EST-based microarrays and assist in the condensation of current pig TCs into clusters representing longer stretches of cDNA sequences. The isolation of genes expressed in backfat tissue is the

  17. GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

    NARCIS (Netherlands)

    Qin Ling,; Prins, P.; Jones, J.T.; Popeijus, H.; Smant, G.; Bakker, J.; Helder, J.

    2001-01-01

    The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power

  18. Flavonoid Biosynthesis Genes Putatively Identified in the Aromatic Plant Polygonum minus via Expressed Sequences Tag (EST Analysis

    Directory of Open Access Journals (Sweden)

    Zamri Zainal

    2012-02-01

    Full Text Available P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic data, the biosynthetic pathway of flavonoids is currently unclear. Identification of candidate genes involved in the flavonoid biosynthetic pathway will significantly contribute to understanding the biosynthesis of active compounds. We have constructed a standard cDNA library from P. minus leaves, and two normalized full-length enriched cDNA libraries were constructed from stem and root organs in order to create a gene resource for the biosynthesis of secondary metabolites, especially flavonoid biosynthesis. Thus, large‑scale sequencing of P. minus cDNA libraries identified 4196 expressed sequences tags (ESTs which were deposited in dbEST in the National Center of Biotechnology Information (NCBI. From the three constructed cDNA libraries, 11 ESTs encoding seven genes were mapped to the flavonoid biosynthetic pathway. Finally, three flavonoid biosynthetic pathway-related ESTs chalcone synthase, CHS (JG745304, flavonol synthase, FLS (JG705819 and leucoanthocyanidin dioxygenase, LDOX (JG745247 were selected for further examination by quantitative RT-PCR (qRT-PCR in different P. minus organs. Expression was detected in leaf, stem and root. Gene expression studies have been initiated in order to better understand the underlying physiological processes.

  19. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

    Directory of Open Access Journals (Sweden)

    Ueno Saneyoshi

    2012-04-01

    Full Text Available Abstract Background Microsatellites or simple sequence repeats (SSRs in expressed sequence tags (ESTs are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica. Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54% contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%. The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3% di-SSRs, followed by the AAG motif, found in 342 (25.9% tri-SSRs. Most (72.8% tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size

  20. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

    Science.gov (United States)

    2012-01-01

    Background Microsatellites or simple sequence repeats (SSRs) in expressed sequence tags (ESTs) are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica). Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54%) contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%). The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3%) di-SSRs, followed by the AAG motif, found in 342 (25.9%) tri-SSRs. Most (72.8%) tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO) annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size and number of SSR

  1. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.).

    Science.gov (United States)

    Guo, Qi; Wang, Jin-Xing; Su, Li-Zhuo; Lv, Wei; Sun, Yu-Han; Li, Yun

    2017-07-07

    Black locust ( Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033-0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000-0.931 and 0.035-0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R . pseudoacacia , constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.

  2. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.

    Science.gov (United States)

    Pereira-Leal, José B; Abreu, Isabel A; Alabaça, Cláudia S; Almeida, Maria Helena; Almeida, Paulo; Almeida, Tânia; Amorim, Maria Isabel; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, Ana Cristina; Costa, Maria Manuela Ribeiro; Costa, Rita; Cravador, Alfredo; Egas, Conceição; Faro, Carlos; Fortes, Ana M; Fortunato, Ana S; Gaspar, Maria João; Gonçalves, Sónia; Graça, José; Horta, Marília; Inácio, Vera; Leitão, José M; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria Margarida; Oliveira, Rute; Pais, Maria Salomé; Paiva, Jorge A; Paulo, Octávio S; Pinheiro, Miguel; Raimundo, João A P; Ramalho, José C; Ribeiro, Ana I; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana Isabel; Rodrigues, José C; Saibo, Nelson J M; Santo, Tatiana E; Santos, Ana Margarida; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria Manuela; Ricardo, Cândido P P

    2014-05-15

    Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

  3. Development of EST-derived markers in Dendrobium from EST of related taxa

    Directory of Open Access Journals (Sweden)

    Narisa Juejun

    2013-04-01

    Full Text Available Public databases are useful for molecular marker development. The major aim of this study was to develop expressedsequence tag (EST-derived markers in Dendrobium from available ESTs of Phalaenopsis and Dendrobium. A total of 6063sequences were screened for simple sequence repeats (SSRs and introns. Primers flanking these regions were generated andtested on genomic DNAs of Phalaenopsis and Dendrobium. Twenty-three percent of amplifiable Phalaenopsis EST-derivedmarkers were cross-genera transferable to Dendrobium. Forty-one markers from both Phalaenopsis and Dendrobium thatamplified in Dendrobium were assessed on six commercial cultivars and six wild accessions. All of them were transferableamong Dendrobium species. High polymorphism and heterozygosity were observed within wild accessions. Sixteen polymorphic markers were evaluated for linkage analysis on an F1 segregating population. Seven markers were mapped into threelinkage groups, two of which showed syntenic relationship between dendrobium and rice. This relationship will facilitatefurther quantitative trait loci (QTL mapping and comparative genomic studies of Dendrobium. Our results indicate thatPhalaenopsis EST-derived markers are valuable tools for genetic research and breeding applications in Dendrobium.

  4. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

    Science.gov (United States)

    Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

    2008-04-10

    Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  5. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

    Directory of Open Access Journals (Sweden)

    Pardinas Jose R

    2008-04-01

    Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  6. CitEST libraries

    Directory of Open Access Journals (Sweden)

    Maria Luísa P. Natividade Targon

    2007-01-01

    Full Text Available In order to obtain a better understanding of what is citrus, 33 cDNA libraries were constructed from different citrus species and genera. Total RNA was extracted from fruits, leaves, flowers, bark, seeds and roots, and subjected or not to different biotic and abiotic stresses (pathogens and drought and at several developmental stages. To identify putative promoter sequences, as well as molecular markers that could be useful for breeding programs, one shotgun library was prepared from sweet orange (Citrus sinensis var. Olimpia. In addition, EST libraries were also constructed for a citrus pathogen, the oomycete Phythophthora parasitica in either virulent or avirulent form. A total of 286,559 cDNA clones from citrus were sequenced from their 5’ end, generating 242,790 valid reads of citrus. A total of 9,504 sequences were produced in the shotgun library and the valid reads were assembled using CAP3. In this procedure, we obtained 1,131 contigs and 4,083 singletons. A total of 19,200 cDNA clones from P. parasitica were sequenced, resulting in 16,400 valid reads. The number of ESTs generated in this project is, to our knowledge, the largest citrus sequence database in the world.

  7. Analysis and functional annotation of expressed sequence tags (ESTs from multiple tissues of oil palm (Elaeis guineensis Jacq.

    Directory of Open Access Journals (Sweden)

    Lee Weng-Wah

    2007-10-01

    Full Text Available Abstract Background Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST analysis on oil palm. Results In this study, six cDNA libraries from oil palm zygotic embryos, suspension cells, shoot apical meristems, young flowers, mature flowers and roots, were constructed. We have generated a total of 14537 expressed sequence tags (ESTs from these libraries, from which 6464 tentative unique contigs (TUCs and 2129 singletons were obtained. Approximately 6008 of these tentative unique genes (TUGs have significant matches to the non-redundant protein database, from which 2361 were assigned to one or more Gene Ontology categories. Predominant transcripts and differentially expressed genes were identified in multiple oil palm tissues. Homologues of genes involved in many aspects of flower development were also identified among the EST collection, such as CONSTANS-like, AGAMOUS-like (AGL2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP etc. Majority of them are the first representatives in oil palm, providing opportunities to explore the cause of epigenetic homeotic flowering abnormality in oil palm, given the importance of flowering in fruit production. The transcript levels of two flowering-related genes, EgSBP and EgSEP were analysed in the flower tissues of various developmental stages. Gene homologues for enzymes involved in oil biosynthesis, utilization of nitrogen sources, and scavenging of oxygen radicals, were also uncovered among the oil palm ESTs. Conclusion The EST sequences generated will allow comparative genomic studies between oil palm and other monocotyledonous and dicotyledonous plants, development of gene-targeted markers for the reference genetic map

  8. Expressed sequence tag (EST) analysis of two subspecies of Metarhizium anisopliae reveals a plethora of secreted proteins with potential activity in insect hosts.

    Science.gov (United States)

    Freimoser, Florian M; Screen, Steven; Bagga, Savita; Hu, Gang; St Leger, Raymond J

    2003-01-01

    Expressed sequence tag (EST) libraries for Metarhizium anisopliae, the causative agent of green muscardine disease, were developed from the broad host-range pathogen Metarhizium anisopliae sf. anisopliae and the specific grasshopper pathogen, M. anisopliae sf. acridum. Approximately 1,700 5' end sequences from each subspecies were generated from cDNA libraries representing fungi grown under conditions that maximize secretion of cuticle-degrading enzymes. Both subspecies had ESTs for virtually all pathogenicity-related genes cloned to date from M. anisopliae, but many novel genes encoding potential virulence factors were also tagged. Enzymes with potential targets in the insect host included proteases, chitinases, phospholipases, lipases, esterases, phosphatases and enzymes producing toxic secondary metabolites. A diverse array of proteases composed 36 % of all M. anisopliae sf. anisopliae ESTs. Eighty percent of the ESTs that could be clustered into functional groups had significant matches (Ehistory of this clade.

  9. Analysis of SSR information in EST resources of sugarcane

    Science.gov (United States)

    Expressed sequence tags ( ESTs) offer the opportunity to exploit single, low -copy, conserved sequence motifs for the development of simple sequence repeats ( SSRs). The total of 262 113 ESTs of sugarcane (Saccharum officinarum) in the database of NCBI were downloaded and analyzed, which resulted in...

  10. BLOG 2.0: a software system for character-based species classification with DNA Barcode sequences. What it does, how to use it

    NARCIS (Netherlands)

    Weitschek, E.; Velzen, van R.; Felici, G.; Bertolazzi, P.

    2013-01-01

    BLOG (Barcoding with LOGic) is a diagnostic and character-based DNA Barcode analysis method. Its aim is to classify specimens to species based on DNA Barcode sequences and on a supervised machine learning approach, using classification rules that compactly characterize species in terms of DNA

  11. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

    Science.gov (United States)

    2011-01-01

    Background Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. Results To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar

  12. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

    Directory of Open Access Journals (Sweden)

    Wynhoven Brian

    2011-03-01

    Full Text Available Abstract Background Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. Results To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt, we have generated Expressed Sequence Tags (ESTs by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores and asexual (germinated urediniospores stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum, 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs. Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt and stripe rust, P. striiformis f. sp

  13. Wheat EST resources for functional genomics of abiotic stress

    Directory of Open Access Journals (Sweden)

    Links Matthew G

    2006-06-01

    Full Text Available Abstract Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets. Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in

  14. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.

    Directory of Open Access Journals (Sweden)

    Yang Jun-Bo

    2010-12-01

    Full Text Available Abstract Background The castor bean (Ricinus communis L., a monotypic species in the spurge family (Euphorbiaceae, 2n = 20, is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85% in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly

  15. An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies.

    Science.gov (United States)

    Frentiu, Francesca D; Adamski, Marcin; McGraw, Elizabeth A; Blows, Mark W; Chenoweth, Stephen F

    2009-01-21

    The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number of important questions, including the evolution of traits under sexual selection and traits involved in climatic adaptation along latitudinal gradients. Understanding the molecular genetic basis of such traits has been limited by a lack of genomic resources for this species. Here, we present the first expressed sequence tag (EST) collection for D. serrata that will enable the identification of genes underlying sexually-selected phenotypes and physiological responses to environmental change and may help resolve controversial phylogenetic relationships within the montium subgroup. A normalized cDNA library was constructed from whole fly bodies at several developmental stages, including larvae and adults. Assembly of 11,616 clones sequenced from the 3' end allowed us to identify 6,607 unique contigs, of which at least 90% encoded peptides. Partial transcripts were discovered from a variety of genes of evolutionary interest by BLASTing contigs against the 12 Drosophila genomes currently sequenced. By incorporating into the cDNA library multiple individuals from populations spanning a large portion of the geographical range of D. serrata, we were able to identify 11,057 putative single nucleotide polymorphisms (SNPs), with 278 different contigs having at least one "double hit" SNP that is highly likely to be a real polymorphism. At least 394 EST-associated microsatellite markers, representing 355 different contigs, were also found, providing an additional set of genetic markers. The assembled EST library is available online at http://www.chenowethlab.org/serrata/index.cgi. We have provided the first gene collection and largest set of polymorphic genetic markers, to date, for the fly D. serrata. The EST collection will provide much needed genomic resources for

  16. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Wei, Chaochun; Brown, Randall H

    2006-01-01

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on trans alignments, in which expressed sequences are aligned to the genomic loci...... with de novo gene prediction by using N-SCAN_EST. N-SCAN_EST is based on a generalized HMM probability model augmented with a phylogenetic conservation model and EST alignments. It can predict complete transcripts by extending or merging EST alignments, but it can also predict genes in regions without EST...

  17. Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster.

    Directory of Open Access Journals (Sweden)

    Shigeharu Kinoshita

    Full Text Available BACKGROUND: Despite its economic importance, we have a limited understanding of the molecular mechanisms underlying shell formation in pearl oysters, wherein the calcium carbonate crystals, nacre and prism, are formed in a highly controlled manner. We constructed comprehensive expressed gene profiles in the shell-forming tissues of the pearl oyster Pinctada fucata and identified novel shell formation-related genes candidates. PRINCIPAL FINDINGS: We employed the GS FLX 454 system and constructed transcriptome data sets from pallial mantle and pearl sac, which form the nacreous layer, and from the mantle edge, which forms the prismatic layer in P. fucata. We sequenced 260477 reads and obtained 29682 unique sequences. We also screened novel nacreous and prismatic gene candidates by a combined analysis of sequence and expression data sets, and identified various genes encoding lectin, protease, protease inhibitors, lysine-rich matrix protein, and secreting calcium-binding proteins. We also examined the expression of known nacreous and prismatic genes in our EST library and identified novel isoforms with tissue-specific expressions. CONCLUSIONS: We constructed EST data sets from the nacre- and prism-producing tissues in P. fucata and found 29682 unique sequences containing novel gene candidates for nacreous and prismatic layer formation. This is the first report of deep sequencing of ESTs in the shell-forming tissues of P. fucata and our data provide a powerful tool for a comprehensive understanding of the molecular mechanisms of molluscan biomineralization.

  18. A structural query system for Han characters

    DEFF Research Database (Denmark)

    Skala, Matthew

    2016-01-01

    The IDSgrep structural query system for Han character dictionaries is presented. This dictionary search system represents the spatial structure of Han characters using Extended Ideographic Description Sequences (EIDSes), a data model and syntax based on the Unicode IDS concept. It includes a query...... language for EIDS databases, with a freely available implementation and format translation from popular third-party IDS and XML character databases. The system is designed to suit the needs of font developers and foreign language learners. The search algorithm includes a bit vector index inspired by Bloom...... filters to support faster query operations. Experimental results are presented, evaluating the effect of the indexing on query performance....

  19. Development and characterization of polymorphic EST based SSR markers in barley (Hordeum vulgare).

    Science.gov (United States)

    Jo, Won-Sam; Kim, Hye-Yeong; Kim, Kyung-Min

    2017-08-01

    In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study. A cDNA library of the cultivar Gwanbori was constructed for use in analysis of genetic relationships, and 58 EST-SSR markers were developed and characterized. In total, 47 SSR markers were employed to analyze polymorphisms. A relationship dendrogram based on the polymorphism data was constructed to compare genetic diversity. We found that the polymorphism information content among the examined cultivars was 0.519, which indicates that there is low genetic diversity among Korean barley cultivars. The results obtained in this study may be useful in preventing redundant investment in new cultivars and in resolving disputes over seed patents. Our approach can be used by companies and government groups to develop different cultivars with distinguishable markers. In addition, the developed markers can be used for quantitative trait locus analysis to improve both the quantity and the quality of cultivated barley.

  20. Trimming and clustering sugarcane ESTs

    Directory of Open Access Journals (Sweden)

    Guilherme P. Telles

    2001-12-01

    Full Text Available The original clustering procedure adopted in the Sugarcane Expressed Sequence Tag project (SUCEST had many problems, for instance too many clusters, the presence of ribosomal sequences, etc. We therefore redesigned the clustering procedure entirely, including a much more careful initial trimming of the reads. In this paper the new trimming and clustering strategies are described in detail and we give the new official figures for the project, 237,954 expressed sequence tags and 43,141 clusters.O método de clustering adotado no Projeto SUCEST (Sugarcane EST Project tinha vários problemas (muitos clusters, presença de seqüências de ribossomo etc. Nós assumimos a tarefa de reprojetar todo o processo de clustering, propondo uma "limpeza" inicial mais cuidadosa das seqüências. Neste artigo as estratégias de limpeza das seqüências e de clustering são descritas em detalhe, incluindo os números oficiais do projeto (237,954 ESTs e 43,141 clusters.

  1. Recognizing Chinese characters in digital ink from non-native language writers using hierarchical models

    Science.gov (United States)

    Bai, Hao; Zhang, Xi-wen

    2017-06-01

    While Chinese is learned as a second language, its characters are taught step by step from their strokes to components, radicals to components, and their complex relations. Chinese Characters in digital ink from non-native language writers are deformed seriously, thus the global recognition approaches are poorer. So a progressive approach from bottom to top is presented based on hierarchical models. Hierarchical information includes strokes and hierarchical components. Each Chinese character is modeled as a hierarchical tree. Strokes in one Chinese characters in digital ink are classified with Hidden Markov Models and concatenated to the stroke symbol sequence. And then the structure of components in one ink character is extracted. According to the extraction result and the stroke symbol sequence, candidate characters are traversed and scored. Finally, the recognition candidate results are listed by descending. The method of this paper is validated by testing 19815 copies of the handwriting Chinese characters written by foreign students.

  2. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology.

    Science.gov (United States)

    Tanase, Koji; Nishitani, Chikako; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Ohmiya, Akemi; Onozaki, Takashi

    2012-07-02

    Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. We constructed a normalized cDNA library and a 3'-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  3. Transcriptome analysis of carnation (Dianthus caryophyllus L. based on next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Tanase Koji

    2012-07-01

    Full Text Available Abstract Background Carnation (Dianthus caryophyllus L., in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. Results We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380 of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. Conclusions We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  4. Genetic variation patterns of American chestnut populations at EST-SSRs

    Science.gov (United States)

    Oliver Gailing; C. Dana Nelson

    2017-01-01

    The objective of this study is to analyze patterns of genetic variation at genic expressed sequence tag - simple sequence repeats (EST-SSRs) and at chloroplast DNA markers in populations of American chestnut (Castanea dentata Borkh.) to assist in conservation and breeding efforts. Allelic diversity at EST-SSRs decreased significantly from southwest to northeast along...

  5. Sugarcane expressed sequences tags (ESTs encoding enzymes involved in lignin biosynthesis pathways

    Directory of Open Access Journals (Sweden)

    Ramos Rose Lucia Braz

    2001-01-01

    Full Text Available Lignins are phenolic polymers found in the secondary wall of plant conductive systems where they play an important role by reducing the permeability of the cell wall to water. Lignins are also responsible for the rigidity of the cell wall and are involved in mechanisms of resistance to pathogens. The metabolic routes and enzymes involved in synthesis of lignins have been largely characterized and representative genes that encode enzymes involved in these processes have been cloned from several plant species. The synthesis of lignins is liked to the general metabolism of the phenylpropanoids in plants, having enzymes (e.g. phenylalanine ammonia-lyase (PAL, cinnamate 4-hydroxylase (C4H and caffeic acid O-methyltransferase (COMT common to other processes as well as specific enzymes such as cinnamoyl-CoA reductase (CCR and cinnamyl alcohol dehydrogenase (CAD. Some maize and sorghum mutants, shown to have defective in CAD and/or COMT activity, are easier to digest because they have a reduced lignin content, something which has motivated different research groups to alter the lignin content and composition of model plants by genetic engineering try to improve, for example, the efficiency of paper pulping and digestibility. In the work reported in this paper, we have made an inventory of the sugarcane expressed sequence tag (EST coding for enzymes involved in lignin metabolism which are present in the sugarcane EST genome project (SUCEST database. Our analysis focused on the key enzymes ferulate-5-hydroxylase (F5H, caffeic acid O-methyltransferase (COMT, caffeoyl CoA O-methyltransferase (CCoAOMT, hydroxycinnamate CoA ligase (4CL, cinnamoyl-CoA reductase (CCR and cinnamyl alcohol dehydrogenase (CAD. The comparative analysis of these genes with those described in other species could be used as molecular markers for breeding as well as for the manipulation of lignin metabolism in sugarcane.

  6. ESTIMA, a tool for EST management in a multi-project environment.

    Science.gov (United States)

    Kumar, Charu G; LeDuc, Richard; Gong, George; Roinishivili, Levan; Lewin, Harris A; Liu, Lei

    2004-11-04

    Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http

  7. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    SERVER

    2008-02-19

    Feb 19, 2008 ... the discovery of the DNA, a new area of modern plant biotechnology begun. In plant ... Marker Assisted Breeding and Sequence Tagged Sites. (STS) are all in use in modern ...... and behaviour in the honey bee. Genome Res.

  8. ESAP plus: a web-based server for EST-SSR marker development.

    Science.gov (United States)

    Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

    2016-12-22

    Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can

  9. DNA repair-related genes in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    R.M.A. Costa

    2001-12-01

    écies. Os mecanismos relacionados à remoção de danos pelo reparo de DNA, bem como suas conseqüências biológicas, já são bem conhecidas em bactérias, leveduras e animais. Entretanto, no que diz respeito a organismos vegetais, ainda há muito a ser investigado. No presente trabalho, apresentamos a identificação dos genes envolvidos nas principais vias de reparo de DNA em cana-de-açúcar, através de uma análise de similaridade do banco de dados do projeto brasileiro Sugarcane Expressed Sequence Tag (SUCEST com seqüências protéicas conhecidas disponíveis em outros bancos de dados públicos (National Center of Biotechnology Information (NCBI e Munich Information Center for Protein Sequences (MIPS Arabidopsis thaliana. Esta busca revelou que a gama de proteínas envolvidas no reparo de DNA em cana-de-açúcar é similar a de outros eucariotos. Mesmo assim, foi possível identificar algumas características interessantes encontradas apenas em vegetais, provavelmente em função do seu processo evolutivo independente. As vias de reparo de DNA aqui representadas incluem fotorreativação, reparo excisão de bases, reparo excisão de nucleotídeos, reparo mismatch, end-joinning não homólogo, reparo por recombinação homóloga e tolerância a lesões. Este trabalho descreve as principais diferenças encontradas na maquinaria de reparo de DNA de células vegetais em relação àquela de organismos nos quais encontra-se bem descrita. Tais diferenças chamam a atenção para um potencial de mecanismos distintos em vegetais, que merecem futuras investigações.

  10. annot8r: GO, EC and KEGG annotation of EST datasets

    Directory of Open Access Journals (Sweden)

    Schmid Ralf

    2008-04-01

    Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non

  11. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

    Directory of Open Access Journals (Sweden)

    Richardson Annette C

    2008-07-01

    Full Text Available Abstract Background Kiwifruit (Actinidia spp. are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs. Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons. Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases and pathways (terpenoid biosynthesis is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

  12. 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, ...

  13. Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum transcriptome

    Directory of Open Access Journals (Sweden)

    Kim Woo Taek

    2008-10-01

    Full Text Available Abstract Background There is no dedicated database available for Expressed Sequence Tags (EST of the chili pepper (Capsicum annuum, although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses. Results We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO, and MIPS Functional Catalogue (FunCat. The Pepper EST database is designed to provide a workbench for (i identifying unigenes in pepper plants, (ii analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/. Conclusion The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.

  14. Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

    Directory of Open Access Journals (Sweden)

    Lanfranchi Gerolamo

    2002-10-01

    Full Text Available Abstract Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 EST clusters from a non-normalized subtracted muscle EST sequencing project (28,074 EST sequences. This set included 369 novel EST clusters showing no match to previously characterized proteins in any database. Each probe set was designed to contain 20–32 25 mer oligonucleotides (10–16 paired perfect match and mismatch probe pairs per gene, with each probe evaluated for hybridization kinetics (Tm and similarity to other sequences. The 120,000 oligonucleotides were synthesized by photolithography and light-activated chemistry on each microarray. Results Hybridization of human muscle cRNAs to this MuscleChip (33 samples showed a correlation of 0.6 between the number of ESTs sequenced in each cluster and hybridization intensity. Out of 369 novel EST clusters not showing any similarity to previously characterized proteins, we focused on 250 EST clusters that were represented by robust probe sets on the MuscleChip fulfilling all stringent rules. 102 (41% were found to be consistently "present" by analysis of hybridization to human muscle RNA, of which 40 ESTs (39% could be genome anchored to potential transcription units in the human genome sequence. 19 ESTs of the 40 ESTs were furthermore computer-predicted as exons by one or more than three gene identification algorithms. Conclusion Our analysis found 40 transcriptionally validated, genome-anchored novel EST clusters to be expressed in human muscle. As most of these ESTs were low copy clusters (duplex and triplex in the original 28,000 EST project, the identification of these as significantly expressed is a robust validation of the transcript units that permits subsequent focus on the novel proteins encoded by these genes.

  15. ESTIMA, a tool for EST management in a multi-project environment

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2004-11-01

    Full Text Available Abstract Background Single-pass, partial sequencing of complementary DNA (cDNA libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs, and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. Results A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA, has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera, cattle (Bos taurus, songbird (Taeniopygia guttata, corn rootworm (Diabrotica vergifera, catfish (Ictalurus punctatus, Ictalurus furcatus, and apple (Malus x domestica. The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. Conclusions The scripts used to create the ESTIMA interface are freely available to academic users in

  16. PAVE: Program for assembling and viewing ESTs

    Directory of Open Access Journals (Sweden)

    Bomhoff Matthew

    2009-08-01

    Full Text Available Abstract Background New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. Results The PAVE (Program for Assembling and Viewing ESTs assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. Conclusion The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

  17. PAVE: program for assembling and viewing ESTs.

    Science.gov (United States)

    Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

    2009-08-26

    New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

  18. Species tree phylogeny and character evolution in the genus Centipeda (Asteraceae): evidence from DNA sequences from coding and non-coding loci from the plastid and nuclear genomes.

    Science.gov (United States)

    Nylinder, Stephan; Cronholm, Bodil; de Lange, Peter J; Walsh, Neville; Anderberg, Arne A

    2013-08-01

    A species tree phylogeny of the Australian/New Zealand genus Centipeda (Asteraceae) is estimated based on nucleotide sequence data. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and three plasmid loci (ndhF, psbA-trnH, and trnL-F) using the multi-species coalescent module in BEAST. A total of 129 individuals from all 10 recognised species of Centipeda were sampled throughout the species distribution ranges, including two subspecies. We conclude that the inferred species tree topology largely conform previous assumptions on species relationships. Centipeda racemosa (Snuffweed) is the sister to remaining species, which is also the only consistently perennial representative in the genus. Centipeda pleiocephala (Tall Sneezeweed) and C. nidiformis (Cotton Sneezeweed) constitute a species pair, as does C. borealis and C. minima (Spreading Sneezeweed), all sharing the symplesiomorphic characters of spherical capitulum and convex receptacle with C. racemosa. Another species group comprising C. thespidioides (Desert Sneezeweed), C. cunninghamii (Old man weed, or Common sneeze-weed), C. crateriformis is well-supported but then include the morphologically aberrant C. aotearoana, all sharing the character of having capitula that mature more slowly relative the subtending shoot. Centipeda elatinoides takes on a weakly supported intermediate position between the two mentioned groups, and is difficult to relate to any of the former groups based on morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.

    Science.gov (United States)

    Watkins, Russell F; Gray, Michael W

    2008-04-01

    From comparative analysis of EST data for five taxa within the eukaryotic supergroup Amoebozoa, including two free-living amoebae (Acanthamoeba castellanii, Hartmannella vermiformis) and three slime molds (Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.), we obtained new broad-range perspectives on the evolution and biosynthetic capacity of this assemblage. Together with genome sequences for the amoebozoans Dictyostelium discoideum and Entamoeba histolytica, and including partial genome sequence available for A. castellanii, we used the EST data to identify genes that appear to be exclusive to the supergroup, and to specific clades therein. Many of these genes are likely involved in cell-cell communication or differentiation. In examining on a broad scale a number of characters that previously have been considered in simpler cross-species comparisons, typically between Dictyostelium and Entamoeba, we find that Amoebozoa as a whole exhibits striking variation in the number and distribution of biosynthetic pathways, for example, ones for certain critical stress-response molecules, including trehalose and mannitol. Finally, we report additional compelling cases of lateral gene transfer within Amoebozoa, further emphasizing that although this process has influenced genome evolution in all examined amoebozoan taxa, it has done so to a variable extent.

  20. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes

    Directory of Open Access Journals (Sweden)

    Runko Suzan J

    2005-10-01

    Full Text Available Abstract Background Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate, female (megasporangiate, and vegetative organs (leaves of Ginkgo biloba. Results RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants – many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Conclusion Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and

  1. Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus root, leaves and nodules in the context of carbohydrate metabolism investigation

    Directory of Open Access Journals (Sweden)

    Boutry Marc

    2009-01-01

    Full Text Available Abstract Background The industrial chicory, Cichorium intybus, is a member of the Asteraceae family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison. Results Approximately 1,000 Expressed Sequence Tags (EST were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution. Conclusion This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.

  2. Neural Semantic Parsing by Character-based Translation: Experiments with Abstract Meaning Representations

    NARCIS (Netherlands)

    van Noord, Rik; Bos, Johannes

    2017-01-01

    We evaluate the character-level translation method for neural semantic parsing on a large corpus of sentences annotated with Abstract Meaning Representations (AMRs). Using a sequence-to-sequence model, and some trivial preprocessing and postprocessing of AMRs, we obtain a baseline accuracy of 53.1

  3. Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp. sativa

    Directory of Open Access Journals (Sweden)

    Zhipeng Liu

    2014-05-01

    Full Text Available The common vetch (Vicia sativa subsp. sativa, a self-pollinating and diploid species, is one of the most important annual legumes in the world due to its short growth period, high nutritional value, and multiple usages as hay, grain, silage, and green manure. The available simple sequence repeat (SSR markers for common vetch, however, are insufficient to meet the developing demand for genetic and molecular research on this important species. Here, we aimed to develop and characterise several polymorphic EST-SSR markers from the vetch Illumina transcriptome. A total number of 1,071 potential EST-SSR markers were identified from 1025 unigenes whose lengths were greater than 1,000 bp, and 450 primer pairs were then designed and synthesized. Finally, 95 polymorphic primer pairs were developed for the 10 common vetch accessions, which included 50 individuals. Among the 95 EST-SSR markers, the number of alleles ranged from three to 13, and the polymorphism information content values ranged from 0.09 to 0.98. The observed heterozygosity values ranged from 0.00 to 1.00, and the expected heterozygosity values ranged from 0.11 to 0.98. These 95 EST-SSR markers developed from the vetch Illumina transcriptome could greatly promote the development of genetic and molecular breeding studies pertaining to in this species.

  4. Signaling pathways in a Citrus EST database

    Directory of Open Access Journals (Sweden)

    Angela Mehta

    2007-01-01

    Full Text Available Citrus spp. are economically important crops, which in Brazil are grown mainly in the State of São Paulo. Citrus cultures are attacked by several pathogens, causing severe yield losses. In order to better understand this culture, the Millenium Project (IAC Cordeirópolis was launched in order to sequence Citrus ESTs (expressed sequence tags from different tissues, including leaf, bark, fruit, root and flower. Plants were submitted to biotic and abiotic stresses and investigated under different development stages (adult vs. juvenile. Several cDNA libraries were constructed and the sequences obtained formed the Citrus ESTs database with almost 200,000 sequences. Searches were performed in the Citrus database to investigate the presence of different signaling pathway components. Several of the genes involved in the signaling of sugar, calcium, cytokinin, plant hormones, inositol phosphate, MAPKinase and COP9 were found in the citrus genome and are discussed in this paper. The results obtained may indicate that similar mechanisms described in other plants, such as Arabidopsis, occur in citrus. Further experimental studies must be conducted in order to understand the different signaling pathways present.

  5. PCR-Based EST Mapping in Wheat (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    J. PERRY GUSTAFSON

    2009-04-01

    Full Text Available Mapping expressed sequence tags (ESTs to hexaploid wheat is aimed to reveal the structure and function of the hexaploid wheat genome. Sixty eight ESTs representing 26 genes were mapped into all seven homologous chromosome groups of wheat (Triticum aestivum L using a polymerase chain reaction technique. The majority of the ESTs were mapped to homologous chromosome group 2, and the least were mapped to homologous chromosome group 6. Comparative analysis between the EST map from this study and the EST map based on RFLPs showed 14 genes that have been mapped by both approaches were mapped to the same arm of the same homologous chromosome, which indicated that using PCR-based ESTs was a reliable approach in mapping ESTs in hexaploid wheat.

  6. Transcriptome analysis of blueberry using 454 EST sequencing

    Science.gov (United States)

    Blueberry (Vaccinium corymbosum) is a major berry crop in the United States, and one that has great nutritional and economical value. Next generation sequencing methodologies, such as 454, have been demonstrated to be successful and efficient in producing a snap-shot of transcriptional activities du...

  7. Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

    Directory of Open Access Journals (Sweden)

    Sugantham Priyanka Annabel

    2010-10-01

    Full Text Available Abstract Background Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs. Results A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 106 clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes. Conclusions The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding

  8. All 5' EST - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...n of data contents 5' EST sequences Data file File name: CSV: kome_est_5end_all.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...fasta.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_est_5end_...se Description Download License Update History of This Database Site Policy | Contact Us All 5' EST - KOME | LSDB Archive ...

  9. All 3' EST - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...n of data contents 3' EST sequences Data file File name: CSV: kome_est_3end_all.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...fasta.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_est_3end_...se Description Download License Update History of This Database Site Policy | Contact Us All 3' EST - KOME | LSDB Archive ...

  10. High-resolution sequence stratigraphic character and sandstone-type uranium ore formation. A case from Saihan Formation in Baiyinwula area, Erlian Basin

    International Nuclear Information System (INIS)

    He Zhongbo; Qin Mingkuan

    2006-01-01

    High-resolution sequence stratigraphy has been applied widely in the petroleum exploration and development, many achievements have been achieved. However, it is in the beginning stage that high-resolution sequence stratigraphy is applied to explore the sandstone-type uranium deposits in Erlian Basin. By applying principles of high-resolution sequence stratigraphy and taking typical boreholes as an example, sedimentary cycles of Saihan Formation, the ore-bearing formation in Baiyinwula area are divided and correlated through cross sections. One long-term cycle (LSC 1 ), two middle-term cycles (MSC 1 , MSC 2 ) have been identified in this study. Based on this and combined with the mineralization character of sandstone uranium deposits in this area, it is presented that the interlayer oxidation zone is developed mainly in the rising hemicycle of MSC 1 and uranium ore bodies predominantly in channel sand bodies that were developed in the system tract with low accommodation; furthermore, it is recognized that these sand bodies are moderate (10-15 m) in thickness, fairly good in interconnectivity, relatively thin (<3 m) with the argillaceous interbed, and good in permeability, abundant in the organic matter and thus it is favorable for the development of the interlayer oxidization zone. (authors)

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

    Directory of Open Access Journals (Sweden)

    Borba Tereza CO

    2011-05-01

    Full Text Available Abstract 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

  12. Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae).

    Science.gov (United States)

    Ju, Miao-Miao; Ma, Huan-Cheng; Xin, Pei-Yao; Zhou, Zhi-Li; Tian, Bin

    2015-04-01

    Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for the species using transcriptome analysis. A total of 33 new EST-SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively. These newly developed EST-SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST-SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.

  13. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis for Crossbreeding

    Directory of Open Access Journals (Sweden)

    Yueting Dai

    2017-11-01

    Full Text Available Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu. However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.

  14. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding

    Science.gov (United States)

    Dai, Yueting; Su, Wenying; Song, Bing; Li, Yu; Fu, Yongping

    2017-01-01

    Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species. PMID:29149037

  15. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae to develop and characterize new EST-SSR markers and construct an EST-SSR database.

    Directory of Open Access Journals (Sweden)

    Fang K Du

    Full Text Available BACKGROUND: Microsatellite markers or Simple Sequence Repeats (SSRs are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS: A total of 94,090 non-redundant Expressed Sequence Tags (ESTs from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37% and hexanucleotides (33% repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs and selected 673 of these pairs at random for further validation. 575 pairs (85% gave successful amplification, of which, 464 (80.7% were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html. CONCLUSIONS: The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.

  16. Construction of new EST-SSRs for Fusarium resistant wheat breeding.

    Science.gov (United States)

    Yumurtaci, Aysen; Sipahi, Hulya; Al-Abdallat, Ayed; Jighly, Abdulqader; Baum, Michael

    2017-06-01

    Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome. Based on the fragment profiling and similarity analysis, a 327bp amplicon, which was a product of contig 1207 (chromosome 5BL), was detected only in Fusarium head blight (FHB) resistant cultivars (CM82036 and Sumai) and the amino acid sequences showed a similarity to pathogen related proteins. Another FHB resistance related EST-SSR, Contig 556 (chromosome 1BL) produced a 151bp fragment in Sumai and was associated to wax2-like protein. A polymorphic 204bp fragment, derived from Contig 578 (chromosome 1DL), was generated from root rot (FRR) resistant cultivars (2-49; Altay2000 and Sunco). A total of 98 alleles were displayed with an average of 1.8 alleles per locus and the polymorphic information content (PIC) ranged from 0.11 to 0.78. Dendrogram tree with two main and five sub-groups were displayed the highest genetic relationship between FRR resistant cultivars (2-49 and Altay2000), FRR sensitive cultivars (Seri82 and Scout66) and FHB resistant cultivars (CM82036 and Sumai). Thus, exploitation of these candidate EST-SSRs may help to genotype other wheat sources for Fusarium resistance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Characters with personality!

    NARCIS (Netherlands)

    Bosch, K. van den; Brandenburgh, A.; Muller, T.J.; Heuvelink, A.

    2012-01-01

    Serious games offer an opportunity for learning communication skills by practicing conversations with one or more virtual characters, provided that the character(s) behave in accordance with their assigned properties and strate-gies. This paper presents an approach for developing virtual characters

  18. Print preparation of the logical INIS-character set for a digital LNO3 printer

    International Nuclear Information System (INIS)

    Mueller, M.; Nevyjel, A.

    1987-09-01

    The implementation of the revised INIS-character set (describedin INIS-Circular Letter No.131) made it necessary to develop a print preparation program, which transfers most of the new INIS logical characters to characters, which are printable on a local LNO3 laser printer. The program is written in PL/I and runs under VAX/VMS on a VAX 11/750. It reads a normal print file and replaces the encoded logical characters by special control sequences, which generate the corresponding images on the LNO3 printer. The program is used for print preparation of any INIS-data records, both input preparation and output tape utilisation on the local VAX system. (Author)

  19. Two EST-derived marker systems for cultivar identification in tree peony.

    Science.gov (United States)

    Zhang, J J; Shu, Q Y; Liu, Z A; Ren, H X; Wang, L S; De Keyser, E

    2012-02-01

    Tree peony (Paeonia suffruticosa Andrews), a woody deciduous shrub, belongs to the section Moutan DC. in the genus of Paeonia of the Paeoniaceae family. To increase the efficiency of breeding, two EST-derived marker systems were developed based on a tree peony expressed sequence tag (EST) database. Using target region amplification polymorphism (TRAP), 19 of 39 primer pairs showed good amplification for 56 accessions with amplicons ranging from 120 to 3,000 bp long, among which 99.3% were polymorphic. In contrast, 7 of 21 primer pairs demonstrated adequate amplification with clear bands for simple sequence repeats (SSRs) developed from ESTs, and a total of 33 alleles were found in 56 accessions. The similarity matrices generated by TRAP and EST-SSR markers were compared, and the Mantel test (r = 0.57778, P = 0.0020) showed a moderate correlation between the two types of molecular markers. TRAP markers were suitable for DNA fingerprinting and EST-SSR markers were more appropriate for discriminating synonyms (the same cultivars with different names due to limited information exchanged among different geographic areas). The two sets of EST-derived markers will be used further for genetic linkage map construction and quantitative trait locus detection in tree peony.

  20. The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

    Science.gov (United States)

    Kozlov, Sergey; Grishin, Eugene

    2011-01-31

    Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

  1. Character Decomposition and Transposition Processes in Chinese Compound Words Modulates Attentional Blink.

    Science.gov (United States)

    Cao, Hongwen; Gao, Min; Yan, Hongmei

    2016-01-01

    The attentional blink (AB) is the phenomenon in which the identification of the second of two targets (T2) is attenuated if it is presented less than 500 ms after the first target (T1). Although the AB is eliminated in canonical word conditions, it remains unclear whether the character order in compound words affects the magnitude of the AB. Morpheme decomposition and transposition of Chinese two-character compound words can provide an effective means to examine AB priming and to assess combinations of the component representations inherent to visual word identification. In the present study, we examined the processing of consecutive targets in a rapid serial visual presentation (RSVP) paradigm using Chinese two-character compound words in which the two characters were transposed to form meaningful words or meaningless combinations (reversible, transposed, or canonical words). We found that when two Chinese characters that form a compound word, regardless of their order, are presented in an RSVP sequence, the likelihood of an AB for the second character is greatly reduced or eliminated compared to when the two characters constitute separate words rather than a compound word. Moreover, the order of the report for the two characters is more likely to be reversed when the normal order of the two characters in a compound word is reversed, especially when the interval between the presentation of the two characters is extremely short. These findings are more consistent with the cognitive strategy hypothesis than the resource-limited hypothesis during character decomposition and transposition of Chinese two-character compound words. These results suggest that compound characters are perceived as a unit, rather than two separate words. The data further suggest that readers could easily understand the text with character transpositions in compound words during Chinese reading.

  2. Peanut (Arachis hypogaea Expressed Sequence Tag Project: Progress and Application

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2012-01-01

    Full Text Available Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.

  3. Identification and Validation of EST-Derived Molecular Markers, TRAP and VNTRs, for Banana Research

    NARCIS (Netherlands)

    Garcia, S.A.L.; Talebi, R.; Ferreira, C.F.; Vroh, B.I.; Paiva, L.V.; Kema, G.H.J.; Souza, M.T.

    2011-01-01

    The advent of high-throughput sequencing technology has generated abundant information on DNA sequences for the genomes of many plant species. Expressed Sequence Tags (ESTs), which are unique DNA sequences derived from a cDNA library and therefore representing genes transcribed in specific tissues

  4. Differential transferability of EST-SSR primers developed from diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Th. elongatum

    Science.gov (United States)

    Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid T...

  5. The mining of toxin-like polypeptides from EST database by single residue distribution analysis

    Directory of Open Access Journals (Sweden)

    Grishin Eugene

    2011-01-01

    Full Text Available Abstract Background Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Results Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. Conclusions The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

  6. Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

    Directory of Open Access Journals (Sweden)

    Nicholas J Schurch

    Full Text Available The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1 gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb; (2 disentangling of gene expression in complex regions; (3 clearer interpretation of small RNA expression and (4 identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.

  7. Applying Agrep to r-NSA to solve multiple sequences approximate matching.

    Science.gov (United States)

    Ni, Bing; Wong, Man-Hon; Lam, Chi-Fai David; Leung, Kwong-Sak

    2014-01-01

    This paper addresses the approximate matching problem in a database consisting of multiple DNA sequences, where the proposed approach applies Agrep to a new truncated suffix array, r-NSA. The construction time of the structure is linear to the database size, and the computations of indexing a substring in the structure are constant. The number of characters processed in applying Agrep is analysed theoretically, and the theoretical upper-bound can approximate closely the empirical number of characters, which is obtained through enumerating the characters in the actual structure built. Experiments are carried out using (synthetic) random DNA sequences, as well as (real) genome sequences including Hepatitis-B Virus and X-chromosome. Experimental results show that, compared to the straight-forward approach that applies Agrep to multiple sequences individually, the proposed approach solves the matching problem in much shorter time. The speed-up of our approach depends on the sequence patterns, and for highly similar homologous genome sequences, which are the common cases in real-life genomes, it can be up to several orders of magnitude.

  8. Seismic echo character northern Hatteras Abyssal Plain

    International Nuclear Information System (INIS)

    McCreery, C.J.; Laine, E.P.

    1985-01-01

    Latest efforts in echo-character mapping of the northern Hatteras Abyssal Plain have discerned variations in thickness in a near-surface sedimentary sequence which has been designated seismic unit A. This unit probably represents the last episode of progradation of the Hatteras Deep Sea Fan in the southern part of the study area, and has infilled probable paleochannels from the Wilmington Canyon and Sohm Gap in the north. Unit A thins to a minimum in the central part of the plain, where older sediments come within 1 meter of the surface. Variations in the character of the surface reflector probably represent differing degrees of microtopography developed on a Late Pleistocene surface overlain by Holocene sediments. With the exception of one area identified as a relict surface outcropping in the western plain, this microtopography seems related to present-day thalweg locations on the abyssal plain. 11 references, 13 figures

  9. Os riscos do texto e da imagem - Em torno de Balinese character (1942, de Gregory Bateson e Margaret Mead

    Directory of Open Access Journals (Sweden)

    Etienne Samain

    2000-11-01

    Full Text Available Balinese character. A photographie analysis (1942 de Gregory Bateson et Margaret Mead est, sans nul doute, un livre fondateur de l’anthropologie visuelle (photographique. Souvent cité, il reste insuffisamment exploré. Cet article soulève - après une brève présentation de l’organisation d’ensemble de l’oeuvre - un questionnement heuristique et une réflexion sur la nature de l’utilisation intégrative de l’image et du texte dans l’élaboration du discours anthropologique. Pour ce faire, nous étudions trois modèles d’organisation des planches photographiques de Balinese character et leurs respectifs commentaires écrits, effectuant des parcours inverses: de l’image au texte, du texte à l’image. S’il est vrai que l'un et l’autre de ces supports communicationnels sont singuliers autant que complémentaires, leurs richesse respective n’est pas à l’abri d’autres risques que cette recherche dévoilera.

  10. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

    Directory of Open Access Journals (Sweden)

    Zhou Sun

    2012-05-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be “unclean”. Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and accurate delineation of transcription ends, but also furthers our understanding of the potential sources of data abnormalities/errors present in the wet-lab procedures for cDNA library construction. Results After analyzing a total of 309,976 raw Pinus taeda ESTs, we uncovered many distinct variations of cDNA termini, some of which prove to be good indicators of wet-lab artifacts, and characterized each raw EST by its cDNA terminus structure patterns. In contrast to the expected patterns, many ESTs displayed complex and/or abnormal patterns that represent potential wet-lab errors such as: a failure of one or both of the restriction enzymes to cut the plasmid vector; a failure of the restriction enzymes to cut the vector at the correct positions; the insertion of two cDNA inserts into a single vector; the insertion of multiple and/or concatenated adapters/linkers; the presence of 3′-end terminal structures in designated 5′-end sequences or vice versa; and so on. With a close examination of these artifacts, many problematic ESTs that have been deposited into public databases by conventional bioinformatics pipelines or tools could be cleaned or filtered by our methodology. We developed a software tool for Abnormality Filtering and Sequence Trimming for ESTs (AFST, http://code.google.com/p/afst/ using a pattern analysis approach. To compare AFST with other pipelines that submitted ESTs into dbEST, we reprocessed 230,783 Pinus taeda and 38,709 Arachis hypogaea GenBank ESTs. We found 7.4% of Pinus taeda and 29.2% of Arachis hypogaea GenBank ESTs are “unclean” or abnormal, all of which could be cleaned

  11. Survey of transposable elements in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Rossi Magdalena

    2001-01-01

    Full Text Available The sugarcane expressed sequence tag (SUCEST project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac, Mutator (MuDR, Suppressor-mutator (En/Spm and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

  12. From biomedicine to natural history research: EST resources for ambystomatid salamanders

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2004-08-01

    Full Text Available Abstract Background Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum and Eastern tiger salamander (A. tigrinum tigrinum, species with deep and diverse research histories. Results Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. Conclusions Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research.

  13. From biomedicine to natural history research: EST resources for ambystomatid salamanders

    Science.gov (United States)

    Putta, Srikrishna; Smith, Jeramiah J; Walker, John A; Rondet, Mathieu; Weisrock, David W; Monaghan, James; Samuels, Amy K; Kump, Kevin; King, David C; Maness, Nicholas J; Habermann, Bianca; Tanaka, Elly; Bryant, Susan V; Gardiner, David M; Parichy, David M; Voss, S Randal

    2004-01-01

    Background Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories. Results Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. Conclusions Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research. PMID:15310388

  14. Effects on Learning Logographic Character Formation in Computer-Assisted Handwriting Instruction

    Science.gov (United States)

    Tsai, Chen-hui; Kuo, Chin-Hwa; Horng, Wen-Bing; Chen, Chun-Wen

    2012-01-01

    This paper reports on a study that investigates how different learning methods might affect the learning process of character handwriting among beginning college learners of Chinese, as measured by tests of recognition, approximate production, precise production, and awareness of conventional stroke sequence. Two methodologies were examined during…

  15. Database Description - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name AcEST Alternative n...hi, Tokyo-to 192-0397 Tel: +81-42-677-1111(ext.3654) E-mail: Database classificat...eneris Taxonomy ID: 13818 Database description This is a database of EST sequences of Adiantum capillus-vene...(3): 223-227. External Links: Original website information Database maintenance site Plant Environmental Res...base Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - AcEST | LSDB Archive ...

  16. Comparison of brain mechanisms underlying the processing of Chinese characters and pseudo-characters: an event-related potential study.

    Science.gov (United States)

    Wang, Ting; Li, Hong; Zhang, Qinglin; Tu, Shen; Yu, Caiyun; Qiu, Jiang

    2010-04-01

    Most Chinese characters are composed of a semantic radical on the left and a phonetic radical on the right. The semantic radical provides the semantic information; the phonetic radical provides information concerning the pronunciation of the whole character. The pseudo-characters in the study consisted of different sub-lexical parts of real Chinese characters and consequently they also had the semantic radical and the phonetic radical. But they were not readable and had no actual meaning. In order to investigate the spatiotemporal cortical activation patterns underlying the orthographic, phonological and semantic processing of Chinese characters, we used event-related brain potentials (ERPs) to explore the processing of Chinese characters and pseudo-characters when 14 healthy Chinese college students viewed the characters passively. Results showed that both Chinese characters and pseudo-characters elicited an evident negative potential peaking around 120 ms (N120), which appeared to reflect initial orthographic distinction and evaluation. Then, Chinese pseudo-characters elicited a more positive ERP deflection (P220) than did Chinese characters 200-250 ms after onset of the stimuli. It was similar to the recognition potential (RP) and might reflect the integration processes of phonological and semantic processing on the basis of early orthographic information. Dipole source analysis of the difference wave (pseudo-characters minus characters) indicated that a generator localized in the left temporal-occipital junction contributed to this effect, which was possibly related to phonological and perceptual-semantic information integration. Between 350-450 ms, a greater negativity (N360) in pseudo-characters as compared to characters was found over midline fronto-central scalp regions. Dipole analysis localized the generator of N360 in the right parahippocampal cortex. Therefore, the N360 might be an N400 component and reflect the higher-level semantic activation on the

  17. Development and Characterization of 37 Novel EST-SSR Markers in Pisum sativum (Fabaceae

    Directory of Open Access Journals (Sweden)

    Xiaofeng Zhuang

    2013-01-01

    Full Text Available Premise of the study: Simple sequence repeat markers were developed based on expressed sequence tags (EST-SSR and screened for polymorphism among 23 Pisum sativum individuals to assist development and refinement of pea linkage maps. In particular, the SSR markers were developed to assist in mapping of white mold disease resistance quantitative trait loci. Methods and Results: Primer pairs were designed for 46 SSRs identified in EST contiguous sequences assembled from a 454 pyrosequenced transcriptome of the pea cultivar, ‘LIFTER’. Thirty-seven SSR markers amplified PCR products, of which 11 (30% SSR markers produced polymorphism in 23 individuals, including parents of recombinant inbred lines, with two to four alleles. The observed and expected heterozygosities ranged from 0 to 0.43 and from 0.31 to 0.83, respectively. Conclusions: These EST-SSR markers for pea will be useful for refinement of pea linkage maps, and will likely be useful for comparative mapping of pea and as tools for marker-based pea breeding.

  18. 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...... 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....

  19. Character animation fundamentals developing skills for 2D and 3D character animation

    CERN Document Server

    Roberts, Steve

    2012-01-01

    Expand your animation toolkit and remain competitive in the industry with this leading resource for 2D and 3D character animation techniques. Apply the industry's best practices to your own workflows and develop 2D, 3D and hybrid characters with ease. With side by side comparisons of 2D and 3D character design, improve your character animation and master traditional principles and processes including weight and balance, timing and walks. Develop characters inspired by humans, birds, fish, snakes and four legged animals. Breathe life into your character and develop a characters personality w

  20. JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

    Science.gov (United States)

    Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

    2006-11-23

    Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to

  1. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers

    Directory of Open Access Journals (Sweden)

    Wallace Richard

    2007-06-01

    Full Text Available Abstract Background The eastern oyster, Crassostrea virginica (Gmelin 1791, is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs. Results A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174 of the unique ESTs had significant hits (E-value ≤ 1e-05 to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. Conclusion A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the

  2. Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis).

    Science.gov (United States)

    Chen, Honglin; Liu, Liping; Wang, Lixia; Wang, Suhua; Somta, Prakit; Cheng, Xuzhen

    2015-01-01

    The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

  3. Optical character recognition of handwritten Arabic using hidden Markov models

    Science.gov (United States)

    Aulama, Mohannad M.; Natsheh, Asem M.; Abandah, Gheith A.; Olama, Mohammed M.

    2011-04-01

    The problem of optical character recognition (OCR) of handwritten Arabic has not received a satisfactory solution yet. In this paper, an Arabic OCR algorithm is developed based on Hidden Markov Models (HMMs) combined with the Viterbi algorithm, which results in an improved and more robust recognition of characters at the sub-word level. Integrating the HMMs represents another step of the overall OCR trends being currently researched in the literature. The proposed approach exploits the structure of characters in the Arabic language in addition to their extracted features to achieve improved recognition rates. Useful statistical information of the Arabic language is initially extracted and then used to estimate the probabilistic parameters of the mathematical HMM. A new custom implementation of the HMM is developed in this study, where the transition matrix is built based on the collected large corpus, and the emission matrix is built based on the results obtained via the extracted character features. The recognition process is triggered using the Viterbi algorithm which employs the most probable sequence of sub-words. The model was implemented to recognize the sub-word unit of Arabic text raising the recognition rate from being linked to the worst recognition rate for any character to the overall structure of the Arabic language. Numerical results show that there is a potentially large recognition improvement by using the proposed algorithms.

  4. Crystallization and preliminary X-ray crystallographic analysis of EstE1, a new and thermostable esterase cloned from a metagenomic library

    Energy Technology Data Exchange (ETDEWEB)

    Byun, Jung-Sue [Department of Biology, Yonsei University, Seoul 120-749 (Korea, Republic of); Protein Network Research Center, Yonsei University, Seoul 120-749 (Korea, Republic of); Rhee, Jin-Kyu [Department of Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Kim, Dong-Uk [Department of Biology, Yonsei University, Seoul 120-749 (Korea, Republic of); Oh, Jong-Won [Department of Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Cho, Hyun-Soo, E-mail: hscho8@yonsei.ac.kr [Department of Biology, Yonsei University, Seoul 120-749 (Korea, Republic of); Protein Network Research Center, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2006-02-01

    Recombinant EstE1 protein with a histidine tag at the C-terminus was overexpressed in Escherichia coli strain BL21(DE3) and then purified by affinity chromatography. The protein was then crystallized at 290 K by the hanging-drop vapour-diffusion method. EstE1, a new thermostable esterase, was isolated by functional screening of a metagenomic DNA library from thermal environment samples. This enzyme showed activity towards short-chain acyl derivatives of length C4–C6 at a temperature of 303–363 K and displayed a high thermostability above 353 K. EstE1 has 64 and 57% amino-acid sequence similarity to est{sub pc}-encoded carboxylesterase from Pyrobaculum calidifontis and AFEST from Archaeoglobus fulgidus, respectively. The recombinant protein with a histidine tag at the C-terminus was overexpressed in Escherichia coli strain BL21(DE3) and then purified by affinity chromatography. The protein was crystallized at 290 K by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.3 Å resolution from an EstE1 crystal; the crystal belongs to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 73.71, c = 234.23 Å. Assuming the presence of four molecules in the asymmetric unit, the Matthews coefficient V{sub M} is calculated to be 2.2 Å{sup 3} Da{sup −1} and the solvent content is 44.1%.

  5. Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane.

    Science.gov (United States)

    Parthiban, S; Govindaraj, P; Senthilkumar, S

    2018-03-01

    Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to

  6. Development and Testing of New Gene-Homologous EST-SSRs for Eucalyptus gomphocephala (Myrtaceae

    Directory of Open Access Journals (Sweden)

    Donna Bradbury

    2013-07-01

    Full Text Available Premise of the study: New microsatellite (simple sequence repeat [SSR] primers were developed from Eucalyptus expressed sequence tags (ESTs and optimized for genetic studies of the southwestern Australian tree E. gomphocephala, which is severely impacted by tree health decline and habitat fragmentation. Methods and Results: A total of 133 gene-homologous EST-SSR primer pairs were designed for Eucalyptus, and 44 were screened in E. gomphocephala. Of these, 17 produced reliable amplification products and 11 were polymorphic. Between two and 13 alleles were observed per locus, and observed heterozygosities ranged from 0.172 to 0.867. All 17 EST-SSRs that amplified E. gomphocephala cross-amplified to at least one of E. marginata, E. camaldulensis, and E. victrix. Conclusions: This set of EST-SSR primer pairs will be valuable tools for future population genetic studies of E. gomphocephala and other eucalypts, particularly for studying gene-linked variation and informing seed-sourcing strategies for ecological restoration.

  7. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Li Yujun

    2011-10-01

    Full Text Available Abstract Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas, which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9% being the most abundant followed by di- (41.2%, tetra- (9.2%, penta- (3.7% and hexa-nucleotide (3.1% repeat types. The top five motifs included AG/CT (26.9%, AAG/CTT (13.5%, AT/TA (10.6%, CCG/CGG (5.8% and AAT/ATT (4.5%. After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30 and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9% and 342 (41.9% primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would

  8. JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

    Directory of Open Access Journals (Sweden)

    Martinez Veronica

    2006-11-01

    Full Text Available Abstract Background Expressed sequence tag (EST analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux, which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in

  9. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  10. Analysis of cassava (Manihot esculenta) ESTs: A tool for the discovery of genes

    International Nuclear Information System (INIS)

    Zapata, Andres; Neme, Rafik; Sanabria, Carolina; Lopez, Camilo

    2011-01-01

    Cassava (Manihot esculenta) is the main source of calories for more than 1,000 millions of people around the world and has been consolidated as the fourth most important crop after rice, corn and wheat. Cassava is considered tolerant to abiotic and biotic stress conditions; nevertheless these characteristics are mainly present in non-commercial varieties. Genetic breeding strategies represent an alternative to introduce the desirable characteristics into commercial varieties. A fundamental step for accelerating the genetic breeding process in cassava requires the identification of genes associated to these characteristics. One rapid strategy for the identification of genes is the possibility to have a large collection of ESTs (expressed sequence tag). In this study, a complete analysis of cassava ESTs was done. The cassava ESTs represent 80,459 sequences which were assembled in a set of 29,231 unique genes (unigen), comprising 10,945 contigs and 18,286 singletones. These 29,231 unique genes represent about 80% of the genes of the cassava's genome. Between 5% and 10% of the unigenes of cassava not show similarity to any sequences present in the NCBI database and could be consider as cassava specific genes. a functional category was assigned to a group of sequences of the unigen set (29%) following the Gene Ontology Vocabulary. the molecular function component was the best represented with 43% of the sequences, followed by the biological process component (38%) and finally the cellular component with 19%. in the cassava ESTs collection, 3,709 microsatellites were identified and they could be used as molecular markers. this study represents an important contribution to the knowledge of the functional genomic structure of cassava and constitutes an important tool for the identification of genes associated to agricultural characteristics of interest that could be employed in cassava breeding programs.

  11. Segmentation of Handwritten Chinese Character Strings Based on improved Algorithm Liu

    Directory of Open Access Journals (Sweden)

    Zhihua Cai

    2014-09-01

    Full Text Available Algorithm Liu attracts high attention because of its high accuracy in segmentation of Japanese postal address. But the disadvantages, such as complexity and difficult implementation of algorithm, etc. have an adverse effect on its popularization and application. In this paper, the author applies the principles of algorithm Liu to handwritten Chinese character segmentation according to the characteristics of the handwritten Chinese characters, based on deeply study on algorithm Liu.In the same time, the author put forward the judgment criterion of Segmentation block classification and adhering mode of the handwritten Chinese characters.In the process of segmentation, text images are seen as the sequence made up of Connected Components (CCs, while the connected components are made up of several horizontal itinerary set of black pixels in image. The author determines whether these parts will be merged into segmentation through analyzing connected components. And then the author does image segmentation through adhering mode based on the analysis of outline edges. Finally cut the text images into character segmentation. Experimental results show that the improved Algorithm Liu obtains high segmentation accuracy and produces a satisfactory segmentation result.

  12. Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database.

    Science.gov (United States)

    Badisco, Liesbeth; Huybrechts, Jurgen; Simonet, Gert; Verlinden, Heleen; Marchal, Elisabeth; Huybrechts, Roger; Schoofs, Liliane; De Loof, Arnold; Vanden Broeck, Jozef

    2011-03-21

    The desert locust (Schistocerca gregaria) displays a fascinating type of phenotypic plasticity, designated as 'phase polyphenism'. Depending on environmental conditions, one genome can be translated into two highly divergent phenotypes, termed the solitarious and gregarious (swarming) phase. Although many of the underlying molecular events remain elusive, the central nervous system (CNS) is expected to play a crucial role in the phase transition process. Locusts have also proven to be interesting model organisms in a physiological and neurobiological research context. However, molecular studies in locusts are hampered by the fact that genome/transcriptome sequence information available for this branch of insects is still limited. We have generated 34,672 raw expressed sequence tags (EST) from the CNS of desert locusts in both phases. These ESTs were assembled in 12,709 unique transcript sequences and nearly 4,000 sequences were functionally annotated. Moreover, the obtained S. gregaria EST information is highly complementary to the existing orthopteran transcriptomic data. Since many novel transcripts encode neuronal signaling and signal transduction components, this paper includes an overview of these sequences. Furthermore, several transcripts being differentially represented in solitarious and gregarious locusts were retrieved from this EST database. The findings highlight the involvement of the CNS in the phase transition process and indicate that this novel annotated database may also add to the emerging knowledge of concomitant neuronal signaling and neuroplasticity events. In summary, we met the need for novel sequence data from desert locust CNS. To our knowledge, we hereby also present the first insect EST database that is derived from the complete CNS. The obtained S. gregaria EST data constitute an important new source of information that will be instrumental in further unraveling the molecular principles of phase polyphenism, in further establishing

  13. Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database.

    Directory of Open Access Journals (Sweden)

    Liesbeth Badisco

    Full Text Available BACKGROUND: The desert locust (Schistocerca gregaria displays a fascinating type of phenotypic plasticity, designated as 'phase polyphenism'. Depending on environmental conditions, one genome can be translated into two highly divergent phenotypes, termed the solitarious and gregarious (swarming phase. Although many of the underlying molecular events remain elusive, the central nervous system (CNS is expected to play a crucial role in the phase transition process. Locusts have also proven to be interesting model organisms in a physiological and neurobiological research context. However, molecular studies in locusts are hampered by the fact that genome/transcriptome sequence information available for this branch of insects is still limited. METHODOLOGY: We have generated 34,672 raw expressed sequence tags (EST from the CNS of desert locusts in both phases. These ESTs were assembled in 12,709 unique transcript sequences and nearly 4,000 sequences were functionally annotated. Moreover, the obtained S. gregaria EST information is highly complementary to the existing orthopteran transcriptomic data. Since many novel transcripts encode neuronal signaling and signal transduction components, this paper includes an overview of these sequences. Furthermore, several transcripts being differentially represented in solitarious and gregarious locusts were retrieved from this EST database. The findings highlight the involvement of the CNS in the phase transition process and indicate that this novel annotated database may also add to the emerging knowledge of concomitant neuronal signaling and neuroplasticity events. CONCLUSIONS: In summary, we met the need for novel sequence data from desert locust CNS. To our knowledge, we hereby also present the first insect EST database that is derived from the complete CNS. The obtained S. gregaria EST data constitute an important new source of information that will be instrumental in further unraveling the molecular

  14. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.

    Directory of Open Access Journals (Sweden)

    Morgan Kullberg

    Full Text Available BACKGROUND: We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human, lagomorphs (rabbit, rodents (rat and mouse, artiodactyls (cow, carnivorans (dog and proboscideans (elephant. METHODOLOGY/PRINCIPAL FINDINGS: We have produced 2000 ESTs (1.2 mega bases from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS: The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.

  15. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.

    Science.gov (United States)

    Chakraborty, Mohua; Dhar, Bishal; Ghosh, Sankar Kumar

    2017-11-01

    The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification. © 2017 John Wiley & Sons Ltd.

  16. Validation of dbEST-SSRs and transferability of some other solanaceous species SSR in ashwagandha [Withania Somnifera (L.) Dunal].

    Science.gov (United States)

    Parmar, Eva K; Fougat, Ranbir S; Patel, Chandni B; Zala, Harshvardhan N; Patel, Mahesh A; Patel, Swati K; Kumar, Sushil

    2015-12-01

    Cross-species transferability and expressed sequence tags (ESTs) in public databases are cost-effective means for developing simple sequence repeats (SSRs) for less-studied species like medicinal plants. In this study, 11 EST-SSR markers developed from 742 available ESTs of Withania Somnifera EST sequences and 95 SSR primer pairs derived from other solanaceous crops (tomato, eggplant, chili, and tobacco) were utilized for their amplification and validation. Out of 11, 10 EST-SSRs showed good amplification quality and produced 13 loci with a product size ranging between 167 and 291 bp. Similarly, of the 95 cross-genera SSR loci assayed, 20 (21 %) markers showed the transferability of 5, 27, 32, and 14.2 % from eggplant, chili, tomato, and tobacco, respectively, to ashwagandha. In toto, these 30 SSR markers reported here will be valuable resources and may be applicable for the analysis of intra- and inter-specific genetic diversity in ashwagandha for which till date no information about SSR is available.

  17. Flashing characters with famous faces improves ERP-based brain-computer interface performance

    Science.gov (United States)

    Kaufmann, T.; Schulz, S. M.; Grünzinger, C.; Kübler, A.

    2011-10-01

    Currently, the event-related potential (ERP)-based spelling device, often referred to as P300-Speller, is the most commonly used brain-computer interface (BCI) for enhancing communication of patients with impaired speech or motor function. Among numerous improvements, a most central feature has received little attention, namely optimizing the stimulus used for eliciting ERPs. Therefore we compared P300-Speller performance with the standard stimulus (flashing characters) against performance with stimuli known for eliciting particularly strong ERPs due to their psychological salience, i.e. flashing familiar faces transparently superimposed on characters. Our results not only indicate remarkably increased ERPs in response to familiar faces but also improved P300-Speller performance due to a significant reduction of stimulus sequences needed for correct character classification. These findings demonstrate a promising new approach for improving the speed and thus fluency of BCI-enhanced communication with the widely used P300-Speller.

  18. Mining of expressed sequence tag libraries of cacao

    Indian Academy of Sciences (India)

    Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available ...

  19. Actor/Character Dualism

    DEFF Research Database (Denmark)

    Riis, Johannes

    2012-01-01

    Our perception of agency may be inherently fallible, and this may explain not only our general awareness of actors when engaged in fictional characters but also the specific case of paradoxical characters...

  20. Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences | Center for Cancer Research

    Science.gov (United States)

    A graphical method is presented for displaying how binding proteins and other macromolecules interact with individual bases of nucleotide sequences. Characters representing the sequence are either oriented normally and placed above a line indicating favorable contact, or upside-down and placed below the line indicating unfavorable contact. The positive or negative height of each letter shows the contribution of that base to the average sequence conservation of the binding site, as represented by a sequence logo.

  1. Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species

    Directory of Open Access Journals (Sweden)

    Kotewong Rattanawadee

    2010-11-01

    Full Text Available Abstract Background Many species of marine shrimp in the Family Penaeidae, viz. Penaeus (Litopenaeus vannamei, Penaeus monodon, Penaeus (Fenneropenaeus chinensis, and Penaeus (Marsupenaeus japonicus, are animals of economic importance in the aquaculture industry. Yet information about their DNA and protein sequences is lacking. In order to predict their collective proteome, we combined over 270,000 available EST and cDNA sequences from the 4 shrimp species with all protein sequences of Drosophila melanogaster and Caenorhabditis elegans. EST data from 4 other crustaceans, the crab Carcinus maenas, the lobster Homarus americanus (Decapoda, the water flea Daphnia pulex, and the brine shrimp Artemia franciscana were also used. Findings Similarity searches from EST collections of the 4 shrimp species matched 64% of the protein sequences of the fruit fly, but only 45% of nematode proteins, indicating that the shrimp proteome content is more similar to that of an insect than a nematode. Combined results with 4 additional non-shrimp crustaceans increased matching to 78% of fruit fly and 56% of nematode proteins, suggesting that present shrimp EST collections still lack sequences for many conserved crustacean proteins. Analysis of matching data revealed the presence of 4 EST groups from shrimp, namely sequences for proteins that are both fruit fly-like and nematode-like, fruit fly-like only, nematode-like only, and non-matching. Gene ontology profiles of proteins for the 3 matching EST groups were analyzed. For non-matching ESTs, a small fraction matched protein sequences from other species in the UniProt database, including other crustacean-specific proteins. Conclusions Shrimp ESTs indicated that the shrimp proteome is comprised of sub-populations of proteins similar to those common to both insect and nematode models, those present specifically in either model, or neither. Combining small EST collections from related species to compensate for their

  2. Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae: Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer

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    Lemieux Claude

    2008-06-01

    Full Text Available Abstract Background To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales, Scenedesmus (Sphaeropleales, and Stigeoclonium (Chaetophorales revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade. Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales. Results Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns, and displays 99 different conserved genes and four long open reading frames (ORFs, three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (int and dpoB revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members

  3. Identification of candidate genes for human pituitary development by EST analysis

    Directory of Open Access Journals (Sweden)

    Xiao Huasheng

    2009-03-01

    Full Text Available Abstract Background The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely that a large number of signaling molecules and transcription factors essential for determination and terminal differentiation of specific cell types remain unidentified. High-throughput methods such as microarray analysis may facilitate the measurement of gene transcriptional levels, while Expressed sequence tag (EST sequencing, an efficient method for gene discovery and expression level analysis, may no-redundantly help to understand gene expression patterns during development. Results A total of 9,271 ESTs were generated from both fetal and adult pituitaries, and assigned into 961 gene/EST clusters in fetal and 2,747 in adult pituitary by homology analysis. The transcription maps derived from these data indicated that developmentally relevant genes, such as Sox4, ST13 and ZNF185, were dominant in the cDNA library of fetal pituitary, while hormones and hormone-associated genes, such as GH1, GH2, POMC, LHβ, CHGA and CHGB, were dominant in adult pituitary. Furthermore, by using RT-PCR and in situ hybridization, Sox4 was found to be one of the main transcription factors expressed in fetal pituitary for the first time. It was expressed at least at E12.5, but decreased after E17.5. In addition, 40 novel ESTs were identified specifically in this tissue. Conclusion The significant changes in gene expression in both tissues suggest a distinct and dynamic switch between embryonic and adult pituitaries. All these data along with Sox4 should be confirmed to further understand the community of multiple signaling pathways that act as a cooperative network that regulates maturation of the pituitary. It was also suggested that EST

  4. Analyses of an expressed sequence tag library from Taenia solium, Cysticerca.

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    Jonas Lundström

    Full Text Available BACKGROUND: Neurocysticercosis is a disease caused by the oral ingestion of eggs from the human parasitic worm Taenia solium. Although drugs are available they are controversial because of the side effects and poor efficiency. An expressed sequence tag (EST library is a method used to describe the gene expression profile and sequence of mRNA from a specific organism and stage. Such information can be used in order to find new targets for the development of drugs and to get a better understanding of the parasite biology. METHODS AND FINDINGS: Here an EST library consisting of 5760 sequences from the pig cysticerca stage has been constructed. In the library 1650 unique sequences were found and of these, 845 sequences (52% were novel to T. solium and not identified within other EST libraries. Furthermore, 918 sequences (55% were of unknown function. Amongst the 25 most frequently expressed sequences 6 had no relevant similarity to other sequences found in the Genbank NR DNA database. A prediction of putative signal peptides was also performed and 4 among the 25 were found to be predicted with a signal peptide. Proposed vaccine and diagnostic targets T24, Tsol18/HP6 and Tso31d could also be identified among the 25 most frequently expressed. CONCLUSIONS: An EST library has been produced from pig cysticerca and analyzed. More than half of the different ESTs sequenced contained a sequence with no suggested function and 845 novel EST sequences have been identified. The library increases the knowledge about what genes are expressed and to what level. It can also be used to study different areas of research such as drug and diagnostic development together with parasite fitness via e.g. immune modulation.

  5. Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

    Science.gov (United States)

    Bosamia, Tejas C.; Mishra, Gyan P.; Thankappan, Radhakrishnan; Dobaria, Jentilal R.

    2015-01-01

    With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut. PMID:26046991

  6. Believable Characters

    Science.gov (United States)

    El-Nasr, Magy Seif; Bishko, Leslie; Zammitto, Veronica; Nixon, Michael; Vasiliakos, Athanasios V.; Wei, Huaxin

    The interactive entertainment industry is one of the fastest growing industries in the world. In 1996, the U.S. entertainment software industry reported 2.6 billion in sales revenue, this figure has more than tripled in 2007 yielding 9.5 billion in revenues [1]. In addition, gamers, the target market for interactive entertainment products, are now reaching beyond the traditional 8-34 year old male to include women, Hispanics, and African Americans [2]. This trend has been observed in several markets, including Japan, China, Korea, and India, who has just published their first international AAA title (defined as high quality games with high budget), a 3D third person action game: Ghajini - The Game [3]. The topic of believable characters is becoming a central issue when designing and developing games for today's game industry. While narrative and character were considered secondary to game mechanics, games are currently evolving to integrate characters, narrative, and drama as part of their design. One can see this pattern through the emergence of games like Assassin's Creed (published by Ubisoft 2008), Hotel Dusk (published by Nintendo 2007), and Prince of Persia series (published by Ubisoft), which emphasized character and narrative as part of their design.

  7. Comparative expression profiling in grape (Vitis vinifera berries derived from frequency analysis of ESTs and MPSS signatures

    Directory of Open Access Journals (Sweden)

    Cook Douglas R

    2008-05-01

    Full Text Available Abstract Background Vitis vinifera (V. vinifera is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS and combined it with available Expressed Sequence Tag (EST data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. Results The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS. A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million. Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. Conclusion The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed

  8. Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

    Directory of Open Access Journals (Sweden)

    Wegnez Maurice

    2007-05-01

    Full Text Available Abstract Background The western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional genomics resource on genes expressed in the nervous system during early embryogenesis and metamorphosis in X. tropicalis. Results A gene index was defined and analysed after the collection of over 48,785 high quality sequences. These partial cDNA sequences were obtained from an embryonic head and retina library (30,272 sequences and from a metamorphic brain and spinal cord library (27,602 sequences. These ESTs are estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. Comparison of these cDNA sequences with protein databases indicates that 46% contain their start codon. Further annotation included Gene Ontology functional classification, InterPro domain analysis, alternative splicing and non-coding RNA identification. Gene expression profiles were derived from EST counts and used to define transcripts specific to metamorphic stages of development. Moreover, these ESTs allowed identification of a set of 225 polymorphic microsatellites that can be used as genetic markers. Conclusion These cDNA sequences permit in silico cloning of numerous genes and will facilitate studies aimed at deciphering the roles of cognate genes expressed in the nervous system during neural development and metamorphosis. The genomic resources developed to study X. tropicalis biology will accelerate exploration of amphibian physiology and genetics. In particular, the model will facilitate analysis of key questions related to anuran embryogenesis and metamorphosis and its associated regulatory processes.

  9. Characterization of variable EST SSR markers for Norway spruce (Picea abies L.

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    Spiess Nadine

    2011-10-01

    Full Text Available Abstract Background Norway spruce is widely distributed across Europe and the predominant tree of the Alpine region. Fast growth and the fact that timber can be harvested cost-effectively in relatively young populations define its status as one of the economically most important tree species of Northern Europe. In this study, EST derived simple sequence repeat (SSR markers were developed for the assessment of putative functional diversity in Austrian Norway spruce stands. Results SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 P. abies individuals sampled across Austria and in an additional screening population of 96 P. abies individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99. Conclusions We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.

  10. Regularity of C*-algebras and central sequence algebras

    DEFF Research Database (Denmark)

    Christensen, Martin S.

    The main topic of this thesis is regularity properties of C*-algebras and how these regularity properties are re ected in their associated central sequence algebras. The thesis consists of an introduction followed by four papers [A], [B], [C], [D]. In [A], we show that for the class of simple...... Villadsen algebra of either the rst type with seed space a nite dimensional CW complex, or the second type, tensorial absorption of the Jiang-Su algebra is characterized by the absence of characters on the central sequence algebra. Additionally, in a joint appendix with Joan Bosa, we show that the Villadsen...... algebra of the second type with innite stable rank fails the corona factorization property. In [B], we consider the class of separable C*-algebras which do not admit characters on their central sequence algebra, and show that it has nice permanence properties. We also introduce a new divisibility property...

  11. 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 ...

  12. Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests.

    Science.gov (United States)

    Noda, Hiroaki; Kawai, Sawako; Koizumi, Yoko; Matsui, Kageaki; Zhang, Qiang; Furukawa, Shigetoyo; Shimomura, Michihiko; Mita, Kazuei

    2008-03-03

    The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site. The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.

  13. Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

    Directory of Open Access Journals (Sweden)

    Arias Covadonga

    2007-06-01

    Full Text Available Abstract Background The ciliate protozoan Ichthyophthirius multifiliis (Ich is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs. Results We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate. Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan. BLASTX searches produced 2,518 significant (E-value -5 hits and further Gene Ontology (GO analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289. Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.

  14. A REVIEW: OPTICAL CHARACTER RECOGNITION

    OpenAIRE

    Swati Tomar*1 & Amit Kishore2

    2018-01-01

    This paper presents detailed review in the field of Optical Character Recognition. Various techniques are determine that have been proposed to realize the center of character recognition in an optical character recognition system. Even though, sufficient studies and papers are describes the techniques for converting textual content from a paper document into machine readable form. Optical character recognition is a process where the computer understands automatically the image of handwritten ...

  15. Knowing Chinese character grammar.

    Science.gov (United States)

    Myers, James

    2016-02-01

    Chinese character structure has often been described as representing a kind of grammar, but the notion of character grammar has hardly been explored. Patterns in character element reduplication are particularly grammar-like, displaying discrete combinatoriality, binarity, phonology-like final prominence, and potentially the need for symbolic rules (X→XX). To test knowledge of these patterns, Chinese readers were asked to judge the acceptability of fake characters varying both in grammaticality (obeying or violating reduplication constraints) and in lexicality (of the reduplicative configurations). While lexical knowledge was important (lexicality improved acceptability and grammatical configurations were accepted more quickly when also lexical), grammatical knowledge was important as well, with grammaticality improving acceptability equally for lexical and nonlexical configurations. Acceptability was also higher for more frequent reduplicative elements, suggesting that the reduplicative configurations were decomposed. Chinese characters present an as-yet untapped resource for exploring fundamental questions about the nature of the human capacity for grammar. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. ESTminer: a Web interface for mining EST contig and cluster databases.

    Science.gov (United States)

    Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

    2005-03-01

    ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

  17. Character Apps for Children's Snacks: Effects of Character Awareness on Snack Selection and Consumption Patterns.

    Science.gov (United States)

    Putnam, Marisa M; Cotto, Caroline E; Calvert, Sandra L

    2018-04-01

    Media characters are used to market snacks that are typically of poor nutritional value, which has been linked to childhood obesity. This study examines whether children's snack selections and consumption patterns are influenced by an app depicting a popular children's media character, as well as the role that children's awareness of the character plays. The results can increase our understanding of how to encourage healthier snack selection and consumption in newer game-based marketing venues, such as apps. Four- and 5-year-old children (N = 132) played a bowling game on an iPad with no character or with a character holding either healthier or unhealthy snacks. After app-play, children selected and consumed healthier or unhealthy snacks. Children's awareness of the character was measured by children's verbalizations of the character's name during or after app-play. An ordered logistic regression found no significant effect of treatment conditions compared with the control group. Within treatment conditions, awareness of the character led to selection and consumption of more healthy snacks in the healthier condition (odds ratio β = 10.340, P = 0.008), and of unhealthy snacks in the unhealthy condition (odds ratio β = 0.228, P = 0.033), but children were unaware that the character influenced their decisions. Results suggest that young children will choose and consume healthier, not just unhealthy, products when they are aware that a popular character in an app is associated with the snack, potentially leading to healthier eating patterns.

  18. EST and transcriptome analysis of cephalochordate amphioxus--past, present and future.

    Science.gov (United States)

    Wang, Yu-Bin; Chen, Shu-Hwa; Lin, Chun-Yen; Yu, Jr-Kai

    2012-03-01

    The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.

  19. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    Science.gov (United States)

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  20. Distorted Character Recognition Via An Associative Neural Network

    Science.gov (United States)

    Messner, Richard A.; Szu, Harold H.

    1987-03-01

    The purpose of this paper is two-fold. First, it is intended to provide some preliminary results of a character recognition scheme which has foundations in on-going neural network architecture modeling, and secondly, to apply some of the neural network results in a real application area where thirty years of effort has had little effect on providing the machine an ability to recognize distorted objects within the same object class. It is the author's belief that the time is ripe to start applying in ernest the results of over twenty years of effort in neural modeling to some of the more difficult problems which seem so hard to solve by conventional means. The character recognition scheme proposed utilizes a preprocessing stage which performs a 2-dimensional Walsh transform of an input cartesian image field, then sequency filters this spectrum into three feature bands. Various features are then extracted and organized into three sets of feature vectors. These vector patterns that are stored and recalled associatively. Two possible associative neural memory models are proposed for further investigation. The first being an outer-product linear matrix associative memory with a threshold function controlling the strength of the output pattern (similar to Kohonen's crosscorrelation approach [1]). The second approach is based upon a modified version of Grossberg's neural architecture [2] which provides better self-organizing properties due to its adaptive nature. Preliminary results of the sequency filtering and feature extraction preprocessing stage and discussion about the use of the proposed neural architectures is included.

  1. Evolving Lattices for Analyzing Behavioral Dynamics of Characters in Literary Text

    Directory of Open Access Journals (Sweden)

    Eugene S Kitamura

    2011-10-01

    Full Text Available This paper is about an application of rough set derived lattices in order to analyze the dynamics of literary text. Due to the double approximation nature of rough set theory, a pseudo-closure obtained from two different equivalence relations allows us to form arbitrary lattices. Moreover, such double approximations with different equivalence relations permit us to obtain lattice fixed points based on two interpretations. The two interpretations used for literary text analysis are subjects and their attributes. The attributes chosen for this application are verbs. The progression of a story is defined by the sequence of verbs (or event occurrences. By fixing a window size and sliding the window down the story steps, we obtain a lattice representing the relationship between subjects and their attributes within that window frame. The resulting lattice provides information such as complementarity (lattice complement existence rate and distributivity (lattice complement possession rate. These measurements depend on the overlap and the lack of overlap among the attributes of characters. As the story develops and new character and attributes are provided as the source of lattices, one can observe its evolution. In fact, a dramatic change in the behavior dynamics in a scene is reflected in the particular shifts in the character-attribute relationship. This method lets us quantify the developments of character behavioral dynamics in a story.

  2. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-05-23

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

  3. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.

    Directory of Open Access Journals (Sweden)

    Byregowda Munishamappa

    2010-03-01

    Full Text Available Abstract Background Pigeonpea (Cajanus cajan (L. Millsp is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW, sterility mosaic disease (SMD, etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs. Results A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376' and SMD ('ICP 7035' and 'TTB 7' and a total of 9,888 (9,468 high quality ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%, rice (28.3%, Arabidopsis (33.7% and poplar (35.4%. As expected, pigeonpea ESTs are more closely related to soybean (60.3% and cowpea ESTs (43.6% than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1% out of 4,557 total unigenes correspond to known proteins in the UniProt database (≤ 1E-08. Functional categorization of the annotated unigenes sequences showed that 153 (3.3% genes were assigned to cellular component category, 132 (2.8% to biological process, and 132 (2

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

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

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

  5. Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states.

    Science.gov (United States)

    Pedersen, Niklas; Holyoak, David T; Newton, Angela E

    2007-06-01

    The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.

  6. A Missing Piece of the Contemporary Character Education Puzzle: The Individualisation of Moral Character

    Science.gov (United States)

    Chen, Yi-Lin

    2013-01-01

    The different sorts of virtuous people who display various virtues to a remarkable degree have brought the issue of individualisation of moral character to the forefront. It signals a more personal dimension of character development which is notoriously ignored in the current discourse on character education. The case is made that since in…

  7. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  8. Character Issues: Reality Character Problems and Solutions through Education in Indonesia

    Science.gov (United States)

    Saidek, Abdul Rahim; Islami, Raisul; Abdoludin

    2016-01-01

    Weak character education raises the problem of corruption, a fight between students, free sex, drugs and rape/abortion indicate that the issue of character education of the nation must be improved and the concern of all parties, the nation's leaders, law enforcement officers, educators, religious leaders, groups and other etc. There are two…

  9. Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: A genomic resource for studying agricultural pests

    Directory of Open Access Journals (Sweden)

    Zhang Qiang

    2008-03-01

    Full Text Available Abstract Background The brown planthopper (BPH, Nilaparvata lugens (Hemiptera, Delphacidae, is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. Results More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site. Conclusion The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.

  10. Seqüência de estímulos durante o fortalecimento da resposta de bicar: efeitos sobre a aquisição de desempenhos em matching e oddity Stimuli sequencing during pecking responses build up: effects upon matching and oddity acquisitions

    Directory of Open Access Journals (Sweden)

    Katia Damiani

    2002-01-01

    Full Text Available Este estudo investigou o efeito da seqüência de apresentação de estímulos durante o fortalecimento da resposta (pré-treino de bicar em pombos, sobre a aquisição do matching de identidade (IMTS e oddity-from-sample (OFS com 3 cores como estímulos e 2 escolhas. O problema se remete à disparidade no desempenho inicial em OFS em relação aos níveis do acaso, reiteradamente relatado na literatura. Durante o pré-treino, apenas uma cor era apresentada em qualquer uma de 3 chaves de resposta. O sorteio da seqüência de estímulos nas tentativas foi realizado com a restrição de que a probabilidade de 2 estímulos iguais serem apresentados em tentativas consecutivas foi semelhante à probabilidade de 2 estímulos diferentes serem apresentados em tentativas consecutivas. Em seguida, os sujeitos foram submetidos ou ao treino IMTS ou ao OFS. Os resultados replicaram aqueles descritos na literatura, indicando que o controle realizado sobre a seqüência de tentativas no pré-treino não teve efeito sobre a aquisição do IMTS e OFS.This study was aimed to investigate the question why oddity-from-sample acquisition in animals always start at above chance level. A question was raised concerning the role of stimuli sequences and a possible bias introduced in responding. Thus, this study analyzed the effects of stimuli sequencing during response build up in the pigeon (pre-training upon the acquisition of identity matching (IMTS and oddity-from-sample (OFS with three color stimuli and two comparisons. During pre-training one color was presented at the time in any one of three response key. Color presentation was randomized but for the restriction that the probability of two like colors being presented consecutively was the same as the probability of two non-like colors being presented consecutively. This controlled for any sequencing bias effects upon responding. Following, subjects were submitted either to IMTS or to OFS training. Results

  11. The character and behaviour of circumstellar shells at T Tauri stars

    International Nuclear Information System (INIS)

    Goetz, W.

    1988-01-01

    T Tauri stars are extremely young low-mass stars in the pre-main sequence stage. A brief review of investigations made at the Sonneberg observatory concerning the character and the behaviour of circumstellar shells at T Tauri stars is given. They lead to the construction of a shell model on the basis of observational facts. The idea rests upon the causal connection between the gas and dust shell phenomenon and the cosmogonic mass loss of the stars, which is the connecting link between the stars and their shells and which appears in the early phase of the pre-main sequence stage and decreases, like the accompanying shell phenomena, during the evolution of the stars. (author)

  12. Cloning and characterization of a pyrethroid pesticide decomposing esterase gene, Est3385, from Rhodopseudomonas palustris PSB-S.

    Science.gov (United States)

    Luo, Xiangwen; Zhang, Deyong; Zhou, Xuguo; Du, Jiao; Zhang, Songbai; Liu, Yong

    2018-05-09

    Full length open reading frame of pyrethroid detoxification gene, Est3385, contains 963 nucleotides. This gene was identified and cloned based on the genome sequence of Rhodopseudomonas palustris PSB-S available at the GneBank. The predicted amino acid sequence of Est3385 shared moderate identities (30-46%) with the known homologous esterases. Phylogenetic analysis revealed that Est3385 was a member in the esterase family I. Recombinant Est3385 was heterologous expressed in E. coli, purified and characterized for its substrate specificity, kinetics and stability under various conditions. The optimal temperature and pH for Est3385 were 35 °C and 6.0, respectively. This enzyme could detoxify various pyrethroid pesticides and degrade the optimal substrate fenpropathrin with a Km and Vmax value of 0.734 ± 0.013 mmol·l -1 and 0.918 ± 0.025 U·µg -1 , respectively. No cofactor was found to affect Est3385 activity but substantial reduction of enzymatic activity was observed when metal ions were applied. Taken together, a new pyrethroid degradation esterase was identified and characterized. Modification of Est3385 with protein engineering toolsets should enhance its potential for field application to reduce the pesticide residue from agroecosystems.

  13. Contribution to automatic handwritten characters recognition. Application to optical moving characters recognition

    International Nuclear Information System (INIS)

    Gokana, Denis

    1986-01-01

    This paper describes a research work on computer aided vision relating to the design of a vision system which can recognize isolated handwritten characters written on a mobile support. We use a technique which consists in analyzing information contained in the contours of the polygon circumscribed to the character's shape. These contours are segmented and labelled to give a new set of features constituted by: - right and left 'profiles', - topological and algebraic unvarying properties. A new method of character's recognition induced from this representation based on a multilevel hierarchical technique is then described. In the primary level, we use a fuzzy classification with dynamic programming technique using 'profiles'. The other levels adjust the recognition by using topological and algebraic unvarying properties. Several results are presented and an accuracy of 99 pc was reached for handwritten numeral characters, thereby attesting the robustness of our algorithm. (author) [fr

  14. Leading Character?s Antisocial Personality Disorder In James B Stewart?s Blind Eye

    OpenAIRE

    Lestari, Ayu

    2016-01-01

    110705043 The title of this thesis isLeading Character?s Antisocial Personality Disorder in James B Stewart?s Blind Eyethat is research about antisocial personality of leading character in the novel, namely Dr. Michael Swango. The purpose of this thesis is to find out characteristic of Swango that show he has antisocial personality disorder and to know the causes of his disorder. The writer refers to theory antisocial personality disorder that take in a research of APA (American Psychiatri...

  15. MytiBase: a knowledgebase of mussel (M. galloprovincialis transcribed sequences

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    Roch Philippe

    2009-02-01

    Full Text Available Abstract Background Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel challenged with toxic pollutants, temperature and potentially pathogenic bacteria. Results We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01 was constructed as determined by the high rate of gene discovery (65.6%. Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database http://mussel.cribi.unipd.it. Conclusion We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.

  16. Construction of a cDNA library from female adult of Toxocara canis, and analysis of EST and immune-related genes expressions.

    Science.gov (United States)

    Zhou, Rongqiong; Xia, Qingyou; Huang, Hancheng; Lai, Min; Wang, Zhenxin

    2011-10-01

    Toxocara canis is a widespread intestinal nematode parasite of dogs, which can also cause disease in humans. We employed an expressed sequence tag (EST) strategy in order to study gene-expression including development, digestion and reproduction of T. canis. ESTs provided a rapid way to identify genes, particularly in organisms for which we have very little molecular information. In this study, a cDNA library was constructed from a female adult of T. canis and 215 high-quality ESTs from 5'-ends of the cDNA clones representing 79 unigenes were obtained. The titer of the primary cDNA library was 1.83×10(6)pfu/mL with a recombination rate of 99.33%. Most of the sequences ranged from 300 to 900bp with an average length of 656bp. Cluster analysis of these ESTs allowed identification of 79 unique sequences containing 28 contigs and 51 singletons. BLASTX searches revealed that 18 unigenes (22.78% of the total) or 70 ESTs (32.56% of the total) were novel genes that had no significant matches to any protein sequences in the public databases. The rest of the 61 unigenes (77.22% of the total) or 145 ESTs (67.44% of the total) were closely matched to the known genes or sequences deposited in the public databases. These genes were classified into seven groups based on their known or putative biological functions. We also confirmed the gene expression patterns of several immune-related genes using RT-PCR examination. This work will provide a valuable resource for the further investigations in the stage-, sex- and tissue-specific gene transcription or expression. Copyright © 2011. Published by Elsevier Inc.

  17. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta.

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    Shanmei Zou

    Full Text Available Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.

  18. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)

    Science.gov (United States)

    Zou, Shanmei; Fei, Cong; Song, Jiameng; Bao, Yachao; He, Meilin; Wang, Changhai

    2016-01-01

    Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella–like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential “specific barcode” for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes. PMID:27092945

  19. ANALYSIS OF THE INTERACTIONS BETWEEN IMMIGRANT/FOREIGN CHARACTERS AND NATIONAL/AUTOCHTHONOUS CHARACTERS IN SPANISH TELEVISION FICTION

    Directory of Open Access Journals (Sweden)

    María Marcos Ramos

    2014-10-01

    Full Text Available In this paper we present the results of an empirical research in which it were analysed the interactions between immigrants and national characters in a sample of Spanish television fictional programs broadcasted on prime time. This study is a content analysis of 282 interactions between immigrant/foreign and national characters. Thus, it was found that the largest number of relationships between the characters involved was produced in a working context. Moreover, there was a higher proportion of the use of aggressive humour from the national characters to the immigrant/foreigners than in the reverse way. It was also observed that the immigrant/foreigner characters hardly spoke about their feelings, nor were heard by the nationals when they did it, although there were a high number of interactions in which immigrant characters were expressing their opinions and these were attended by national characters. The analysis of the interactions between immigrant and national characters in television fiction is a very important research issue, because it has been proposed that the parasocial interactions are complementary of the interpersonal interactions taking place in daily life (Müller, 2009; Park, 2012.

  20. THE NEED FOR CHARACTER EDUCATION

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    Aynur Pala

    2011-07-01

    Full Text Available Character education is a national movement creatingschools that foster ethical,responsible and caring young people by modelling and teaching good characterthrough emphasis on universal values that we all share. It is the intentional,proactive effort by schools, districts and states to instil in their students importantcore ethical values such as caring, honesty, fairness, responsibility and respect forself and others.Good character is not formed automatically; it is developed over time through asustained process of teaching, example, learning and practice. It is developedthrough character education. The intentional teaching of good character isparticularly important in today’s society since ouryouth face many opportunitiesand dangers unknown to earlier generations. They are bombarded with many morenegative influences through the media and other external sources prevalent intoday’s culture. Since children spend about 900 hours a year in school, it isessential that schools resume a proactive role in assisting families andcommunities by developing caring, respectful environments where students learncore, ethical values. When a comprehensive approachto character education isused, a positive moral culture is created in the school—a total school environmentthat supports the values taught in the classroom (Character Education Partnership,2010.The aim of this study is to provide guidelines forthe elements need for effectiveand comprehensive character education. And to emphasize the need of charactereducation to help students develop good character, which includes knowing,caring about and acting upon core ethical values such as respect, responsibility,honesty, fairness and compassion.

  1. Maya Studio Projects Photorealistic Characters

    CERN Document Server

    Palamar, Todd

    2011-01-01

    Create realistic characters with Maya tools and this project-based book Maya character generation tools are extremely sophisticated, and there's no better way to learn all their capabilities than by working through the projects in this hands-on book. This official guide focuses on understanding and implementing Maya's powerful tools for creating realistic characters for film, games, and TV. Use a variety of tools to create characters from skeleton to clothing, including hairstyles and facial hair, and learn how to use Performance Capture. A DVD includes supplementary videos, project support fi

  2. Holistic Processing of Chinese Characters

    Directory of Open Access Journals (Sweden)

    Alan Chun-Nang Wong

    2011-05-01

    Full Text Available Enhanced holistic processing (obligatory attention to all parts of an object has been associated with different types of perceptual expertise involving faces, cars, fingerprints, musical notes, English words, etc. Curiously Chinese characters are regarded as an exception, as indicated by the lack of holistic processing found for experts (Hsiao and Cottrell, 2009. The ceiling performance of experts, however, may have caused this null effect. We revisit this issue by adopting the often-used face-composite sequential-matching task to two-part Chinese characters. Participants matched the target halves (left or right of two characters while ignoring the irrelevant halves. Both Chinese readers (experts and non-Chinese readers (novices showed holistic processing. Follow-up experiments suggested different origins of the effects for the two groups. For experts, holistic processing was sensitive to the amount of experience with the characters, as it was larger for words than non-words (formed by swapping the two parts of a valid character. Novices, however, showed similar degree of holistic processing to words and non-words, suggesting that their effects were more related to their inefficient decomposition of a complex, character-like pattern into parts. Overall these findings suggest that holistic processing may be a marker of expertise with Chinese characters, contrary to previous claims.

  3. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-22

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

  4. PASSIOMA: Exploring Expressed Sequence Tags during Flower Development in Passiflora spp.

    Directory of Open Access Journals (Sweden)

    Lucas Cutri

    2012-01-01

    Full Text Available The genus Passiflora provides a remarkable example of floral complexity and diversity. The extreme variation of Passiflora flower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs as an approach for the characterization of genes expressed during Passiflora reproductive development. Analyzing the Passiflora floral EST database (named PASSIOMA, we found sequences showing significant sequence similarity to genes known to be involved in reproductive development such as MADS-box genes. Some of these sequences were studied using RT-PCR and in situ hybridization confirming their expression during Passiflora flower development. The detection of these novel sequences can contribute to the development of EST-based markers for important agronomic traits as well as to the establishment of genomic tools to study the naturally occurring floral diversity among Passiflora species.

  5. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

    Directory of Open Access Journals (Sweden)

    Brahmbhatt Sonal

    2008-11-01

    Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

  6. Character order processing in Chinese reading.

    Science.gov (United States)

    Gu, Junjuan; Li, Xingshan; Liversedge, Simon P

    2015-02-01

    We explored how character order information is encoded in isolated word processing or Chinese sentence reading in 2 experiments using a masked priming paradigm and a gaze-contingent display-change paradigm. The results showed that response latencies in the lexical decision task and reading times on the target word region were longer in the unrelated condition (the prime or the preview was unrelated with the target word) than the transposed-character condition (the prime or the preview was a transposition of the 2 characters of the target word), which were respectively longer than in the identity condition (the prime or preview was identical to the target word). These results show that character order is encoded at an early stage of processing in Chinese reading, but character position encoding was not strict. We also found that character order encoding was similar for single-morpheme and multiple-morpheme words, suggesting that morphemic status does not affect character order encoding. The current results represent an early contribution to our understanding of character order encoding during Chinese reading.

  7. Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers.

    Science.gov (United States)

    Pandey, Sudhakar; Ansari, Waquar Akhter; Pandey, Maneesh; Singh, Bijendra

    2018-02-01

    In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2-6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079-1.753, 0.074-0.428 and 0.074-0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon ( Cucumis melo var. momordica ), muskmelon ( Cucumis melo L.), pickling melon ( Cucumis melo var. conomon ) and wild muskmelon ( Cucumis melo var. agrestis ) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.

  8. Construction, database integration, and application of an Oenothera EST library.

    Science.gov (United States)

    Mrácek, Jaroslav; Greiner, Stephan; Cho, Won Kyong; Rauwolf, Uwe; Braun, Martha; Umate, Pavan; Altstätter, Johannes; Stoppel, Rhea; Mlcochová, Lada; Silber, Martina V; Volz, Stefanie M; White, Sarah; Selmeier, Renate; Rudd, Stephen; Herrmann, Reinhold G; Meurer, Jörg

    2006-09-01

    Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

  9. AcEST: [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL2194Contig1 771 2 Adiantum capillus-veneris contig: CL2194contig1 sequence. Link to clone list...apillus-veneris contig: CL2194contig1 sequence. Link to clone list Link to clone list Clone ID BP915172 DK95

  10. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

    Directory of Open Access Journals (Sweden)

    Voorrips Roeland E

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. Results We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. Conclusion QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at

  11. Recalling visual serial order for verbal sequences

    NARCIS (Netherlands)

    Logie, R.H.; Saito, S.; Morita, A.; Varma, S.; Norris, D.

    2016-01-01

    We report three experiments in which participants performed written serial recall of visually presented verbal sequences with items varying in visual similarity. In Experiments 1 and 2 native speakers of Japanese recalled visually presented Japanese Kanji characters. In Experiment 3, native speakers

  12. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

    Science.gov (United States)

    Knudsen, Vegeir; Caetano-Anollés, Gustavo

    2008-01-01

    The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

  13. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

    Energy Technology Data Exchange (ETDEWEB)

    Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

    2010-01-27

    Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in

  14. Character profiles and life satisfaction.

    Science.gov (United States)

    Park, Hwanjin; Suh, Byung Seong; Kim, Won Sool; Lee, Hye-Kyung; Park, Seon-Cheol; Lee, Kounseok

    2015-04-01

    There is a surge of interest in subjective well-being (SWB), which concerns how individuals feel about their happiness. Life satisfaction tends to be influenced by individual psychological traits and external social factors. The aim of this study was to examine the relationship between individual character and SWB. Data from 3522 university students were analyzed in this study. Character profiles were evaluated using the Temperament and Character Inventory-Revised Short version (TCI-RS). Life satisfaction was assessed using the Satisfaction with Life Scale (SWLS). All statistical tests regarding the correlations between each character profile and life satisfaction were conducted using ANOVAs, t-tests, multiple linear regression models and correlation analyses. The creative (SCT) profile was associated with the highest levels of life satisfaction, whereas the depressive (sct) profile was associated with the lowest levels of life satisfaction. Additionally, high self-directedness, self-transcendence and cooperation were associated with high life satisfaction. The results of gender-adjusted multiple regression analysis showed that the effects of self-directedness were the strongest in the assessment of one's quality of life, followed by self-transcendence and cooperativeness, in that order. All of the three-character profiles were significantly correlated with one's quality of life, and the character profiles of TCI-RS explained 27.6% of life satisfaction in total. Among the three-character profiles, the self-directedness profile was most associated with life satisfaction. Our study was cross-sectional, and self-reported data from students at a single university were analyzed. The results of this study showed that, among the character profiles, the effects of self-directedness were the strongest for predicting life satisfaction. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

    Science.gov (United States)

    Pirooznia, Mehdi; Gong, Ping; Guan, Xin; Inouye, Laura S; Yang, Kuan; Perkins, Edward J; Deng, Youping

    2007-01-01

    Background Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. Results A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Conclusion The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at . PMID:18047730

  16. Character Development in Adolescents.

    Science.gov (United States)

    Kessler, Glenn R.; And Others

    1986-01-01

    Explored the effects of a program consisting of communication and counseling skills, assertiveness training and moral dilemmas on the character development of high school students. The results demonstrated that the character development of the students in the experimental treatment group was affected significantly over time by the program.…

  17. Evolution of developmental sequences in lepidosaurs

    Directory of Open Access Journals (Sweden)

    Tomasz Skawiński

    2017-04-01

    Full Text Available Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular. Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.

  18. Budding yeast cDNA sequencing project: S03036-05_I15 [Budding yeast cDNA sequencing project

    Lifescience Database Archive (English)

    Full Text Available EST - Link to UCSC Genome Browser - Sequence >S03036-05_I15.phd NNNTNNTNNNNCNCTCACATANAAGACGGANNAGNNNGCTGGGC...CAATGCGTTCCATATGCG AAAATTCTTGGNCAATGTATTCTCTAGCAATCTNTNCTTTTGTACANTCGGAGGNTTNTC ATGNTCCTTTCATANATTATANAAANNG

  19. The use of Open Reading frame ESTs (ORESTES for analysis of the honey bee transcriptome

    Directory of Open Access Journals (Sweden)

    Soares Ademilson EE

    2004-11-01

    Full Text Available Abstract Background The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES strategy to generate profiles for the life cycle of Apis mellifera workers. Results Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41% represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria, and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52% did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22% should represent Apis-specific genes. Conclusions The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes.

  20. Phylogeny and character evolution of the fern genus Tectaria (Tectariaceae) in the Old World inferred from chloroplast DNA sequences.

    Science.gov (United States)

    Ding, Hui-Hui; Chao, Yi-Shan; Callado, John Rey; Dong, Shi-Yong

    2014-11-01

    In this study we provide a phylogeny for the pantropical fern genus Tectaria, with emphasis on the Old World species, based on sequences of five plastid regions (atpB, ndhF plus ndhF-trnL, rbcL, rps16-matK plus matK, and trnL-F). Maximum parsimony, maximum likelihood, and Bayesian inference are used to analyze 115 individuals, representing ca. 56 species of Tectaria s.l. and 36 species of ten related genera. The results strongly support the monophyly of Tectaria in a broad sense, in which Ctenitopsis, Hemigramma, Heterogonium, Psomiocarpa, Quercifilix, Stenosemia, and Tectaridium should be submerged. Such broadly circumscribed Tectaria is supported by the arising pattern of veinlets and the base chromosome number (x=40). Four primary clades are well resolved within Tectaria, one from the Neotropic (T. trifoliata clade) and three from the Old World (T. subtriphylla clade, Ctenitopsis clade, and T. crenata clade). Tectaria crenata clade is the largest one including six subclades. Of the genera previously recognized as tectarioid ferns, Ctenitis, Lastreopsis, and Pleocnemia, are confirmed to be members in Dryopteridaceae; while Pteridrys and Triplophyllum are supported in Tectariaceae. To infer morphological evolution, 13 commonly used characters are optimized on the resulting phylogenetic trees and in result, are all homoplastic in Tectaria. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

    Directory of Open Access Journals (Sweden)

    Vingron Martin

    2004-09-01

    Full Text Available Abstract Background Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts. Methods We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones represented only by ESTs derived from normalized libraries. A subset of the predicted tissue and tumor specific isoforms are then validated via RT-PCR experiments over a spectrum of 40 tissue types. Results Our strategy revealed 427 genes with at least one tissue specific transcript as well as 1120 genes showing tumor specific isoforms. While our experimental evaluation of computationally predicted tissue-specific isoforms revealed a high success rate in confirming the expression of these isoforms in the respective tissue, the strategy frequently failed to detect the expected restricted expression pattern. The analysis of putative lowly expressed transcripts using normalized cDNA libraries suggests that our ability to detect tissue-specific isoforms strongly depends on the expression level of the respective transcript as well as on the sensitivity of the experimental methods. Especially splice isoforms predicted to be disease-specific tend to represent transcripts that are expressed in a set of healthy tissues rather than novel isoforms. Conclusions We propose to combine the computational prediction of alternative splice isoforms with experimental validation for

  2. Social character of materialism.

    Science.gov (United States)

    Chatterjee, A; Hunt, J M; Kernan, J B

    2000-06-01

    Scores for 170 undergraduates on Richins and Dawson's Materialism scale were correlated with scores on Kassarjian's Social Preference Scale, designed to measure individuals' character structure. A correlation of .26 between materialism and other-directed social character suggested that an externally oriented reference system guides materialists' perceptions, judgments, acquisitions, and possessions.

  3. APLIKASI SPOKES-CHARACTERS DALAM KAITAN DENGAN MEREK PRODUK

    Directory of Open Access Journals (Sweden)

    Caroline Widjoyo

    2004-01-01

    Full Text Available Advertisement by using spokes-characters have potency to alter the choice of consumer brand with the compared to bigger impact which do not use the spokes-character. A lot of producer which hence spokes-character to increase assess to sell from a product. Spokes-Characters experience of the evolution from time to time keep abreast of the era%2C now emerge the new type of spokes-character and its application. Abstract in Bahasa Indonesia : Iklan dengan spokes-characters berpotensi mengubah pilihan merek konsumen dengan dampak lebih besar dibanding yang tidak menggunakan spokes-character. Banyak produsen yang memakai spokes-character untuk meningkatkan nilai jual dari sebuah produk. Spokes-characters mengalami evolusi dari masa ke masa mengikuti perkembangan jaman%2C sekarang muncul jenis baru spokes-character dan aplikasinya. spokes-characters%2C advertising%2C branding.

  4. Character Play – The use of game characters in multi- player Role Playing Games across platforms

    DEFF Research Database (Denmark)

    Tychsen, Anders; Hitchens, M.; Brolund, T.

    2008-01-01

    histories of game characters. This article presents results from a comprehensive empirical study of the way complex game characters are utilized by players in multiplayer role-playing games across two different media platforms. The results indicate that adult players are capable of comprehending...... and utilizing game characters with well-defined personalities and backgrounds, as well as rules-based components. Furthermore, that the game format plays a significant role in the pattern of usage of the character elements. This pattern appears directly linked with variations in the way that the different game...

  5. Marvel and DC Characters Inspired by Arachnids

    Directory of Open Access Journals (Sweden)

    Elidiomar Ribeiro Da-Silva

    2014-12-01

    Full Text Available This article compares arachnid-based Marvel and DC comics characters. The composition of a comic book character often has interesting ‘real-life’ influences. Given the strong connection between arachnids (especially spiders, scorpions and mites, all belonging to the zoological class 'Arachnida' and human beings it is not surprising that they have inspired many fictional characters. We recorded 84 Marvel Comics characters and 40 DC Comics characters, detailed in the dataset that accompanies the article (Da-Silva 2014. Most characters have been created recently, since the 1990s. Marvel has significantly more arachnid characters than DC. As for taxonomic classification, the characters were based mostly on spiders (zoological order 'Araneae'. Of the total characters, the majority are human beings, but an overwhelming number have at least some typical arachnid features. Villains (60.91% of total are significantly more numerous, considering the sum of the two publishers. Arachnids have bad reputation for being dangerous (Thorp and Woodson 1976; Ruppert and Barnes 1996. Since the public usually considers spiders, scorpions and mites “harmful” in general, we expected a larger contingent of villains. However, there was no statistical difference between the amount of villains and heroes in Marvel characters. It did not happen probably due to the success of one character: the Amazing Spider-Man.

  6. Handwritten Sindhi Character Recognition Using Neural Networks

    Directory of Open Access Journals (Sweden)

    Shafique Ahmed Awan

    2018-01-01

    Full Text Available OCR (OpticalCharacter Recognition is a technology in which text image is used to understand and write text by machines. The work on languages containing isolated characters such as German, English, French and others is at its peak. The OCR and ICR (Intelligent Character Recognition research in Sindhi script is currently at in starting stages and not sufficient work have been cited in this area even though Sindhi language is rich in culture and history. This paper presents one of the initial steps in recognizing Sindhi handwritten characters. The isolated characters of Sindhi script written by thesubjects have been recognized. The various subjects were asked to write Sindhi characters in unconstrained form and then the written samples were collected and scanned through a flatbed scanner. The scanned documents were preprocessedwith the help of binary conversion, removing noise by pepper noise and the lines were segmented with the help of horizontal profile technique. The segmented lines were used to extract characters from scanned pages.This character segmentation was done by vertical projection. The extracted characters have been used to extract features so that the characters can be classified easily. Zoning was used for the feature extraction technique. For the classification, neural network has been used. The recognized characters converted into editable text with an average accuracy of 85%.

  7. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik

    2007-01-01

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

  8. Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.).

    Science.gov (United States)

    Mornkham, T; Wangsomnuk, P P; Mo, X C; Francisco, F O; Gao, L Z; Kurzweil, H

    2016-10-24

    Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

  9. Degraded character recognition based on gradient pattern

    Science.gov (United States)

    Babu, D. R. Ramesh; Ravishankar, M.; Kumar, Manish; Wadera, Kevin; Raj, Aakash

    2010-02-01

    Degraded character recognition is a challenging problem in the field of Optical Character Recognition (OCR). The performance of an optical character recognition depends upon printed quality of the input documents. Many OCRs have been designed which correctly identifies the fine printed documents. But, very few reported work has been found on the recognition of the degraded documents. The efficiency of the OCRs system decreases if the input image is degraded. In this paper, a novel approach based on gradient pattern for recognizing degraded printed character is proposed. The approach makes use of gradient pattern of an individual character for recognition. Experiments were conducted on character image that is either digitally written or a degraded character extracted from historical documents and the results are found to be satisfactory.

  10. Moral character in the workplace.

    Science.gov (United States)

    Cohen, Taya R; Panter, A T; Turan, Nazli; Morse, Lily; Kim, Yeonjeong

    2014-11-01

    Using two 3-month diary studies and a large cross-sectional survey, we identified distinguishing features of adults with low versus high levels of moral character. Adults with high levels of moral character tend to: consider the needs and interests of others and how their actions affect other people (e.g., they have high levels of Honesty-Humility, empathic concern, guilt proneness); regulate their behavior effectively, specifically with reference to behaviors that have positive short-term consequences but negative long-term consequences (e.g., they have high levels of Conscientiousness, self-control, consideration of future consequences); and value being moral (e.g., they have high levels of moral identity-internalization). Cognitive moral development, Emotionality, and social value orientation were found to be relatively undiagnostic of moral character. Studies 1 and 2 revealed that employees with low moral character committed harmful work behaviors more frequently and helpful work behaviors less frequently than did employees with high moral character, according to their own admissions and coworkers' observations. Study 3 revealed that adults with low moral character committed more delinquent behavior and had more lenient attitudes toward unethical negotiation tactics than did adults with high moral character. By showing that individual differences have consistent, meaningful effects on employees' behaviors, after controlling for demographic variables (e.g., gender, age, income) and basic attributes of the work setting (e.g., enforcement of an ethics code), our results contest situationist perspectives that deemphasize the importance of personality. Moral people can be identified by self-reports in surveys, and these self-reports predict consequential behaviors months after the initial assessment.

  11. Character Education and Students Social Behavior

    Directory of Open Access Journals (Sweden)

    Syamsu A. Kamaruddin

    2012-09-01

    Full Text Available

    In an educational environment, in the form of character education program has been done both formally and informally. It's intended as one of the supporting ideas for follow-up in the form of design activities. Character education should basically refers to the vision and mission of the institution concerned. It shows the orientation of the two things in the character of the students are: aspects of human character and individual learners hallmark institution. In this paper, these two aspects is the author trying to ideas by referring to some other writings. The end result, the authors expect the birth of a design patent as early referral to spearhead a character development program learners.

  12. Effects of word width and word length on optimal character size for reading of horizontally scrolling Japanese words

    Directory of Open Access Journals (Sweden)

    Wataru eTeramoto

    2016-02-01

    Full Text Available The present study investigated whether word width and length affect the optimal character size for reading of horizontally scrolling Japanese words, using reading speed as a measure. In Experiment 1, three Japanese words, each consisting of 4 Hiragana characters, sequentially scrolled on a display screen from right to left. Participants, all Japanese native speakers, were instructed to read the words aloud as accurately as possible, irrespective of their order within the sequence. To quantitatively measure their reading performance, we used rapid serial visual presentation paradigm, where the scrolling rate was increased until the participants began to make mistakes. Thus, the highest scrolling rate at which the participants’ performance exceeded 88.9% correct rate was calculated for each character size (0.3, 0.6, 1.0, and 3.0° and scroll window size (5 or 10 character spaces. Results showed that the reading performance was highest in the range of 0.6° to 1.0°, irrespective of the scroll window size. Experiment 2 investigated whether the optimal character size observed in Experiment 1 was applicable for any word width and word length (i.e., the number of characters in a word. Results showed that reading speeds were slower for longer than shorter words and the word width of 3.6° was optimal among the word lengths tested (3, 4, and 6 character words. Considering that character size varied depending on word width and word length in the present study, this means that the optimal character size can be changed by word width and word length.

  13. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis.

    Science.gov (United States)

    Sabourault, Cécile; Ganot, Philippe; Deleury, Emeline; Allemand, Denis; Furla, Paola

    2009-07-23

    Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zooxanthellae. These algae are photosynthetic and the cnidarian-zooxanthellae association is based on nutritional exchanges. Maintenance of such an intimate cellular partnership involves many crosstalks between the partners. To better characterize symbiotic relationships between a cnidarian host and its dinoflagellate symbionts, we conducted a large-scale EST study on a symbiotic sea anemone, Anemonia viridis, in which the two tissue layers (epiderm and gastroderm) can be easily separated. A single cDNA library was constructed from symbiotic tissue of sea anemones A. viridis in various environmental conditions (both normal and stressed). We generated 39,939 high quality ESTs, which were assembled into 14,504 unique sequences (UniSeqs). Sequences were analysed and sorted according to their putative origin (animal, algal or bacterial). We identified many new repeated elements in the 3'UTR of most animal genes, suggesting that these elements potentially have a biological role, especially with respect to gene expression regulation. We identified genes of animal origin that have no homolog in the non-symbiotic starlet sea anemone Nematostella vectensis genome, but in other symbiotic cnidarians, and may therefore be involved in the symbiosis relationship in A. viridis. Comparison of protein domain occurrence in A. viridis with that in N. vectensis demonstrated an increase in abundance of some molecular functions, such as protein binding or antioxidant activity, suggesting that these functions are essential for the symbiotic state and may be specific adaptations. This large dataset of sequences provides a valuable resource for future studies on symbiotic interactions in Cnidaria. The comparison with the closest available genome, the sea anemone N. vectensis, as well as

  14. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis

    Directory of Open Access Journals (Sweden)

    Deleury Emeline

    2009-07-01

    Full Text Available Abstract Background Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zooxanthellae. These algae are photosynthetic and the cnidarian-zooxanthellae association is based on nutritional exchanges. Maintenance of such an intimate cellular partnership involves many crosstalks between the partners. To better characterize symbiotic relationships between a cnidarian host and its dinoflagellate symbionts, we conducted a large-scale EST study on a symbiotic sea anemone, Anemonia viridis, in which the two tissue layers (epiderm and gastroderm can be easily separated. Results A single cDNA library was constructed from symbiotic tissue of sea anemones A. viridis in various environmental conditions (both normal and stressed. We generated 39,939 high quality ESTs, which were assembled into 14,504 unique sequences (UniSeqs. Sequences were analysed and sorted according to their putative origin (animal, algal or bacterial. We identified many new repeated elements in the 3'UTR of most animal genes, suggesting that these elements potentially have a biological role, especially with respect to gene expression regulation. We identified genes of animal origin that have no homolog in the non-symbiotic starlet sea anemone Nematostella vectensis genome, but in other symbiotic cnidarians, and may therefore be involved in the symbiosis relationship in A. viridis. Comparison of protein domain occurrence in A. viridis with that in N. vectensis demonstrated an increase in abundance of some molecular functions, such as protein binding or antioxidant activity, suggesting that these functions are essential for the symbiotic state and may be specific adaptations. Conclusion This large dataset of sequences provides a valuable resource for future studies on symbiotic interactions in Cnidaria. The comparison with the closest

  15. Essays on Character & Opportunity

    Science.gov (United States)

    Center on Children and Families at Brookings, 2014

    2014-01-01

    These essays provide richer set of writings on the philosophical, empirical and practical issues raised by a focus on character, and in particular its relationship to questions of opportunity. Each one is an intellectual pemmican: sharp and to the point. Two scholars draw attention to the gendered nature of character formation (Segal and Lexmond);…

  16. Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

    Directory of Open Access Journals (Sweden)

    Matthew W. Blair

    2011-11-01

    Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

  17. Reproducibility analysis to validate language processes involving Kanji and Chinese characters under different MRI scanner environments

    International Nuclear Information System (INIS)

    Chen Shensing Annabel; Matsuo, Kayako; Tseng Wenyih Isaac; Hue Chiwei; Nakai, Toshiharu; Bagarinao, E.; Ho Moonho Ringo; Liou Michelle

    2009-01-01

    Reading Japanese kanji is similar to reading Chinese characters in that orthography-to-phonology conversion is required. However, a notable difference between kanji and Chinese characters or alphabets is that the majority of kanji are heterophonic-homographic characters, id est (i.e.), one character is mapped to more than one pronunciation. With the goal of developing a standardized functional MRI language task for Japanese and Chinese, we conducted a series of homophone judgment tasks in both populations. Since the Japanese and Chinese data were acquired using MRI scanners with different magnetic field strengths (1.5 T and 3 T, respectively), direct comparison of the activation maps from the two populations using conventional statistical methods was not appropriate. Informal evaluation of the group activations for the homophonic-heterographic condition showed that this homophone judgment task with similar content and standardized design elicited common areas of activation for language in general for the two populations. Further, it is interesting to note that strong activations in the left posterior superior and middle temporal regions were found to be unique to the Taiwanese population. To further investigate this, we applied reproducibility analysis to verify the likelihood that this finding is unique to the Chinese population. The results are presented and the possibility of using reproducibility analysis to evaluate and compare data from different populations and with different scanner strengths is discussed. (author)

  18. Building Character through Literacy with Children's Literature

    Science.gov (United States)

    Almerico, Gina M.

    2014-01-01

    Character education is described as curriculum specifically developed to teach children about the quality and traits of good character. One means in which children can learn about good character is through the pages of high quality children's literature. In this study, the author defines the characteristics of an effective character development…

  19. The Effect of Realistic Appearance of Virtual Characters in Immersive Environments - Does the Character's Personality Play a Role?

    Science.gov (United States)

    Zibrek, Katja; Kokkinara, Elena; Mcdonnell, Rachel

    2018-04-01

    Virtual characters that appear almost photo-realistic have been shown to induce negative responses from viewers in traditional media, such as film and video games. This effect, described as the uncanny valley, is the reason why realism is often avoided when the aim is to create an appealing virtual character. In Virtual Reality, there have been few attempts to investigate this phenomenon and the implications of rendering virtual characters with high levels of realism on user enjoyment. In this paper, we conducted a large-scale experiment on over one thousand members of the public in order to gather information on how virtual characters are perceived in interactive virtual reality games. We were particularly interested in whether different render styles (realistic, cartoon, etc.) would directly influence appeal, or if a character's personality was the most important indicator of appeal. We used a number of perceptual metrics such as subjective ratings, proximity, and attribution bias in order to test our hypothesis. Our main result shows that affinity towards virtual characters is a complex interaction between the character's appearance and personality, and that realism is in fact a positive choice for virtual characters in virtual reality.

  20. Development of EST Intron-Targeting SNP Markers for Panax ginseng and Their Application to Cultivar Authentication.

    Science.gov (United States)

    Wang, Hongtao; Li, Guisheng; Kwon, Woo-Saeng; Yang, Deok-Chun

    2016-06-04

    Panax ginseng is one of the most valuable medicinal plants in the Orient. The low level of genetic variation has limited the application of molecular markers for cultivar authentication and marker-assisted selection in cultivated ginseng. To exploit DNA polymorphism within ginseng cultivars, ginseng expressed sequence tags (ESTs) were searched against the potential intron polymorphism (PIP) database to predict the positions of introns. Intron-flanking primers were then designed in conserved exon regions and used to amplify across the more variable introns. Sequencing results showed that single nucleotide polymorphisms (SNPs), as well as indels, were detected in four EST-derived introns, and SNP markers specific to "Gopoong" and "K-1" were first reported in this study. Based on cultivar-specific SNP sites, allele-specific polymerase chain reaction (PCR) was conducted and proved to be effective for the authentication of ginseng cultivars. Additionally, the combination of a simple NaOH-Tris DNA isolation method and real-time allele-specific PCR assay enabled the high throughput selection of cultivars from ginseng fields. The established real-time allele-specific PCR assay should be applied to molecular authentication and marker assisted selection of P. ginseng cultivars, and the EST intron-targeting strategy will provide a potential approach for marker development in species without whole genomic DNA sequence information.

  1. Promoting Character Development through Coach Education

    Science.gov (United States)

    Power, F. Clark; Seroczynski, A. D.

    2015-01-01

    Can youth sports build character? Research suggests that the answer to this question leads to 2 further questions: (1) can youth sport coaches be effectively prepared to become character educators, and (2) can character education take place in today's competitive youth sport environment? (Bredemeier & Shields, 2006; Power, 2015; Power &…

  2. Braille Character Recognition Using Artificial Neural Network

    OpenAIRE

    Subur, Joko; Sardjono, Tri Arief; Mardiyanto, Ronny

    2015-01-01

    Braille letter is characters designed for the blind, consist of six embossed points, arranged in a standard braille character. Braille letters is touched and read using fingers, therefore the sensitivity of the fingers is important. Those characters need to be memorized, so it is very difficult to be learned. The aim of this research is to create a braille characters recognition system and translate it to alpha-numeric text. Webcam camera is used to capture braille image from braille characte...

  3. The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

    Science.gov (United States)

    Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

    2014-01-01

    Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

  4. A Study of Character among Collegiate Athletes

    Science.gov (United States)

    Heupel, Jill D.

    2017-01-01

    The idea that sport builds character has been around for a long time. However, sports may not build the type of character once thought. Character of athletes was defined based on differing views held by sport scholars, coaches, athletes, and sport enthusiast. Sport scholars tend to view character of athletes from a moral perspective. Coaches,…

  5. Isolation, sequence identification and tissue expression profile of a ...

    African Journals Online (AJOL)

    The complete expressed sequence tag (CDS) sequence of Banna mini-pig inbred line (BMI) ribokinase gene (RBKS) was amplified using the reverse transcription-polymerase chain reaction (RT-PCR) based on the conserved sequence information of the cattle or other mammals and known highly homologous swine ESTs.

  6. IMAGE PROCESSING BASED OPTICAL CHARACTER RECOGNITION USING MATLAB

    OpenAIRE

    Jyoti Dalal*1 & Sumiran Daiya2

    2018-01-01

    Character recognition techniques associate a symbolic identity with the image of character. In a typical OCR systems input characters are digitized by an optical scanner. Each character is then located and segmented, and the resulting character image is fed into a pre-processor for noise reduction and normalization. Certain characteristics are the extracted from the character for classification. The feature extraction is critical and many different techniques exist, each having its strengths ...

  7. Body Language Advanced 3D Character Rigging

    CERN Document Server

    Allen, Eric; Fong, Jared; Sidwell, Adam G

    2011-01-01

    Whether you're a professional Character TD or just like to create 3D characters, this detailed guide reveals the techniques you need to create sophisticated 3D character rigs that range from basic to breathtaking. Packed with step-by-step instructions and full-color illustrations, Body Language walks you through rigging techniques for all the body parts to help you create realistic and believable movements in every character you design. You'll learn advanced rigging concepts that involve MEL scripting and advanced deformation techniques and even how to set up a character pipeline.

  8. Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries

    Science.gov (United States)

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources such as SSRs, SNPs and InDels in several model and non-model plant species. Yam (Dioscorea spp.) i...

  9. An attempt to reconstruct phylogenetic relationships within Caribbean nummulitids: simulating relationships and tracing character evolution

    Science.gov (United States)

    Eder, Wolfgang; Ives Torres-Silva, Ana; Hohenegger, Johann

    2017-04-01

    chamber length and P/D ratio) and some growth-invariant characters of the chamber sequence (e.g., backbend angle, initial chamber base length and chamber length increase) are evident.

  10. Effects of Word Width and Word Length on Optimal Character Size for Reading of Horizontally Scrolling Japanese Words.

    Science.gov (United States)

    Teramoto, Wataru; Nakazaki, Takuyuki; Sekiyama, Kaoru; Mori, Shuji

    2016-01-01

    The present study investigated, whether word width and length affect the optimal character size for reading of horizontally scrolling Japanese words, using reading speed as a measure. In Experiment 1, three Japanese words, each consisting of four Hiragana characters, sequentially scrolled on a display screen from right to left. Participants, all Japanese native speakers, were instructed to read the words aloud as accurately as possible, irrespective of their order within the sequence. To quantitatively measure their reading performance, we used rapid serial visual presentation paradigm, where the scrolling rate was increased until the participants began to make mistakes. Thus, the highest scrolling rate at which the participants' performance exceeded 88.9% correct rate was calculated for each character size (0.3°, 0.6°, 1.0°, and 3.0°) and scroll window size (5 or 10 character spaces). Results showed that the reading performance was highest in the range of 0.6° to 1.0°, irrespective of the scroll window size. Experiment 2 investigated whether the optimal character size observed in Experiment 1 was applicable for any word width and word length (i.e., the number of characters in a word). Results showed that reading speeds were slower for longer than shorter words and the word width of 3.6° was optimal among the word lengths tested (three, four, and six character words). Considering that character size varied depending on word width and word length in the present study, this means that the optimal character size can be changed by word width and word length in scrolling Japanese words.

  11. Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

    Science.gov (United States)

    Scaglione, Davide; Acquadro, Alberto; Portis, Ezio; Taylor, Christopher A; Lanteri, Sergio; Knapp, Steven J

    2009-01-01

    Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species. PMID:19785740

  12. On Hemingway’s Literary Characters

    Directory of Open Access Journals (Sweden)

    Maria-Miruna Ciocoi-Pop

    2013-01-01

    Full Text Available The present paper is a brief outline of Hemingway’s characters and the way in which they correspond to the author himself. It is known for a fact that Hemingway evinced a tendency to imitate his characters when they were coming to grips with diverse situations. Thus I have tried to briefly pinpoint the fading boundaries between reality and imagination in his work. By doing so, I have focused on both male and female characters, underlining the major dissimilarities between these two categories, as well as their main features.

  13. Moral character effects in endorser perception

    Directory of Open Access Journals (Sweden)

    Chang Joseph W.

    2017-06-01

    Full Text Available This research consists of two experimental studies investigating the influence of moral character on endorser perception, and the influence of perceiver characteristics on tarnished endorser perception and brand evaluations. Perceiver characteristics are discussed from the perspectives of dispositional tendency, innate moral intuitions and self-location. The first study compared the influences of moral character and warmth on endorser perception. The second study examined the impact of perceiver characteristics on tarnished endorsers and brand evaluations. The findings reveal that moral character is more influential than warmth on endorser evaluations. Tarnished endorsers with immoral character exert more negative influence than tarnished endorsers with coldness character on brand evaluations. Innate moral intuitions and self-location moderate brand evaluations. High-morality consumers and heart-locators are more vulnerable than low-morality and brain-locators to the brands endorsed by tarnished endorsers, respectively.

  14. Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki.

    Science.gov (United States)

    Luo, C; Zhang, F; Zhang, Q L; Guo, D Y; Luo, Z R

    2013-01-09

    We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.

  15. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  16. Video Game Characters. Theory and Analysis

    Directory of Open Access Journals (Sweden)

    Felix Schröter

    2014-06-01

    Full Text Available This essay develops a method for the analysis of video game characters based on a theoretical understanding of their medium-specific representation and the mental processes involved in their intersubjective construction by video game players. We propose to distinguish, first, between narration, simulation, and communication as three modes of representation particularly salient for contemporary video games and the characters they represent, second, between narrative, ludic, and social experience as three ways in which players perceive video game characters and their representations, and, third, between three dimensions of video game characters as ‘intersubjective constructs’, which usually are to be analyzed not only as fictional beings with certain diegetic properties but also as game pieces with certain ludic properties and, in those cases in which they function as avatars in the social space of a multiplayer game, as representations of other players. Having established these basic distinctions, we proceed to analyze their realization and interrelation by reference to the character of Martin Walker from the third-person shooter Spec Ops: The Line (Yager Development 2012, the highly customizable player-controlled characters from the role-playing game The Elder Scrolls V: Skyrim (Bethesda 2011, and the complex multidimensional characters in the massively multiplayer online role-playing game Star Wars: The Old Republic (BioWare 2011-2014.

  17. Identity of the xerophilic species Aspergillus penicillioides: Integrated analysis of the genotypic and phenotypic characters.

    Science.gov (United States)

    Tamura, Miki; Kawasaki, Hiroko; Sugiyama, Junta

    1999-02-01

    We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamorphic species, using an integrated analysis of the genotypic and phenotypic characters. Our experimental methods on two genotypic characters, i.e., DNA base composition using the HPLC method and DNA relatedness using the nitrocellulose filter hybridization technique between A. flavus, A. oryzae, and their close relations revealed a good agreement with the values by buoyant density (for DNA base composition) and spectrophotometric determination (for DNA relatedness) reported by Kurtzman et al. in 1986. On the basis of these comparisons, we examined DNA base composition and DNA relatedness of six selected strains of A. penicillioides, including IFO 8155 (originally described as A. vitricola), one strain of A. restrictus, and the respective strains from Eurotium amstelodami, E. repens, and E. rubrum. As a result, five strains within A. penicillioides, including the neotype strain NRRL 4548, had G+C contents of 46 to 49 mol%, whereas IFO 8155 had 50 mol%. A. restrictus had 52 mol%, and three Eurotium species ranged from 46 to 49 mol%. The DNA relatedness between A. penicillioides (five strains), except for IFO 8155, exhibited values greater than 70%, but the DNA complementarity between four strains and IFO 8155 in A. penicillioides revealed values of less than 40%. DNA relatedness values between three species of Eurotium were 65 to 72%. We determined 18S, 5.8S, and ITS rDNA sequences as other genotypic characters from A. penicillioides (six strains), A. restrictus, and related teleomorphic species of Eurotium. In three phylogenetic trees inferred from these sequences, five strains of A. penicillioides, including the neotype strain, were closely related to each other, whereas IFO 8155 was distantly related and grouped with other xerophilic species. Our results have suggested that A. penicillioides typified by NRRL 4548 and A. penicillioides IFO 8155 (ex holotype of A

  18. Modeling the Semiotic Structure of Player-Characters

    DEFF Research Database (Denmark)

    Vella, Daniel

    2014-01-01

    When game studies has tackled the player-character, it has tended to do so by means of an opposition to the notion of the avatar, with the result that the ontological and semiotic nature of the character in itself has not been given due attention. This paper draws on understandings of character...... from the fields of narratology and literary theory to highlight the double-layered ontology of character as both a possible individual and as a semiotic construction. Uri Margolin’s narratological model of character signification is used as the basis for developing a semiotic-structural model...

  19. Building innovative and creative character through mathematics

    Science.gov (United States)

    Suyitno, Hardi; Suyitno, Amin

    2018-03-01

    21st century is predicted as the century with rapid development in all aspects of life. People require creative and innovative character to exist. Specifically, mathematics has been given to students from the kindergarten until the middle school. Thus, building character through mathematics should begin since the early age. The problem is how to build creative and innovative character through mathematics education? The goal expected from this question is to build innovative and creative characters to face the challenges of the 21st century. This article discusses the values of mathematics, the values in mathematics education, innovative and creative character, and the integration of these values in teaching mathematics that support the innovative and creative character building, and applying the values in structurely programmed, measurable, and applicable learning activities.

  20. Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Asp, Torben; Frei, Ursula

    2008-01-01

    An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was te...

  1. Abiotic Stress-Related Expressed Sequence Tags from the Diploid Strawberry Fragaria vesca f. semperflorens

    Directory of Open Access Journals (Sweden)

    Maximo. Rivarola

    2011-03-01

    Full Text Available Strawberry ( spp. is a eudicotyledonous plant that belongs to the Rosaceae family, which includes other agronomically important plants such as raspberry ( L. and several tree-fruit species. Despite the vital role played by cultivated strawberry in agriculture, few stress-related gene expression characterizations of this crop are available. To increase the diversity of available transcriptome sequence, we produced 41,430 L. expressed sequence tags (ESTs from plants growing under water-, temperature-, and osmotic-stress conditions as well as a combination of heat and osmotic stresses that is often found in irrigated fields. Clustering and assembling of the ESTs resulted in a total of 11,836 contigs and singletons that were annotated using Gene Ontology (GO terms. Furthermore, over 1200 sequences with no match to available Rosaceae ESTs were found, including six that were assigned the “response to stress” GO category. Analysis of EST frequency provided an estimate of steady state transcript levels, with 91 sequences exhibiting at least a 20-fold difference between treatments. This EST collection represents a useful resource to advance our understanding of the abiotic stress-response mechanisms in strawberry. The sequence information may be translated to valuable tree crops in the Rosaceae family, where whole-plant treatments are not as simple or practical.

  2. Virtual Character Personality Influences Participant Attitudes and Behavior - An Interview with a Virtual Human Character about Her Social Anxiety

    Directory of Open Access Journals (Sweden)

    Xueni ePan

    2015-02-01

    Full Text Available We introduce a novel technique for the study of human-virtual character interaction in immersive virtual reality. The human participants verbally administered a standard questionnaire about social anxiety to a virtual female character, that responded to each question through speech and body movements. The purpose was to study the extent to which participants responded differently to characters that exhibited different personalities, even though the verbal content of their answers was always the same. A separate online study provided evidence that our intention to create two different personality types had been successful. In the main between-groups experiment that utilized a Cave system there were 24 male participants, where 12 interacted with a female virtual character portrayed to exhibit shyness and the remaining 12 with an identical but more confident virtual character. Our results indicate that although the content of the verbal responses of both virtual characters was the same, participants showed different subjective and behavioral responses to the two different personalities. In particular participants evaluated the shy character more positively, for example, expressing willingness to spend more time with her. Participants evaluated the confident character more negatively and waited for a significantly longer time to call her back after she had left the scene in order to answer a telephone call. The method whereby participants interviewed the virtual character allowed naturalistic conversation while avoiding the necessity of speech processing and generation, and natural language understanding. It is therefore a useful method for the study of the impact of virtual character personality on participant responses.

  3. Artificial Neural Network Based Optical Character Recognition

    OpenAIRE

    Vivek Shrivastava; Navdeep Sharma

    2012-01-01

    Optical Character Recognition deals in recognition and classification of characters from an image. For the recognition to be accurate, certain topological and geometrical properties are calculated, based on which a character is classified and recognized. Also, the Human psychology perceives characters by its overall shape and features such as strokes, curves, protrusions, enclosures etc. These properties, also called Features are extracted from the image by means of spatial pixel-...

  4. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

  5. Character Education in Print: Content Analysis of Character Education in Introduction to Education Textbooks

    Science.gov (United States)

    Protz, Babette Marisa

    2013-01-01

    Albert Einstein is credited with saying that the most important component of education is the development of students' character. While debate exists as to the delivery of character education in the public schools, it must be recognized that not all students have a support system outside of the schoolhouse. Consequently, when character…

  6. Landscape Character of Pongkor Mining Ecotourism Area

    Science.gov (United States)

    Kusumoarto, A.; Gunawan, A.; Machfud; Hikmat, A.

    2017-10-01

    Pongkor Mining Ecotourism Area has a diverse landscape character as a potential landscape resources for the development of ecotourism destination. This area is part of the Mount of Botol Resort, Halimun Salak National Park (HSNP). This area also has a fairly high biodiversity. This study aims to identify and analysis the category of landscape character in the Pongkor Mining Ecotourism Area for the development of ecotourism destination. This study used a descriptive approach through field surveys and interviews, was carried out through two steps : 1) identify the landscape character, and 2) analysis of the landscape character. The results showed that in areas set aside for ecotourism destination in Pongkor Mining, landscape character category scattered forests, tailing ponds, river, plain, and the built environment. The Category of landscape character most dominant scattered in the area is forest, here is the river, plain, tailing ponds, the built environment, and plain. The landscape character in a natural environment most preferred for ecotourism activities. The landscape character that spread in the natural environment and the built environment is a potential that must be protected and modified such as elimination of incongruous element, accentuation of natural form, alteration of the natural form, intensification and enhanced visual quality intensively to be developed as a ecotourism destination area.

  7. Data set for Tifinagh handwriting character recognition

    Directory of Open Access Journals (Sweden)

    Omar Bencharef

    2015-09-01

    Full Text Available The Tifinagh alphabet-IRCAM is the official alphabet of the Amazigh language widely used in North Africa [1]. It includes thirty-one basic letter and two letters each composed of a base letter followed by the sign of labialization. Normalized only in 2003 (Unicode [2], ICRAM-Tifinagh is a young character repertoire. Which needs more work on all levels. In this context we propose a data set for handwritten Tifinagh characters composed of 1376 image; 43 Image For Each character. The dataset can be used to train a Tifinagh character recognition system, or to extract the meaning characteristics of each character.

  8. EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi

    Directory of Open Access Journals (Sweden)

    Mahomed Waheed

    2011-11-01

    Full Text Available Abstract Background Avocado (Persea americana belongs to the Lauraceae family and is an important commercial fruit crop in over 50 countries. The most serious pathogen affecting avocado production is Phytophthora cinnamomi which causes Phytophthora root rot (PRR. Root pathogens such as P. cinnamomi and their interactions with hosts are poorly understood and despite the importance of both the avocado crop and the effect Phytophthora has on its cultivation, there is a lack of molecular knowledge underpinning our understanding of defence strategies against the pathogen. In order to initiate a better understanding of host-specific defence we have generated EST data using 454 pyrosequencing and profiled nine defence-related genes from Pc-infected avocado roots. Results 2.0 Mb of data was generated consisting of ~10,000 reads on a single lane of the GS FLX platform. Using the Newbler assembler 371 contigs were assembled, of which 367 are novel for Persea americana. Genes were classified according to Gene Ontology terms. In addition to identifying root-specific ESTs we were also able to identify and quantify the expression of nine defence-related genes that were differentially regulated in response to P. cinnamomi. Genes such as metallothionein, thaumatin and the pathogenesis related PsemI, mlo and profilin were found to be differentially regulated. Conclusions This is the first study in elucidating the avocado root transcriptome as well as identifying defence responses of avocado roots to the root pathogen P. cinnamomi. Our data is currently the only EST data that has been generated for avocado rootstocks, and the ESTs identified in this study have already been useful in identifying defence-related genes as well as providing gene information for other studies looking at processes such as ROS regulation as well as hypoxia in avocado roots. Our EST data will aid in the elucidation of the avocado transcriptome and identification of markers for improved

  9. DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES

    Directory of Open Access Journals (Sweden)

    Nur Kholilatul Izzah

    2017-01-01

    Full Text Available Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.

  10. READING LITERATURE, TAKING PHILOSOPHICAL IDEAS, AND OBTAINING CHARACTERS

    Directory of Open Access Journals (Sweden)

    Siti Maisaroh

    2017-05-01

    Full Text Available This study aims to describe the philosophical ideas and characters containing in trilogy of 'RaraMendut's' novel by YB Mangunwijaya. The method used is the knowledge archeology of Michel Foucault. The research proves that the philosophical ideas as follows: 1 wife's faithfulness contains characters of wife’s strong determination and true faithfulness sense; 2 The women seizing fate's  contains the character of high struggle spirit;3 women as a glory’s symbol contains character of self-actualization ability; 4 women and a country's defense contains a character of clever to take on the role / responsive; 5 women and their benefits contains the character as a source of love and life spirit; 6 women as good mothers contains the character of conciliatory, reassuring, joyful, sincere, and full of love; 7 the anxiety to old age contains the character of religious and strong self-awareness; 8 the glory contains the character of the glory of battle with themselves; 9 the child's nature contains the character of belief in the skill/ creativity of children and believe to God the Evolver; And 10 the essence of wisdom and usefulness of life contain  the characters of uniting the scattered things, receiving and embracing sincerely things bad/ broken/ waste, understanding and forgiving, voice sincerity and excitement, not easy to complain.

  11. A Classification Scheme for Literary Characters

    Directory of Open Access Journals (Sweden)

    Matthew Berry

    2017-10-01

    Full Text Available There is no established classification scheme for literary characters in narrative theory short of generic categories like protagonist vs. antagonist or round vs. flat. This is so despite the ubiquity of stock characters that recur across media, cultures, and historical time periods. We present here a proposal of a systematic psychological scheme for classifying characters from the literary and dramatic fields based on a modification of the Thomas-Kilmann (TK Conflict Mode Instrument used in applied studies of personality. The TK scheme classifies personality along the two orthogonal dimensions of assertiveness and cooperativeness. To examine the validity of a modified version of this scheme, we had 142 participants provide personality ratings for 40 characters using two of the Big Five personality traits as well as assertiveness and cooperativeness from the TK scheme. The results showed that assertiveness and cooperativeness were orthogonal dimensions, thereby supporting the validity of using a modified version of TK’s two-dimensional scheme for classifying characters.

  12. Character, attitude and disposition

    OpenAIRE

    Webber, Jonathan

    2015-01-01

    Recent debate over the empirical psychological presuppositions of virtue ethics has focused on reactive behavioural dispositions. But there are many character traits that cannot be understood properly in this way. Such traits are well described by attitude psychology. Moreover, the findings of attitude psychology support virtue ethics in three ways. First, they confirm the role of habituation in the development of character. Further, they show virtue ethics to be compatible with the situation...

  13. Development of a novel set of EST-SSR markers and cross-species amplification in Tamarix africana (Tamaricaceae).

    Science.gov (United States)

    Terzoli, Serena; Beritognolo, Isacco; Sabatti, Maurizio; Kuzminsky, Elena

    2010-06-01

    Tamarix plants are resistant to abiotic stresses and have become invasive in North America. Their taxonomy is troublesome, and few molecular makers are available to enable species identification or to track the spread of specific invasive genotypes. Transcriptome sequencing projects offer a potential source for the development of new markers. • Thirteen polymorphic simple sequence repeats (SSRs) markers derived from Expressed Sequence Tags (ESTs) from Tamarix hispida, T. androssowii, T. ramosissima, and T. albiflonum were identified and screened on 24 samples of T. africana to detect polymorphism. The number of alleles per locus ranged from two to eight, with an average of 4.3 alleles per locus, and the mean expected heterozygosity was 0.453. • Amplification products of these 13 loci were also generated for T. gallica. These new EST-SSR markers will be useful in genetic characterization of Tamarix, as additional tools for taxonomic clarification, and for studying invasive populations where they are a threat.

  14. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  15. Genome-wide analysis of immune system genes by EST profiling

    Science.gov (United States)

    Giallourakis, Cosmas; Benita, Yair; Molinie, Benoit; Cao, Zhifang; Despo, Orion; Pratt, Henry E.; Zukerberg, Lawrence R.; Daly, Mark J.; Rioux, John D.; Xavier, Ramnik J.

    2013-01-01

    Profiling studies of mRNA and miRNA, particularly microarray-based studies, have been extensively used to create compendia of genes that are preferentially expressed in the immune system. In some instances, functional studies have been subsequently pursued. Recent efforts such as ENCODE have demonstrated the benefit of coupling RNA-Seq analysis with information from expressed sequence tags (ESTs) for transcriptomic analysis. However, the full characterization and identification of transcripts that function as modulators of human immune responses remains incomplete. In this study, we demonstrate that an integrated analysis of human ESTs provides a robust platform to identify the immune transcriptome. Beyond recovering a reference set of immune-enriched genes and providing large-scale cross-validation of previous microarray studies, we discovered hundreds of novel genes preferentially expressed in the immune system, including non-coding RNAs. As a result, we have established the Immunogene database, representing an integrated EST “road map” of gene expression in human immune cells, which can be used to further investigate the function of coding and non-coding genes in the immune system. Using this approach, we have uncovered a unique metabolic gene signature of human macrophages and identified PRDM15 as a novel overexpressed gene in human lymphomas. Thus we demonstrate the utility of EST profiling as a basis for further deconstruction of physiologic and pathologic immune processes. PMID:23616578

  16. Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae).

    Science.gov (United States)

    Yang, Chien-Hui; Bracken-Grissom, Heather; Kim, Dohyup; Crandall, Keith A; Chan, Tin-Yam

    2012-01-01

    The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Madness in Shakespeare's Characters

    Directory of Open Access Journals (Sweden)

    Nuno Borja-Santos

    2014-10-01

    Full Text Available This paper begins with an introduction where the aims are explained: a psychopathological analysis of a Shakespearean character - Othello – followed by the discussion of the English dramatist’s importance in helping us understand madness in the emergent world of Renaissance. The main characteristics of Othello’s personality, which allowed the development of his jealousy delusion, are described. Finally, the conclusions underline the overlap of the symptoms developed by the character with the DSM-IV classification.

  18. Optical character recognition based on nonredundant correlation measurements.

    Science.gov (United States)

    Braunecker, B; Hauck, R; Lohmann, A W

    1979-08-15

    The essence of character recognition is a comparison between the unknown character and a set of reference patterns. Usually, these reference patterns are all possible characters themselves, the whole alphabet in the case of letter characters. Obviously, N analog measurements are highly redundant, since only K = log(2)N binary decisions are enough to identify one out of N characters. Therefore, we devised K reference patterns accordingly. These patterns, called principal components, are found by digital image processing, but used in an optical analog computer. We will explain the concept of principal components, and we will describe experiments with several optical character recognition systems, based on this concept.

  19. Leadership, character and its development: A qualitative exploration

    Directory of Open Access Journals (Sweden)

    Roslyn de Braine

    2007-11-01

    Full Text Available The purpose of this study was to explore (1 what organisational leaders consider to be character elements of leaders within the workplace, (2 what influences leaders’ character development, and (3 how an organisation can continue the process of character development. The literature review and findings revealed that leadership, integrity, industriousness, empathy, loyalty, optimism, fairness and compassion are the most sought after character elements within leaders in the workplace. Leadership and integrity were found to be the most supported character elements. The findings also indicate that work environmental factors, a person’s own efforts, and the daily experiences of work life contribute towards character development.

  20. Generation of EST and Microarray Resources for Functional Genomic Studies on Chicken Intestinal Health

    NARCIS (Netherlands)

    Hemert, van S.; Ebbelaar, B.H.; Smits, M.A.; Rebel, J.M.J.

    2003-01-01

    Expressed sequenced tags (ESTs) and microarray resources have a great impact on the ability to study host response in mice and humans. Unfortunately, these resources are not yet available for domestic farm animals. The aim of this study was to provide genomic resources to study chicken intestinal

  1. Differential Expression ESTs Associated with Fluorosis in Rats Liver

    Directory of Open Access Journals (Sweden)

    Y. Q. He

    2012-01-01

    Full Text Available The fluoride has volcanic activity and abundantly exists in environment combining with other elements as fluoride compounds. Recent researches indicated that the molecular mechanisms of intracellular fluoride toxicity were very complex. However, the molecular mechanisms underlying the effects on gene expression of chronic fluoride-induced damage is unknown, especially the detailed regulatory process of mitochondria. In the present study, we screened the differential expression ESTs associated with fluorosis by DDRT-PCR in rat liver. We gained 8 genes, 3 new ESTs, and 1 unknown function sequence and firstly demonstrated that microsomal glutathione S-transferase 1 (MGST1, ATP synthase H+ transporting mitochondrial F0 complex subunit C1, selenoprotein S, mitochondrial IF1 protein, and mitochondrial succinyl-CoA synthetase alpha subunit were participated in mitochondria metabolism, functional and structural damage process caused by chronic fluorosis. This information will be very helpful for understanding the molecular mechanisms of fluorosis.

  2. Sequence Stratigraphic Appraisal: Coastal Swamp Depobelt In The ...

    African Journals Online (AJOL)

    Mid-Lower Miocene Agbada sedimentary intercalations of “AB” Field in the coastal swamp depobelt, Western Niger-Delta, were evaluated to determine their sequence stratigraphic character. The analysis was based on a combination of data sets including logs of six wells to describe lithic variations of the Agbada Formation ...

  3. 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.

  4. Understanding the Properties of Interactive Televised Characters

    Science.gov (United States)

    Claxton, Laura J.; Ponto, Katelyn C.

    2013-01-01

    Children's television programming frequently uses interactive characters that appear to directly engage the viewers. These characters encourage children to answer questions and perform actions to help the characters solve problems in the televised world. Children readily engage in these interactions; however, it is unclear why they do so. To…

  5. AcEST: DK945751 [AcEST

    Lifescience Database Archive (English)

    Full Text Available p. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value... - Report - TrEMBL (release 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  6. AcEST: BP916868 [AcEST

    Lifescience Database Archive (English)

    Full Text Available . Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrEMBL (rele...ase 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  7. AcEST: DK947351 [AcEST

    Lifescience Database Archive (English)

    Full Text Available op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value... - Report - TrEMBL (release 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  8. Genetic divergence through joint analysis of morphoagronomic and molecular characters in accessions of Jatropha curcas.

    Science.gov (United States)

    Pestana-Caldas, C N; Silva, S A; Machado, E L; de Souza, D R; Cerqueira-Pereira, E C; Silva, M S

    2016-10-05

    The aim of this study was to investigate the genetic divergence between accessions of Jatropha curcas through joint analysis of morphoagronomic and molecular characters. To this end, we investigated 11 morphoagronomic characters and performed molecular genotyping, using 23 inter-simple sequence repeat (ISSR) primers in 46 accessions of J. curcas. We calculated the contribution of each character on divergence using analysis of variance. The grouping among accessions was performed using the Ward-MLM (modified location model) method, using morphoagronomic and molecular data, whereas the cophenetic correlation was obtained based on Gower's algorithm. There were significant differences in all growth-related characteristics: number of primary and secondary branches per plant, plant height, and stem diameter. For characters related to grain production, differences were found for number of fruit clusters per plant and number of inflorescence clusters per plant and average number of seeds per fruit. The greatest phenotypic variation was found in plant height (59.67- 222.33 cm), whereas the smallest variation was found in average number of seeds per fruit (0-2.90), followed by the number of fruit clusters per plant (0-8.67). In total, 94 polymorphic ISSR fragments were obtained. The genotypic grouping identified six groups, indicating that there is genetic divergence among the accessions. The most promising crossings for future hybridization were identified among accessions UFRB60 and UFVJC45, and UFRB61 and UFVJC18. In conclusion, the joint analysis of morphoagronomic characters and ISSR markers is an efficient method to assess the genetic divergence in J. curcas.

  9. Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

    Directory of Open Access Journals (Sweden)

    Kenyon Fiona

    2011-07-01

    Full Text Available Abstract Background Sheep scab is caused by Psoroptes ovis and is arguably the most important ectoparasitic disease affecting sheep in the UK. The disease is highly contagious and causes and considerable pruritis and irritation and is therefore a major welfare concern. Current methods of treatment are unsustainable and in order to elucidate novel methods of disease control a more comprehensive understanding of the parasite is required. To date, no full genomic DNA sequence or large scale transcript datasets are available and prior to this study only 484 P. ovis expressed sequence tags (ESTs were accessible in public databases. Results In order to further expand upon the transcriptomic coverage of P. ovis thus facilitating novel insights into the mite biology we undertook a larger scale EST approach, incorporating newly generated and previously described P. ovis transcript data and representing the largest collection of P. ovis ESTs to date. We sequenced 1,574 ESTs and assembled these along with 484 previously generated P. ovis ESTs, which resulted in the identification of 1,545 unique P. ovis sequences. BLASTX searches identified 961 ESTs with significant hits (E-value P. ovis ESTs. Gene Ontology (GO analysis allowed the functional annotation of 880 ESTs and included predictions of signal peptide and transmembrane domains; allowing the identification of potential P. ovis excreted/secreted factors, and mapping of metabolic pathways. Conclusions This dataset currently represents the largest collection of P. ovis ESTs, all of which are publicly available in the GenBank EST database (dbEST (accession numbers FR748230 - FR749648. Functional analysis of this dataset identified important homologues, including house dust mite allergens and tick salivary factors. These findings offer new insights into the underlying biology of P. ovis, facilitating further investigations into mite biology and the identification of novel methods of intervention.

  10. AcEST: BP920443 [AcEST

    Lifescience Database Archive (English)

    Full Text Available op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrEMBL (r...elease 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  11. AcEST: DK947324 [AcEST

    Lifescience Database Archive (English)

    Full Text Available ast op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value... - Report - TrEMBL (release 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  12. AcEST: BP912655 [AcEST

    Lifescience Database Archive (English)

    Full Text Available t op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrEMBL (...release 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  13. AcEST: BP919873 [AcEST

    Lifescience Database Archive (English)

    Full Text Available ast op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrEMBL... (release 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  14. AcEST: BP915916 [AcEST

    Lifescience Database Archive (English)

    Full Text Available p. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrEMBL (rel...ease 39.9) Link to BlastX Result : TrEMBL (No blast op. Sequence too short.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

  15. An EST dataset for Metasequoia glyptostroboides buds: the first EST resource for molecular genomics studies in Metasequoia.

    Science.gov (United States)

    Zhao, Ying; Thammannagowda, Shivegowda; Staton, Margaret; Tang, Sha; Xia, Xinli; Yin, Weilun; Liang, Haiying

    2013-03-01

    The "living fossil" Metasequoia glyptostroboides Hu et Cheng, commonly known as dawn redwood or Chinese redwood, is the only living species in the genus and is valued for its essential oil and crude extracts that have great potential for anti-fungal activity. Despite its paleontological significance and economical value as a rare relict species, genomic resources of Metasequoia are very limited. In order to gain insight into the molecular mechanisms behind the formation of reproductive buds and the transition from vegetative phase to reproductive phase in Metasequoia, we performed sequencing of expressed sequence tags from Metasequoia vegetative buds and female buds. By using the 454 pyrosequencing technology, a total of 1,571,764 high-quality reads were generated, among which 733,128 were from vegetative buds and 775,636 were from female buds. These EST reads were clustered and assembled into 114,124 putative unique transcripts (PUTs) with an average length of 536 bp. The 97,565 PUTs that were at least 100 bp in length were functionally annotated by a similarity search against public databases and assigned with Gene Ontology (GO) terms. A total of 59 known floral gene families and 190 isotigs involved in hormone regulation were captured in the dataset. Furthermore, a set of PUTs differentially expressed in vegetative and reproductive buds, as well as SSR motifs and high confidence SNPs, were identified. This is the first large-scale expressed sequence tags ever generated in Metasequoia and the first evidence for floral genes in this critically endangered deciduous conifer species.

  16. Factorized combinations of Virasoro characters

    International Nuclear Information System (INIS)

    Bytsko, A.G.; Fring, A.

    2000-01-01

    We investigate linear combinations of characters for minimal Virasoro models which are representable as a product of several basic blocks. Our analysis is based on consideration of asymptotic behaviour of the characters in the quasi-classical limit. In particular, we introduce a notion of the secondary effective central charge. We find all possible cases for which factorization occurs on the base of the Gauss-Jacobi or the Watson identities. Exploiting these results, we establish various types of identities between different characters. In particular, we present several identities generalizing the Rogers-Ramanujan identities. Applications to quasi-particle representations, modular invariant partition functions, super-conformal theories and conformal models with boundaries are briefly discussed. (orig.)

  17. Character Recognition Using Genetically Trained Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Diniz, C.; Stantz, K.M.; Trahan, M.W.; Wagner, J.S.

    1998-10-01

    Computationally intelligent recognition of characters and symbols addresses a wide range of applications including foreign language translation and chemical formula identification. The combination of intelligent learning and optimization algorithms with layered neural structures offers powerful techniques for character recognition. These techniques were originally developed by Sandia National Laboratories for pattern and spectral analysis; however, their ability to optimize vast amounts of data make them ideal for character recognition. An adaptation of the Neural Network Designer soflsvare allows the user to create a neural network (NN_) trained by a genetic algorithm (GA) that correctly identifies multiple distinct characters. The initial successfid recognition of standard capital letters can be expanded to include chemical and mathematical symbols and alphabets of foreign languages, especially Arabic and Chinese. The FIN model constructed for this project uses a three layer feed-forward architecture. To facilitate the input of characters and symbols, a graphic user interface (GUI) has been developed to convert the traditional representation of each character or symbol to a bitmap. The 8 x 8 bitmap representations used for these tests are mapped onto the input nodes of the feed-forward neural network (FFNN) in a one-to-one correspondence. The input nodes feed forward into a hidden layer, and the hidden layer feeds into five output nodes correlated to possible character outcomes. During the training period the GA optimizes the weights of the NN until it can successfully recognize distinct characters. Systematic deviations from the base design test the network's range of applicability. Increasing capacity, the number of letters to be recognized, requires a nonlinear increase in the number of hidden layer neurodes. Optimal character recognition performance necessitates a minimum threshold for the number of cases when genetically training the net. And, the

  18. Exploiting a wheat EST database to assess genetic diversity.

    Science.gov (United States)

    Karakas, Ozge; Gurel, Filiz; Uncuoglu, Ahu Altinkut

    2010-10-01

    Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.

  19. Exploiting a wheat EST database to assess genetic diversity

    Directory of Open Access Journals (Sweden)

    Ozge Karakas

    2010-01-01

    Full Text Available Expressed sequence tag (EST markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum. In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29% contigs and 96 (10% singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs and metabolism and energy (singletons. EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725 being between Harmankaya99 and Sönmez2001, and the lowest (0.622 between Aytin98 and Izgi01.

  20. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

    Science.gov (United States)

    Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja

    2012-08-01

    Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.

  1. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  2. Good character at school: positive classroom behavior mediates the link between character strengths and school achievement.

    Science.gov (United States)

    Wagner, Lisa; Ruch, Willibald

    2015-01-01

    Character strengths have been found to be substantially related to children's and adolescents' well-being. Initial evidence suggests that they also matter for school success (e.g., Weber and Ruch, 2012). The present set of two studies aimed at replicating and extending these findings in two different age groups, primary school students (N = 179; mean age = 11.6 years) and secondary school students (N = 199; mean age = 14.4 years). The students completed the VIA-Youth (Values in Action Inventory of Strengths for Youth), a self-report measure of the 24 character strengths in the VIA classification. Their teachers rated the students' positive behavior in the classroom. Additionally, school achievement was assessed: For the primary school students (Study 1), teachers rated the students' overall school achievement and for the secondary school students (Study 2), we used their grades as a measure of school achievement. We found that several character strengths were associated with both positive classroom behavior and school achievement. Across both samples, school achievement was correlated with love of learning, perseverance, zest, gratitude, hope, and perspective. The strongest correlations with positive classroom behavior were found for perseverance, self-regulation, prudence, social intelligence, and hope. For both samples, there were indirect effects of some of the character strengths on school achievement through teacher-rated positive classroom behavior. The converging findings from the two samples support the notion that character strengths contribute to positive classroom behavior, which in turn enhances school achievement. Results are discussed in terms of their implications for future research and for school interventions based on character strengths.

  3. Good character at school: Positive classroom behavior mediates the link between character strengths and school achievement

    Directory of Open Access Journals (Sweden)

    Lisa eWagner

    2015-05-01

    Full Text Available Character strengths have been found to be substantially related to children’s and adolescents’ well-being. Initial evidence suggests that they also matter for school success (e.g., Weber and Ruch, 2012. The present set of two studies aimed at replicating and extending these findings in two different age groups, primary school students (N = 179; mean age = 11.6 years and secondary school students (N = 199; mean age = 14.4 years. The students completed the VIA-Youth, a self-report measure of the 24 character strengths in the VIA classification. Their teachers rated the students’ positive behavior in the classroom. Additionally, school achievement was assessed: For the primary school students (Study 1, teachers rated the students’ overall school achievement and for the secondary school students (Study 2, we used their grades as a measure of school achievement. We found that several character strengths were associated with both positive classroom behavior and school achievement. Across both samples school achievement was correlated with love of learning, perseverance, zest, gratitude, hope, and perspective. The strongest correlations with positive classroom behavior were found for perseverance, self-regulation, prudence, social intelligence, and hope. For both samples, there were indirect effects of most of the character strengths on school achievement through teacher-rated positive classroom behavior. The converging findings from the two samples support the notion that character strengths contribute to positive classroom behavior, which in turn enhances school achievement. Results are discussed in terms of their implications for future research and for school interventions based on character strengths.

  4. Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam).

    Science.gov (United States)

    Kim, Jin-Hee; Chung, Il Kyung; Kim, Kyung-Min

    2017-01-01

    The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.

  5. On the information content of discrete phylogenetic characters.

    Science.gov (United States)

    Bordewich, Magnus; Deutschmann, Ina Maria; Fischer, Mareike; Kasbohm, Elisa; Semple, Charles; Steel, Mike

    2017-12-16

    Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be grouped together. However, it has long been known that some characters contain more information than others. For instance, a character that assigns the same state to each species groups all of them together and so provides no insight into the relationships of the species considered. At the other extreme, a character that assigns a different state to each species also conveys no phylogenetic signal. In this manuscript, we study a natural combinatorial measure of the information content of an individual character and analyse properties of characters that provide the maximum phylogenetic information, particularly, the number of states such a character uses and how the different states have to be distributed among the species or taxa of the phylogenetic tree.

  6. Analysis of xylem formation in pine by cDNA sequencing

    Science.gov (United States)

    Allona, I.; Quinn, M.; Shoop, E.; Swope, K.; St Cyr, S.; Carlis, J.; Riedl, J.; Retzel, E.; Campbell, M. M.; Sederoff, R.; hide

    1998-01-01

    Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (Pinus taeda L.). A total of 1,097 single-pass sequences were obtained from 5' ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.

  7. Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

    Science.gov (United States)

    Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Peng, Hui; Li, Pirui; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

    2013-01-01

    Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera. PMID:23626799

  8. Which "Character" Should Sport Develop?

    Science.gov (United States)

    Rudd, Andy

    2005-01-01

    For years, strong claims have been made that sport builds character. Despite such claims, a "winning at all cost" mentality can frequently be seen within all of sport. The reason for this paradox may relate to confusion around what it means to demonstrate character. The purpose of this article is to show that there are indeed two distinct types of…

  9. EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum

    Directory of Open Access Journals (Sweden)

    Vandenberg Albert

    2011-06-01

    Full Text Available Abstract Background Colletotrichum truncatum is a haploid, hemibiotrophic, ascomycete fungal pathogen that causes anthracnose disease on many economically important leguminous crops. This pathogen exploits sequential biotrophic- and necrotrophic- infection strategies to colonize the host. Transition from biotrophy to a destructive necrotrophic phase called the biotrophy-necrotrophy switch is critical in symptom development. C. truncatum likely secretes an arsenal of proteins that are implicated in maintaining a compatible interaction with its host. Some of them might be transition specific. Results A directional cDNA library was constructed from mRNA isolated from infected Lens culinaris leaflet tissues displaying the biotrophy-necrotrophy switch of C. truncatum and 5000 expressed sequence tags (ESTs with an average read of > 600 bp from the 5-prime end were generated. Nearly 39% of the ESTs were predicted to encode proteins of fungal origin and among these, 162 ESTs were predicted to contain N-terminal signal peptides (SPs in their deduced open reading frames (ORFs. The 162 sequences could be assembled into 122 tentative unigenes comprising 32 contigs and 90 singletons. Sequence analyses of unigenes revealed four potential groups: hydrolases, cell envelope associated proteins (CEAPs, candidate effectors and other proteins. Eleven candidate effector genes were identified based on features common to characterized fungal effectors, i.e. they encode small, soluble (lack of transmembrane domain, cysteine-rich proteins with a putative SP. For a selected subset of CEAPs and candidate effectors, semiquantitative RT-PCR showed that these transcripts were either expressed constitutively in both in vitro and in planta or induced during plant infection. Using potato virus X (PVX based transient expression assays, we showed that one of the candidate effectors, i. e. contig 8 that encodes a cerato-platanin (CP domain containing protein, unlike CP proteins

  10. THE CHARACTER ANALYSIS OF GLEN HANSARD IN ONCE FILM

    Directory of Open Access Journals (Sweden)

    Nani Rosnani Thamrin

    2013-12-01

    Full Text Available This paper analyzed the characterization of talented actor named Glen Hansard in Once film. This study employed a descriptive qualitative research design based on theories of Rahardjo (1985, Robert (1965, and Card (1988. Primary data sources were whole Once scenes film directed by John Carney which had low-budgeting production with two stars, Glen Hansard and Irglova, while secondary data sources were collected from the articles related to this study. This research mainly investigated two aspects involved two character analyses of the main actor, Hansard. The first one was the construction of Hansard’s characters and the second one was the effect between his character and another actors’ character. The study showed that Hansard’s characters were constructed by five factors: from what the character did and said, what the other characters said about him, how the appearance and its milieu were, influencing one and another.The study also found that he had struggle, visionary, ambitious, introvert, sensitive, straightforward and curious characters, but more characters that showed strong characters of his were struggle, visionary and ambitious, because the scenes reflected them more.

  11. Technology development for gene discovery and full-length sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Marcelo Bento Soares

    2004-07-19

    In previous years, with support from the U.S. Department of Energy, we developed methods for construction of normalized and subtracted cDNA libraries, and constructed hundreds of high-quality libraries for production of Expressed Sequence Tags (ESTs). Our clones were made widely available to the scientific community through the IMAGE Consortium, and millions of ESTs were produced from our libraries either by collaborators or by our own sequencing laboratory at the University of Iowa. During this grant period, we focused on (1) the development of a method for preferential cloning of tissue-specific and/or rare transcripts, (2) its utilization to expedite EST-based gene discovery for the NIH Mouse Brain Molecular Anatomy Project, (3) further development and optimization of a method for construction of full-length-enriched cDNA libraries, and (4) modification of a plasmid vector to maximize efficiency of full-length cDNA sequencing by the transposon-mediated approach. It is noteworthy that the technology developed for preferential cloning of rare mRNAs enabled identification of over 2,000 mouse transcripts differentially expressed in the hippocampus. In addition, the method that we optimized for construction of full-length-enriched cDNA libraries was successfully utilized for the production of approximately fifty libraries from the developing mouse nervous system, from which over 2,500 full-ORF-containing cDNAs have been identified and accurately sequenced in their entirety either by our group or by the NIH-Mammalian Gene Collection Program Sequencing Team.

  12. Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp..

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    Full Text Available Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively. The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.

  13. AcEST: DK948090 [AcEST

    Lifescience Database Archive (English)

    Full Text Available erase A OS=Aspergillus tubingen... 50 1e-05 sp|P0C1S9|DGLB_RAT Sn1-specific diacy...|P47145|YJ77_YEAST Putative lipase YJR107W OS=Saccharomyces ce... 50 8e-06 sp|O42815|FAEA_ASPTU Feruloyl est

  14. The character of free topological groups II

    Directory of Open Access Journals (Sweden)

    Peter Nickolas

    2005-04-01

    Full Text Available A systematic analysis is made of the character of the free and free abelian topological groups on metrizable spaces and compact spaces, and on certain other closely related spaces. In the first case, it is shown that the characters of the free and the free abelian topological groups on X are both equal to the “small cardinal” d if X is compact and metrizable, but also, more generally, if X is a non-discrete k!-space all of whose compact subsets are metrizable, or if X is a non-discrete Polish space. An example is given of a zero-dimensional separable metric space for which both characters are equal to the cardinal of the continuum. In the case of a compact space X, an explicit formula is derived for the character of the free topological group on X involving no cardinal invariant of X other than its weight; in particular the character is fully determined by the weight in the compact case. This paper is a sequel to a paper by the same authors in which the characters of the free groups were analysed under less restrictive topological assumptions.

  15. Analysis of long-range correlation in sequences data of proteins

    OpenAIRE

    ADRIANA ISVORAN; LAURA UNIPAN; DANA CRACIUN; VASILE MORARIU

    2007-01-01

    The results presented here suggest the existence of correlations in the sequence data of proteins. 32 proteins, both globular and fibrous, both monomeric and polymeric, were analyzed. The primary structures of these proteins were treated as time series. Three spatial series of data for each sequence of a protein were generated from numerical correspondences between each amino acid and a physical property associated with it, i.e., its electric charge, its polar character and its dipole moment....

  16. DIALOGUE AND CHARACTER CLASSIFICATION IN WOLE ...

    African Journals Online (AJOL)

    position, level of education, character and habits of a character are reflected in the speech .... Dictators are averse to any form of ... breaks out shouting slogans of praises of himself. ..... Task easier if I can get all the Obas settled before our.

  17. Aristotelian versus Virtue Ethical Character Education

    Science.gov (United States)

    Curren, Randall

    2016-01-01

    This article examines some central aspects of Kristján Kristjánsson's book, "Aristotelian Character Education," beginning with the claim that contemporary virtue ethics provides methodological, ontological, epistemological, and moral foundations for Aristotelian character education. It considers three different formulations of what…

  18. A Review of Virtual Character's Emotion Model

    Science.gov (United States)

    Liu, Zhen

    2008-11-01

    Emotional virtual characters are essential to digital entertainment, an emotion is related to virtual environment and a virtual character's inner variables, emotion model of virtual character is a hot topic in many fields, domain knowledge is very important for modeling emotion, and the current research of emotion expression in the world was also summarized, and some new research directions of emotion model are presented.

  19. Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

    Directory of Open Access Journals (Sweden)

    Koh Eunhee

    2007-07-01

    Full Text Available Abstract Background EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information. Results Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1. Conclusion Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.

  20. Distribution of some sequences of points on elliptic curves

    DEFF Research Database (Denmark)

    Lange, Tanja; Shparlinski, Igor

    2007-01-01

    We estimate character sums over points on elliptic curves over a finite field of q elements. Pseudorandom sequences can be constructed by taking linear combinations with small coefficients (for example, from the set {−1, 0, 1}) of a fixed vector of points, which forms the seed of the generator. We...... consider several particular cases of this general approach which are of special practical interest and have occurred in the literature. For each of them we show that the resulting sequence has good uniformity of distribution properties....

  1. The influence of media characters on children's food choices.

    Science.gov (United States)

    Kotler, Jennifer A; Schiffman, Jennifer M; Hanson, Katherine G

    2012-01-01

    Two experiments were conducted to assess the role of media characters in influencing children's food choices; the first focused on children's self-reported preference, whereas the second focused on actual choice. The results of the experiments suggest that popular characters can make a difference in encouraging children to select one food over another. In the first experiment, children were more likely to indicate a preference for one food over another when one was associated with characters that they liked and with whom they were familiar. This effect was particularly strong when a sugary or salty snack branded by a favored character was competing with a healthier option branded by an unknown character or no character. Alternatively, when children were asked to choose between a healthy food and a sugary or salty snack, branding of the healthy food with a favored character did not significantly change appeal of that healthy snack. However, when foods within the same category (i.e., 2 vegetables, 2 fruits, or 2 grains) were asked to compete against each other, character branding strongly influenced children's food choice. Findings from the second experiment suggest that children are more willing to try more pieces of a healthy food if a favored character, in comparison with an unknown character, is promoting that food.

  2. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  3. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

    Directory of Open Access Journals (Sweden)

    Hahn Daniel A

    2009-05-01

    Full Text Available Abstract Background Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly Sarcophaga crassipalpis. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription. Results We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (ES. crassipalpis unigenes among GO Biological Process functional groups with that of the Drosophila melanogaster transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among S. crassipalpis, D. melanogaster, and Anopheles gambiae. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs. Conclusion Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic

  4. The Proximate Unit in Chinese Handwritten Character Production

    Directory of Open Access Journals (Sweden)

    Jenn-Yeu eChen

    2013-08-01

    Full Text Available In spoken word production, a proximate unit is the first phonological unit at the sublexical level that is selectable for production (O’Seaghdha, Chen, & Chen, 2010. The present study investigated whether the proximate unit in Chinese handwritten word production is the stroke, the radical, or something in between. A written version of the form preparation task was adopted. Chinese participants learned sets of two-character words, later were cued with the first character of each word, and had to write down the second character (the target. Response times were measured from the onset of a cue character to the onset of a written response. In Experiment 1, the target characters within a block shared (homogeneous or did not share (heterogeneous the first stroke. In Experiment 2, the first two strokes were shared in the homogeneous blocks. Response times in the homogeneous blocks and in the heterogeneous blocks were comparable in both experiments (Exp. 1: 687 ms vs. 684 ms, Exp. 2: 717 vs. 716. In Experiment 3 and 4, the target characters within a block shared or did not share the first radical. Response times in the homogeneous blocks were significantly faster than those in the heterogeneous blocks (Exp. 3: 685 vs. 704, Exp. 4: 594 vs. 650. In Experiment 5 and 6, the shared component was a Gestalt-like form that is more than a stroke, constitutes a portion of the target character, can be a stand-alone character itself, can be a radical of another character but is not a radical of the target character (e.g., 士in聲, 鼓, 穀, 款; called a logographeme. Response times in the homogeneous blocks were significantly faster than those in the heterogeneous blocks (Exp. 5: 576 vs. 625, Exp. 6: 586 vs. 620. These results suggest a model of Chinese handwritten character production in which the stroke is not a functional unit, the radical plays the role of a morpheme, and the logographeme is the proximate unit.

  5. Dynamic Obstacle Clearing for Real-time Character Animation

    OpenAIRE

    Glardon, Pascal; Boulic, Ronan; Thalmann, Daniel

    2006-01-01

    This paper proposes a novel method to control virtual characters in dynamic environments. A virtual character is animated by a locomotion and jumping engine, enabling production of continuous parameterized motions. At any time during runtime, flat obstacles (e.g. a puddle of water) can be created and placed in front of a character. The method first decides whether the character is able to get around or jump over the obstacle. Then the motion parameters are accordingly modified. The transition...

  6. Character feature integration of Chinese calligraphy and font

    Science.gov (United States)

    Shi, Cao; Xiao, Jianguo; Jia, Wenhua; Xu, Canhui

    2013-01-01

    A framework is proposed in this paper to effectively generate a new hybrid character type by means of integrating local contour feature of Chinese calligraphy with structural feature of font in computer system. To explore traditional art manifestation of calligraphy, multi-directional spatial filter is applied for local contour feature extraction. Then the contour of character image is divided into sub-images. The sub-images in the identical position from various characters are estimated by Gaussian distribution. According to its probability distribution, the dilation operator and erosion operator are designed to adjust the boundary of font image. And then new Chinese character images are generated which possess both contour feature of artistical calligraphy and elaborate structural feature of font. Experimental results demonstrate the new characters are visually acceptable, and the proposed framework is an effective and efficient strategy to automatically generate the new hybrid character of calligraphy and font.

  7. Character education in perspective of chemistry pre-service teacher

    Science.gov (United States)

    Merdekawati, Krisna

    2017-12-01

    As one of the pre-service teacher education programs, Chemistry Education Department Islamic University of Indonesia (UII) is committed to providing quality education. It is an education that can produce competent and characteristic chemistry pre-service teacher. The focus of research is to describe the perception of students as a potential teacher of chemistry on character education and achievement of character education. The research instruments include questionnaires and observation sheets. Research data show that students have understood the importance of character education and committed to organizing character education later in schools. Students have understood the ways in which character education can be used. The students stated that Chemistry Education Department has tried to equip students with character education. The observation result shows that students generally have character as a pre-service teacher.

  8. High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production.

    Science.gov (United States)

    Augusto, Raphael; Maranho, Rone Charles; Mangolin, Claudete Aparecida; Pires da Silva Machado, Maria de Fátima

    2015-01-01

    High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations.

  9. Online Sequence Training of Recurrent Neural Networks with Connectionist Temporal Classification

    OpenAIRE

    Hwang, Kyuyeon; Sung, Wonyong

    2015-01-01

    Connectionist temporal classification (CTC) based supervised sequence training of recurrent neural networks (RNNs) has shown great success in many machine learning areas including end-to-end speech and handwritten character recognition. For the CTC training, however, it is required to unroll (or unfold) the RNN by the length of an input sequence. This unrolling requires a lot of memory and hinders a small footprint implementation of online learning or adaptation. Furthermore, the length of tr...

  10. Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

    Science.gov (United States)

    Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

    2013-01-01

    The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

  11. Handwritten Javanese Character Recognition Using Several Artificial Neural Network Methods

    Directory of Open Access Journals (Sweden)

    Gregorius Satia Budhi

    2015-07-01

    Full Text Available Javanese characters are traditional characters that are used to write the Javanese language. The Javanese language is a language used by many people on the island of Java, Indonesia. The use of Javanese characters is diminishing more and more because of the difficulty of studying the Javanese characters themselves. The Javanese character set consists of basic characters, numbers, complementary characters, and so on. In this research we have developed a system to recognize Javanese characters. Input for the system is a digital image containing several handwritten Javanese characters. Preprocessing and segmentation are performed on the input image to get each character. For each character, feature extraction is done using the ICZ-ZCZ method. The output from feature extraction will become input for an artificial neural network. We used several artificial neural networks, namely a bidirectional associative memory network, a counterpropagation network, an evolutionary network, a backpropagation network, and a backpropagation network combined with chi2. From the experimental results it can be seen that the combination of chi2 and backpropagation achieved better recognition accuracy than the other methods.

  12. Alterations in subspecific characters of groundnut

    International Nuclear Information System (INIS)

    Mouli, C.; Patil, S.H.; Kale, D.M.

    1983-01-01

    Recombination of beneficial characters associated in the cultivars of groundnut (Arachis hypogaea, L.) belonging to the two subspecies hypogaea and fastigiata had little success in conventional breeding programme. The cultures of ssp. hypogaea have the desirable characters for the crop improvement viz; various growth habits, profuse branching, large pod, seed dormancy and stress tolerance. Sequential flowering, early maturity, compact fruiting habit and high kernel outturn are the other useful characters present in ssp. fastigiata cultures. Mutation research in a popular variety, Spanish Improved belonging to ssp. fastigiata led to the selection of various mutants. One among the mutants had large pod, a characteristic of hypogaea ssp. Hybridization among the mutants and improved cultivars as well as radiation treatment of selected cultures resulted in the isolation of cultures having not only combinations and alterations of characters in both subspecies, but also modifications. These cultures are classified into major groups and their significance in the groundnut improvement is discussed. (author)

  13. 454 sequencing of pooled BAC clones on chromosome 3H of barley

    Directory of Open Access Journals (Sweden)

    Yamaji Nami

    2011-05-01

    Full Text Available Abstract Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp. Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

  14. Character & Cane

    Science.gov (United States)

    Sartorius, Tara Cady

    2009-01-01

    They say first impressions can be deceiving. The difficulty of getting to know someone increases when that person is mostly fictional. Whatever the author writes is all readers can know. Whatever they read about the character is all they have to go on. Now take it another step back, and imagine a portrait drawing, painting or print of that…

  15. 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...

  16. Data set incongruence and correlated character evolution: An example of functional convergence in the hind-limbs of stifftail diving ducks

    Science.gov (United States)

    McCracken, K.G.; Harshman, J.; Mcclellan, D.A.; Afton, A.D.

    1999-01-01

    The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable by using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. mnccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Likewise, null models of

  17. Noisy: Identification of problematic columns in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2008-06-01

    Full Text Available Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i phylogenetically informative and (ii effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1 the average bootstrap support obtained from the original alignment is low, and (2 there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

  18. Identification Of Minangkabau Landscape Characters

    Science.gov (United States)

    Asrina, M.; Gunawan, A.; Aris, Munandar

    2017-10-01

    Minangkabau is one of cultures in indonesia which occupies landscape intact. Landscape of Minangkabau have a very close relationship with the culture of the people. Uniqueness of Minangkabau culture and landscape forming an inseparable characterunity. The landscape is necessarily identified to know the inherent landscape characters. The objective of this study was to identify the character of the Minangkabau landscape characterizes its uniqueness. The study was conducted by using descriptive method comprised literature review and field observasion. Observed the landscape characters comprised two main features, they were major and minor features. Indetification of the features was conducted in two original areas (darek) of the Minangkabau traditional society. The research results showed that major features or natural features of the landscape were predominantly landform, landcover, and hidrology. All luhak (districts) of Minangkabau showed similar main features such as hill, canyon, lake, valley, and forest. The existence of natural features such as hills, canyon and valleys characterizes the nature of minangkabau landscape. Minor features formed by Minangkabau cultural society were agricultural land and settlement. Rumah gadang (big house) is one of famous minor features characterizes the Minangkabau culture. In addition, several historical artefacts of building and others structure may strengthen uniqueness of the Minangkabau landscape character, such as The royal palace, inscription, and tunnels.

  19. CHARACTER EDUCATION IN ISLAMIC BOARDING SCHOOL- BASED SMA AMANAH

    Directory of Open Access Journals (Sweden)

    Nana Herdiana Abdurrahman

    2016-06-01

    Full Text Available This paper aims to describe findings of the study in pesantren-based SMA Amanah covering: 1 the principal policy in developing character education, 2 the methods used in developing character education, 3 students’ characteristics as the result of the character education process, 4 the problems encountered in the implementation of character education and the efforts made in addressing the implementation of character education at the school. This study applied qualitative method using descriptive technique. The data were collected through observation, interviews, and documentation. The findings of study showed that: 1 the principal’s policy in developing character education was carried out by implementing government policies in line with the school’s vision, mission, and programs; 2 the methods used in the process of character education were through role-modelling, assignments and nurturing, habituation, training programs, and  students’ participation in various types of activities, as well as the application of rewards and punishments; 3 the student's characteristics resulted from the character  education process were piousness and devotion as well as being able to apply their knowledge and piety in everyday life; 4 problems encountered in the implementation of character education  were different values and norms students brought from home; imbalance of facilities compared to the number of students; as well as teachers’ readiness to actually implement the new program, which  was character education. Meanwhile the efforts made to overcome those problems were namely developing personal, family, neighborhood or community characters, and making commitment of all related parties/stakeholdres of SMA Amanah.

  20. AcEST: DK944068 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK944068 - Show DK944068 Clone id YMU02A01NGRL0004_O03 Library YMU02 Length 116 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_O03. 5' end sequence. Accession DK944068 Tissue t...YMU02A01NGRL0004_O03 116 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_O0

  1. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

    Science.gov (United States)

    Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

    2012-01-01

    Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

  2. Generation and analysis of expressed sequence tags (ESTs) of Camelina sativa to mine drought stress-responsive genes.

    Science.gov (United States)

    Kanth, Bashistha Kumar; Kumari, Shipra; Choi, Seo Hee; Ha, Hye-Jeong; Lee, Geung-Joo

    2015-11-06

    Camelina sativa is an oil-producing crop belonging to the family of Brassicaceae. Due to exceptionally high content of omega fatty acid, it is commercially grown around the world as edible oil, biofuel, and animal feed. A commonly referred 'false flax' or gold-of-pleasure Camelina sativa has been interested as one of biofuel feedstocks. The species can grow on marginal land due to its superior drought tolerance with low requirement of agricultural inputs. This crop has been unexploited due to very limited transcriptomic and genomic data. Use of gene-specific molecular markers is an important strategy for new cultivar development in breeding program. In this study, Illumina paired-end sequencing technology and bioinformatics tools were used to obtain expression profiling of genes responding to drought stress in Camelina sativa BN14. A total of more than 60,000 loci were assembled, corresponding to approximately 275 K transcripts. When the species was exposed to 10 kPa drought stress, 100 kPa drought stress, and rehydrated conditions, a total of 107, 2,989, and 982 genes, respectively, were up-regulated, while 146, 3,659, and 1189 genes, respectively, were down-regulated compared to control condition. Some unknown genes were found to be highly expressed under drought conditions, together with some already reported gene families such as senescence-associated genes, CAP160, and LEA under 100 kPa soil water condition, cysteine protease, 2OG, Fe(II)-dependent oxygenase, and RAD-like 1 under rehydrated condition. These genes will be further validated and mapped to determine their function and loci. This EST library will be favorably applied to develop gene-specific molecular markers and discover genes responsible for drought tolerance in Camelina species. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Features fusion based approach for handwritten Gujarati character recognition

    Directory of Open Access Journals (Sweden)

    Ankit Sharma

    2017-02-01

    Full Text Available Handwritten character recognition is a challenging area of research. Lots of research activities in the area of character recognition are already done for Indian languages such as Hindi, Bangla, Kannada, Tamil and Telugu. Literature review on handwritten character recognition indicates that in comparison with other Indian scripts research activities on Gujarati handwritten character recognition are very less.  This paper aims to bring Gujarati character recognition in attention. Recognition of isolated Gujarati handwritten characters is proposed using three different kinds of features and their fusion. Chain code based, zone based and projection profiles based features are utilized as individual features. One of the significant contribution of proposed work is towards the generation of large and representative dataset of 88,000 handwritten Gujarati characters. Experiments are carried out on this developed dataset. Artificial Neural Network (ANN, Support Vector Machine (SVM and Naive Bayes (NB classifier based methods are implemented for handwritten Gujarati character recognition. Experimental results show substantial enhancement over state-of-the-art and authenticate our proposals.

  4. Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Nielsen, Henrik

    1997-01-01

    Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role.This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known...

  5. Character and Characterization in “Palms and Men” novel

    Directory of Open Access Journals (Sweden)

    Fariedeh Khajehpour

    2013-11-01

    Full Text Available Abstract Nowadays one of the most significant elements in story writing is character and characterization. Character in a narrative or a play, is a person that his mental and moral qualities reflect in his deeds and what he says and does. Creating such characters in a story or a novel that seem to be like real people to the reader is called characterization (Mir Sadeghi, 1382: p 85. In this article character and characterization in one of the novels about the eight year war between Iran and Iraq, calling “Palms and Men”, is investigated. Character types, methods of characterization, character appearance, prototype, the relation of character with other elements, and characterization defects are some of the subjects studied in this article.  Character types: these characters are generally categorized in two groups of stereotype and type. Samir, Touraj, Reza, Hamid etc. all belong to Sepah forces category which are type characters. Some women characters such as Zeinab, Samir’s mother, Kolsoum, Hanieh’s mother etc. are stereotype characters.   Methods of characterization in “Palms and Men” novel:   The description of characters is done in two methods by Mr. Nematollah Soleimani:   a Direct characterization: If not all the characters, most of them are certainly characterized in this way. For example in expressing Hamid’s characteristic who is the commander of the mission, he writes, “Hamid didn’t bat an eyelid in any incidents. Hamid was lion-hearted”. (Soleimani, 1380: 128. In describing uncle Heidar, he writes, “wisdom and insight, and the effects of years of suffering, difficulty, and experiencing could be clearly seen in his limpid eyes. The rural man was indeed a wise and experienced man” (the same: 264_265.   b Indirect Characterization: Although in novels and long stories, direct characterization method is often used, in “Palms and Men” this kind of characterization is also appeared in different conversations

  6. Character and Characterization in “Palms and Men” novel

    Directory of Open Access Journals (Sweden)

    F. Khajeh pour

    Full Text Available Nowadays one of the most significant elements in story writing is character and characterization. Character in a narrative or a play, is a person that his mental and moral qualities reflect in his deeds and what he says and does. Creating such characters in a story or a novel that seem to be like real people to the reader is called characterization (Mir Sadeghi, 1382: p 85. In this article character and characterization in one of the novels about the eight year war between Iran and Iraq, calling “Palms and Men”, is investigated. Character types, methods of characterization, character appearance, prototype, the relation of character with other elements, and characterization defects are some of the subjects studied in this article.Character types: these characters are generally categorized in two groups of stereotype and type. Samir, Touraj, Reza, Hamid etc. all belong to Sepah forces category which are type characters. Some women characters such as Zeinab, Samir’s mother, Kolsoum, Hanieh’s mother etc. are stereotype characters.Methods of characterization in “Palms and Men” novel:The description of characters is done in two methods by Mr. Nematollah Soleimani:aDirect characterization: If not all the characters, most of them are certainly characterized in this way. For example in expressing Hamid’s characteristic who is the commander of the mission, he writes, “Hamid didn’t bat an eyelid in any incidents. Hamid was lion-hearted”. (Soleimani, 1380: 128. In describing uncle Heidar, he writes, “wisdom and insight, and the effects of years of suffering, difficulty, and experiencing could be clearly seen in his limpid eyes. The rural man was indeed a wise and experienced man” (the same: 264_265.bIndirect Characterization: Although in novels and long stories, direct characterization method is often used, in “Palms and Men” this kind of characterization is also appeared in different conversations, stream of consciousness, deeds

  7. WWC Evidence Review Protocol for Character Education Interventions

    Science.gov (United States)

    What Works Clearinghouse, 2014

    2014-01-01

    Character education is an inclusive concept regarding all aspects of how families, schools, and related social institutions support the positive character development of children and adults. "Character" in this context refers to the moral and ethical qualities of persons as well as the demonstration of those qualities in their emotional…

  8. Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda

    Science.gov (United States)

    Deng, Youping; Dong, Yinghua; Thodima, Venkata; Clem, Rollie J; Passarelli, A Lorena

    2006-01-01

    Background Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interactions. In addition, cell lines derived from Spodoptera frugiperda and other lepidopteran insects are routinely used for baculovirus foreign gene expression. This study reports the results of an expressed sequence tag (EST) sequencing project in cells from the lepidopteran insect S. frugiperda, the fall armyworm. Results We have constructed an EST database using two cDNA libraries from the S. frugiperda-derived cell line, SF-21. The database consists of 2,367 ESTs which were assembled into 244 contigs and 951 singlets for a total of 1,195 unique sequences. Conclusion S. frugiperda is an agriculturally important pest insect and genomic information will be instrumental for establishing initial transcriptional profiling and gene function studies, and for obtaining information about genes manipulated during infections by insect pathogens such as baculoviruses. PMID:17052344

  9. Drawing and Recognizing Chinese Characters with Recurrent Neural Network.

    Science.gov (United States)

    Zhang, Xu-Yao; Yin, Fei; Zhang, Yan-Ming; Liu, Cheng-Lin; Bengio, Yoshua

    2018-04-01

    Recent deep learning based approaches have achieved great success on handwriting recognition. Chinese characters are among the most widely adopted writing systems in the world. Previous research has mainly focused on recognizing handwritten Chinese characters. However, recognition is only one aspect for understanding a language, another challenging and interesting task is to teach a machine to automatically write (pictographic) Chinese characters. In this paper, we propose a framework by using the recurrent neural network (RNN) as both a discriminative model for recognizing Chinese characters and a generative model for drawing (generating) Chinese characters. To recognize Chinese characters, previous methods usually adopt the convolutional neural network (CNN) models which require transforming the online handwriting trajectory into image-like representations. Instead, our RNN based approach is an end-to-end system which directly deals with the sequential structure and does not require any domain-specific knowledge. With the RNN system (combining an LSTM and GRU), state-of-the-art performance can be achieved on the ICDAR-2013 competition database. Furthermore, under the RNN framework, a conditional generative model with character embedding is proposed for automatically drawing recognizable Chinese characters. The generated characters (in vector format) are human-readable and also can be recognized by the discriminative RNN model with high accuracy. Experimental results verify the effectiveness of using RNNs as both generative and discriminative models for the tasks of drawing and recognizing Chinese characters.

  10. First Course in Japanese: Character Workbook.

    Science.gov (United States)

    Niwa, Tamako

    This character workbook is an introduction to Japanese writing designed to be used in conjunction with Parts One and Two of this introductory course in Japanese. All the "hiragana", several "katakana", and 88 Japanese characters are introduced in this text. The workbook, consisting of 30 lessons, is divided into three parts.…

  11. Do Rural Schools Need Character Education?

    Science.gov (United States)

    Reynolds, Janice Carner

    Studies suggest that the challenge of violence in public schools can be met through character education, whether by providing a school culture in which core values are practiced or some form of moral training (indoctrination). To assess the need for character education in rural schools, small-school superintendents and board members in central…

  12. Moral character predominates in person perception and evaluation.

    Science.gov (United States)

    Goodwin, Geoffrey P; Piazza, Jared; Rozin, Paul

    2014-01-01

    What sorts of trait information do people most care about when forming impressions of others? Recent research in social cognition suggests that "warmth," broadly construed, should be of prime importance in impression formation. Yet, some prior research suggests that information about others' specifically moral traits--their moral "character"--may be a primary dimension. Although warmth and character have sometimes been conceived of as interchangeable, we argue that they are separable, and that across a wide variety of contexts, character is usually more important than warmth in impression formation. We first showed that moral character and social warmth traits are indeed separable (Studies 1 and 2). Further studies that used correlational and experimental methods showed that, as predicted, in most contexts, moral character information is more important in impression formation than is warmth information (Studies 2-6). Character information was also more important than warmth information with respect to judgments of traits' perceived fundamentalness to identity, their uniquely human quality, their context-independence, and their controllability (Study 2). Finally, Study 7 used an archival method to show that moral character information appears more prominently than warmth information in obituaries, and more strongly determines the impressions people form of the individuals described in those obituaries. We discuss implications for current theories of person perception and social cognition.

  13. A modification to the SCAR (Sequence Characterized Amplified Region method provides phylogenetic insights within Ceratozamia (Zamiaceae Una modificación al método SCAR (Sequence Characterized Amplified Region aporta entendimiento filogenético en Ceratozamia (Zamiaceae

    Directory of Open Access Journals (Sweden)

    Dolores González

    2012-12-01

    Full Text Available Phylogenetic relationships among closely related plant species are still problematic. DNA intergenic regions often are insufficiently variable to provide desired resolution or support. In this study, a modification to the Sequence Characterized Amplified Region (SCAR method was used to find polymorphic loci for phylogenetic analyses within Ceratozamia. RAPD markers were first used to detect variation in 5 species. Then, equal length fragments found in 2 or more species were excised from the gel, purified and digested with frequent cutter restriction enzymes for isolating both ends, which have the same primer site. Digested fragments were sequenced with the RAPD primer. Variable sequences were used to design specific primers for amplifying and sequencing in all species for phylogenetic analyses. Our results confirmed the previously known high genome sequence resemblance within this genus that contrasts with its high morphological variation. Only 7 parsimony informative characters were found with this approach. Nonetheless, the Digested-SCAR (D-SCAR method provided some phylogenetic insights. Four main clades consistent with distribution ranges of the species were detected. The approach presented here was effective to solve some relationships within the genus and can potentially be implemented in other organisms to find polymorphic loci for phylogenetic studies at any taxonomic level.Las relaciones filogenéticas entre especies de plantas cercanamente relacionadas es aún problemático. Las regiones intergénicas del ADN son a menudo insuficientemente variables para proveer los niveles de resolución y soporte deseados. En este estudio, se usó una modificación al método Sequence Characterized Amplified Region (SCAR para encontrar loci polimórficos para análisis filogenéticos en Ceratozamia. Primero se usaron marcadores RAPD para detectar variación en 5 especies; luego, se cortaron del gel los fragmentos de la misma longitud en 2 o m

  14. Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Pertea Geo

    2007-10-01

    Full Text Available Abstract Background The southern cattle tick, Rhipicephalus (Boophilus microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks. Results We present a global comparative genomic analysis of a gene index of R. microplus comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs, a significant fraction of the complement of R. microplus genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of R. microplus, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology. Conclusion These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes

  15. Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

    Science.gov (United States)

    Cao, Yinhe; Tung, Wen-Wen; Gao, J B

    2004-01-01

    With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

  16. AcEST: DK950801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK950801 - Show DK950801 Clone id TST38A01NGRL0009_K18 Library TST38 Length 645 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0009_K18. 5' end sequence. Accession DK950801 Tissue t...on of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK950801|Adiantum capillus-v...abase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK950801|Adiantum

  17. Cultivating characters (moral value) through internalization strategy in science classroom

    Science.gov (United States)

    Ibrahim, M.; Abadi

    2018-01-01

    It is still in a crucial debate that characters play an important learning outcome to be realized by design. So far, most people think that characters were reached as nurturance effect with the assumption that students who are knowledgeable and skillful will have good characters automatically. Lately, obtained evidence that this assumption is not true. Characters should be taught deliberately or by design. This study was designed to culture elementary school students’ characters through science classroom. The teaching-learning process was conducted to facilitate and bridge the students from the known (concrete images: Science phenomena) to the unknown (abstract ideas: characters: care, and tolerance. Characters were observed five weeks before and after the intervention. Data were analyzed from observation of 24 students in internalization strategy-based courses. Qualitative and quantitative data suggested that the internalization strategy that use of science phenomena to represent abstract ideas (characters) in science classroom positively cultivating characters.

  18. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

    Energy Technology Data Exchange (ETDEWEB)

    Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-20

    Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

  19. Character combinations, convergence and diversification in ectoparasitic arthropods.

    Science.gov (United States)

    Poulin, Robert

    2009-08-01

    Different lineages of organisms diversify over time at different rates, in part as a consequence of the characteristics of the species in these lineages. Certain suites of traits possessed by species within a clade may determine rates of diversification, with some particular combinations of characters acting synergistically to either limit or promote diversification; the most successful combinations may also emerge repeatedly in different clades via convergent evolution. Here, the association between species characters and diversification is investigated amongst 21 independent lineages of arthropods ectoparasitic on vertebrate hosts. Using nine characters (each with two to four states) that capture general life history strategy, transmission mode and host-parasite interaction, each lineage was described by the set of character states it possesses. The results show, firstly, that most possible pair-wise combinations of character states have been adopted at least once, sometimes several times independently by different lineages; thus, ectoparasitic arthropods have explored most of the life history character space available to them. Secondly, lineages possessing commonly observed combinations of character states are not necessarily the ones that have experienced the highest rates of diversification (measured as a clade's species-per-genus ratio). Thirdly, some specific traits are associated with higher rates of diversification. Using more than one host per generation, laying eggs away from the host and intermediate levels of fecundity are features that appear to have promoted diversification. These findings indicate that particular species characters may be evolutionary drivers of diversity, whose effects could also apply in other taxa.

  20. The dark cube: dark and light character profiles

    Directory of Open Access Journals (Sweden)

    Danilo Garcia

    2016-02-01

    Full Text Available Background. Research addressing distinctions and similarities between people’s malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy has detected inconsistent linear associations to temperament traits. Additionally, these dark traits seem to have a common core expressed as uncooperativeness. Hence, some researchers suggest that the dark traits are best represented as one global construct (i.e., the unification argument rather than as ternary construct (i.e., the uniqueness argument. We put forward the dark cube (cf. Cloninger’s character cube comprising eight dark profiles that can be used to compare individuals who differ in one dark character trait while holding the other two constant. Our aim was to investigate in which circumstances individuals who are high in each one of the dark character traits differ in Cloninger’s “light” character traits: self-directedness, cooperativeness, and self-transcendence. We also investigated if people’s dark character profiles were associated to their light character profiles. Method. A total of 997 participants recruited from Amazon’s Mechanical Turk (MTurk responded to the Short Dark Triad and the Short Character Inventory. Participants were allocated to eight different dark profiles and eight light profiles based on their scores in each of the traits and any possible combination of high and low scores. We used three-way interaction regression analyses and t-tests to investigate differences in light character traits between individuals with different dark profiles. As a second step, we compared the individuals’ dark profile with her/his character profile using an exact cell-wise analysis conducted in the ROPstat software (http://www.ropstat.com. Results. Individuals who expressed high levels of Machiavellianism and those who expressed high levels of psychopathy also expressed low self-directedness and low cooperativeness. Individuals with high

  1. Skipping of Chinese characters does not rely on word-based processing.

    Science.gov (United States)

    Lin, Nan; Angele, Bernhard; Hua, Huimin; Shen, Wei; Zhou, Junyi; Li, Xingshan

    2018-02-01

    Previous eye-movement studies have indicated that people tend to skip extremely high-frequency words in sentence reading, such as "the" in English and "/de" in Chinese. Two alternative hypotheses have been proposed to explain how this frequent skipping happens in Chinese reading: one assumes that skipping happens when the preview has been fully identified at the word level (word-based skipping); the other assumes that skipping happens whenever the preview character is easy to identify regardless of whether lexical processing has been completed or not (character-based skipping). Using the gaze-contingent display change paradigm, we examined the two hypotheses by substituting the preview of the third character of a four-character Chinese word with the high-frequency Chinese character "/de", which should disrupt the ongoing word-level processing. The character-based skipping hypothesis predicts that this manipulation will enhance the skipping probability of the target character (i.e., the third character of the target word), because the character "/de" has much higher character frequency than the original character. The word-based skipping hypothesis instead predicts a reduction of the skipping probability of the target character because the presence of the character "/de" is lexically infelicitous at word level. The results supported the character-based skipping hypothesis, indicating that in Chinese reading the decision of skipping a character can be made before integrating it into a word.

  2. AcEST: DK950406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK950406 CL45Contig1 Show DK950406 Clone id TST38A01NGRL0008_J04 Library TST38 Length 64...8 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0008_J04. 5' end sequence. Accession DK950406...SI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK950406... of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK950406

  3. AcEST: DK952801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 9. 5' end sequence. DK952801 - Show DK952801 Clone id TST38A01NGRL0015_B09 Library TST38 Length 646 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0015_B09. 5' end sequence. Accession DK952801 Tissue t...n of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK952801|Adiantum capillus-ve...ase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK952801|Adiantum capillus-veneris mRNA, clone:

  4. AcEST: DK958801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK958801 CL3693Contig1 Show DK958801 Clone id TST39A01NGRL0002_P12 Library TST39 Length ...581 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0002_P12. 5' end sequence. Accession DK958801...protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958801|Adiantum capillus-veneris...ration of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958801|Adiantum capill

  5. AcEST: DK959801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK959801 CL1090Contig1 Show DK959801 Clone id TST39A01NGRL0005_K21 Library TST39 Length ...651 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0005_K21. 5' end sequence. Accession DK959801...ms, Nucleic Acids Res. 25:3389-3402. Query= DK959801|Adiantum capillus-veneris mR...ein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK959801|Adiantum capillus-veneris mRN

  6. AcEST: DK957801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK957801 CL2Contig2 Show DK957801 Clone id TST39A01NGRL0029_F04 Library TST39 Length 752... Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_F04. 5' end sequence. Accession DK957801...of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK957801|Adiantum capillus-vene... search programs, Nucleic Acids Res. 25:3389-3402. Query= DK957801|Adiantum capillus-veneris mRNA, clone: TS

  7. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    Directory of Open Access Journals (Sweden)

    Brejnev Muhizi Muhire

    Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.

  8. Head capsule characters in the Hymenoptera and their phylogenetic implications

    Directory of Open Access Journals (Sweden)

    Lars Vilhelmsen

    2011-09-01

    Full Text Available The head capsule of a taxon sample of three outgroup and 86 ingroup taxa is examined for characters of possible phylogenetic significance within Hymenoptera. 21 morphological characters are illustrated and scored, and their character evolution explored by mapping them onto a phylogeny recently produced from a large morphological data set. Many of the characters are informative and display unambiguous changes. Most of the character support demonstrated is supportive at the superfamily or family level. In contrast, only few characters corroborate deeper nodes in the phylogeny of Hymenoptera.

  9. Submatrices of character tables and basic sets

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Olsson, Jørn Børling

    2012-01-01

    In this investigation of character tables of nite groups we study basic sets and associated representation theoretic data for complementary sets of conjugacy lasses. For the symmetric groups we nd unexpected properties of characters on restricted sets of conjugacy classes, like beautiful...... combinatorial determinant formulae for submatrices of the character table and Cartan matrices with respect to basic sets; we observe that similar phenomena occur for the transition matrices between power sum symmetric functions to bounded partitions and the k-Schur functions dened by Lapointe and Morse...

  10. Visual Antipriming Effect: Evidence from Chinese Character Identification

    Directory of Open Access Journals (Sweden)

    Feng Zhang

    2017-10-01

    Full Text Available Marsolek et al. (2006 have differentiated antipriming effects from priming effects, by adopting a novel priming paradigm comprised of four phases that include a baseline measurement. The general concept of antipriming supports the overlapping representation theory of knowledge. This study extended examination of the Marsolek et al. (2006 paradigm by investigating antipriming and priming effects in a series of Chinese character identification tasks. Results showed that identification accuracy of old characters was significantly higher than baseline measurements (i.e., the priming effect, while identification accuracy of novel characters was significantly lower than baseline measurements (i.e., the antipriming effect. This study demonstrates for the first time the effect of visual antipriming in Chinese character identification. It further provides new evidence for the overlapping representation theory of knowledge, and supports generalizability of the phenomenon to Chinese characters.

  11. Character strengths, social anxiety, and physiological stress reactivity

    Directory of Open Access Journals (Sweden)

    Tingting Li

    2017-05-01

    Full Text Available In this paper, the effects of character strengths on the physiological reactivity to social anxiety induced by the Trier Social Stress Task were reported. On the basis of their scores in the Chinese Virtues Questionnaire, 30 college students were assigned to either high- (n = 15 or low-character-strength (n = 15 groups. Their psychological stress and physiological data across three laboratory stages (namely, baseline, stress exposure, and post-stress were collected. Results indicated that individuals with high character strengths exhibited rapid cardiovascular recovery from baseline to post-stress even if high- and low-character-strength groups showed similar patterns of cardiovascular arousal in response to the stress at baseline and stress exposure. These results prove that character strengths are stress-defense factors that allow for psychological and physiological adaptation to stress.

  12. Representations of deaf characters in children's picture books.

    Science.gov (United States)

    Golos, Debbie B; Moses, Annie M

    2011-01-01

    Picture books can influence how children perceive people of different backgrounds, including people with disabilities whose cultures differ from their own. Researchers have examined the portrayal of multicultural characters with disabilities in children's literature. However, few have specifically considered the portrayal of deaf characters, despite increased inclusion of deaf characters in children's literature over the past two decades. The present study analyzed the portrayal of deaf characters in picture books for children ages 4-8 years. A content analysis of 20 children's picture books was conducted in which the books were analyzed for messages linked to pathological and cultural categories. Results indicated that these books did not portray Deaf characters from a cultural perspective but, rather, highlighted aspects of deafness as a medical condition, one that requires fixing and that perpetuates stereotypes of deafness as a disability.

  13. Influence of a Character-Based App on Children's Learning of Nutritional Information: Should Apps Be Served with a Side of Media Characters?

    Science.gov (United States)

    Putnam, Marisa M; Richmond, Elana M; Brunick, Kaitlin L; Wright, Charlotte A; Calvert, Sandra L

    2018-04-01

    Childhood obesity is a health issue in the United States, associated with marketing practices in which media characters are often used to sell unhealthy products. This study examined exposure to a socially contingent touch-screen gaming app, which replied immediately, reliably, and accurately to children's actions. Children's recall of nutritional content and their liking of the character were assessed. Four- and five-year-old children (N = 114) received no-exposure, single-exposure, or repeated-exposure to a character-based iPad app rewarding healthy and penalizing unhealthy behaviors. Children reported how much they liked the character and recalled healthy and unhealthy items from the app. An ordinary least squares regression was conducted on how much children liked the character by condition. Poisson regressions were conducted on the number of items recalled by condition alone, and in an interacted model of treatment condition by liking the character. Children liked the character more in the repeated app-exposure condition than in the control group (P = 0.018). Children in the repeated and single app-exposure conditions recalled more healthy (P < 0.001) and unhealthy (P < 0.001) items than the control group. Within treatment conditions, liking the character increased recall of healthy items in the single app-exposure compared to the repeated app-exposure condition (P = 0.005). Results revealed that repeated exposure increased children's learning of nutritional information and liking of the character. The results contribute to our understanding of how to deliver effective nutrition information to young children in a new venue, a gaming app.

  14. Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series.

    Science.gov (United States)

    Blair, Matthew W; Hurtado, Natalia; Chavarro, Carolina M; Muñoz-Torres, Monica C; Giraldo, Martha C; Pedraza, Fabio; Tomkins, Jeff; Wing, Rod

    2011-03-22

    Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants. A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers. The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva

  15. Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone ( Haliotis discus hannai)

    Science.gov (United States)

    Li, Qi; Shu, Jing; Zhao, Cui; Liu, Shikai; Kong, Lingfeng; Zheng, Xiaodong

    2010-01-01

    Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone ( Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences, after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2-17, with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922, respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families, with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai, together with the high rate of transportability across Haliotis species, make this set of EST-SSR markers an important tool for comparative mapping, marker-assisted selection, and evolutionary studies, not only in the Pacific abalone, but also in related species.

  16. ESTs Analysis of Putative Genes Engaged in Polyporus umbellatus Sclerotial Development

    Directory of Open Access Journals (Sweden)

    Chao Song

    2014-09-01

    Full Text Available Polyporus umbellatus is one of the most widely used and precious medicinal fungi and the underground sclerotia are known to be with great medicinal value. However, the molecular mechanisms involved in sclerotial development are poorly understood. In the present study, we constructed a forward suppression subtractive hybridization (SSH cDNA library of Polyporus umbellatus to identify genes expressing differently between mycelium and sclerotia. In this library, a total of 1202 clones were sequenced, assembled into 222 contigs and 524 singletons which were further searched against the NCBI nonredundant (NR protein database (E-value cutoff, 10−5. Based on sequence similarity with known proteins, 378 sequences between mycelium and sclerotial were identified and classified into different functional categories through Gene Ontology (GO, Clusters of orthologous Groups of proteins (COGs. We have finally identified a majority of differentially expressed genes (constituting 5.6% of the present library between the two different periods. An expression level of 32 selected expressed sequence tags (ESTs generated from the above SSH cDNA library was studied through RT-PCR. This study provides the first global overview of genes putatively involved in Polyporus umbellatus sclerotial development and provides a preliminary basis for further functional research in terms of regulated gene expression in sclerotial production.

  17. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea.

    Directory of Open Access Journals (Sweden)

    Oliver Voigt

    Full Text Available Calcareous sponges (Phylum Porifera, Class Calcarea are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU rDNA and the almost complete large subunit (LSU rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae and Leucettidae and between Leucascandra (Jenkinidae and Sycon carteri (Sycettidae. According to our results, the taxonomy of Calcarea is in

  18. AcEST: DK959406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 7. 5' end sequence. DK959406 CL3039Contig1 Show DK959406 Clone id TST39A01NGRL0004_J17 Library TST39 Length ...621 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0004_J17. 5' end sequence. Accession DK959406...ed BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK959406...rch programs, Nucleic Acids Res. 25:3389-3402. Query= DK959406|Adiantum capillus-veneris mRNA, clone: TST39A

  19. AcEST: DK958406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK958406 CL15Contig1 Show DK958406 Clone id TST39A01NGRL0030_O18 Library TST39 Length 60...7 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0030_O18. 5' end sequence. Accession DK958406...LAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958406...database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958406|Adiantum capillus-veneris mRNA, c

  20. AcEST: DK944406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 7. 5' end sequence. DK944406 CL1Contig2 Show DK944406 Clone id YMU02A01NGRL0005_P07 Library YMU02 Length 175... Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0005_P07. 5' end sequence. Accession DK944406...rams, Nucleic Acids Res. 25:3389-3402. Query= DK944406|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL00...AST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944406|

  1. AcEST: DK948406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK948406 CL33Contig1 Show DK948406 Clone id TST38A01NGRL0003_D18 Library TST38 Length 58...1 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0003_D18. 5' end sequence. Accession DK948406...ic Acids Res. 25:3389-3402. Query= DK948406|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0003_D18, 5' ... a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948406|Adia

  2. AcEST: DK952406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK952406 CL1615Contig1 Show DK952406 Clone id TST38A01NGRL0014_A01 Library TST38 Length ...618 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0014_A01. 5' end sequence. Accession DK952406...ein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK952406|Adiantum capillus-veneris mRN... Acids Res. 25:3389-3402. Query= DK952406|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0014_A01, 5' (6

  3. AcEST: DK955406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 5. 5' end sequence. DK955406 CL689Contig1 Show DK955406 Clone id TST39A01NGRL0023_A05 Library TST39 Length 5...18 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0023_A05. 5' end sequence. Accession DK955406...Res. 25:3389-3402. Query= DK955406|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0023_A05, 5' (518 lett...-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK955406

  4. AcEST: DK951406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK951406 - Show DK951406 Clone id TST38A01NGRL0011_F06 Library TST38 Length 670 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0011_F06. 5' end sequence. Accession DK951406 Tissue t...AST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK951406...), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK951406

  5. AcEST: DK957406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 5. 5' end sequence. DK957406 - Show DK957406 Clone id TST39A01NGRL0028_E15 Library TST39 Length 641 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0028_E15. 5' end sequence. Accession DK957406 Tissue t...ed BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK957406... PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK957406

  6. AcEST: DK961801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK961801 CL4094Contig1 Show DK961801 Clone id TST39A01NGRL0011_C13 Library TST39 Length ...664 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0011_C13. 5' end sequence. Accession DK961801...tein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK961801|A...ms, Nucleic Acids Res. 25:3389-3402. Query= DK961801|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0011

  7. AcEST: DK943801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK943801 CL1Contig2 Show DK943801 Clone id YMU02A01NGRL0003_P23 Library YMU02 Length 178... Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0003_P23. 5' end sequence. Accession DK943801...rograms, Nucleic Acids Res. 25:3389-3402. Query= DK943801|Adiantum capillus-veneris mRNA, clone: YMU02A01NGR...-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK943801

  8. AcEST: DK956801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK956801 CL1196Contig1 Show DK956801 Clone id TST39A01NGRL0026_L02 Library TST39 Length ...585 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0026_L02. 5' end sequence. Accession DK956801...apped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK956801...on of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK956801|Adiantum capillus-v

  9. AcEST: DK954801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 5. 5' end sequence. DK954801 CL674Contig1 Show DK954801 Clone id TST39A01NGRL0021_G15 Library TST39 Length 6...16 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0021_G15. 5' end sequence. Accession DK954801...a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK954801|Adian...earch programs, Nucleic Acids Res. 25:3389-3402. Query= DK954801|Adiantum capillus-veneris mRNA, clone: TST3

  10. AcEST: DK947801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK947801 CL89Contig1 Show DK947801 Clone id YMU02A01NGRM0001_B06 Library YMU02 Length 26...9 Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRM0001_B06. 5' end sequence. Accession DK947801...eic Acids Res. 25:3389-3402. Query= DK947801|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRM0001_B06, 5'...LAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK947801

  11. AcEST: DK945801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK945801 CL1Contig3 Show DK945801 Clone id YMU02A01NGRL0010_H21 Library YMU02 Length 497... Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0010_H21. 5' end sequence. Accession DK945801...atabase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK945801|Adiantum capillus-veneris mRNA, cl...atabase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK945801|Adiantum capillus-veneris mRNA, cl

  12. AcEST: DK953801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK953801 - Show DK953801 Clone id TST39A01NGRL0018_L21 Library TST39 Length 572 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0018_L21. 5' end sequence. Accession DK953801 Tissue t...cleic Acids Res. 25:3389-3402. Query= DK953801|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0018_L21, ...se search programs, Nucleic Acids Res. 25:3389-3402. Query= DK953801|Adiantum capillus-veneris mRNA, clone:

  13. AcEST: DK951801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK951801 - Show DK951801 Clone id TST38A01NGRL0012_F22 Library TST38 Length 582 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0012_F22. 5' end sequence. Accession DK951801 Tissue t...25:3389-3402. Query= DK951801|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0012_F22, 5' (582 letters) ...: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK951801|Adi

  14. AcEST: DK948801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK948801 - Show DK948801 Clone id TST38A01NGRL0004_E11 Library TST38 Length 549 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0004_E11. 5' end sequence. Accession DK948801 Tissue t...new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948801|Adiantu...AST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948801

  15. AcEST: DK955801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK955801 CL19Contig1 Show DK955801 Clone id TST39A01NGRL0024_B03 Library TST39 Length 62...2 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0024_B03. 5' end sequence. Accession DK955801...ST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK955801...LAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK955801

  16. OD (order-disorder) character of the crystal structure of godlevskite Ni9S8

    DEFF Research Database (Denmark)

    Merlino, Stefano; Makovicky, Emil

    2009-01-01

    Godlevskite Ni9S8 has been found to be an OD (order-disorder) structure consisting of two kinds of OD layers in strict alternation; these layers display stacking disorder. They have layer symmetries P( )2m and P212(2), respectively (symmetry elements in parentheses are perpendicular to OD layers......). Two structures with maximum degree of order (MDO polytypes), with space-group symmetries A222 and I4122, respectively, exist, together with more complex polytypes or disordered sequences. The OD character is in keeping with the frequent twinning of godlevskite....

  17. The Implementation of Character Education at Senior High School

    Directory of Open Access Journals (Sweden)

    Julia

    2018-01-01

    Full Text Available This paper is aimed at analyzing the implementation of character education at Senior High School in Sumedang Regency, West Java, Indonesia. A content analysis method was employed to collect the data with interviews with six teachers from six different senior high schools, which represent the rural, transitional, and urban areas. The findings revealed that: (1 not all teachers understand the concept of character education; (2 the character education has not been done systematically or has not had the specific design/model for the teaching and learning process. Most teachers embedded the character values during the teaching and learning process as a form of character education. For example, through Qur’an recitation, learning tasks, group discussion, lecture, socio-drama, observation and admonition, and even through teachers’ model. Meanwhile, outside the class, character education was implemented through competition and extracurricular activities; (3 the evaluation of character education was relatively varied, such as an observation followed by admonition, group guidance, and also focusing on behavior and affective assessment in the classroom learning process. This research implied that it is needed to make a policy on a program development through the Bureau of Education to improve Senior High School teachers’ knowledge and skills in implementing the character education.

  18. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

    OpenAIRE

    Hasebe, M; Omori, T; Nakazawa, M; Sano, T; Kato, M; Iwatsuki, K

    1994-01-01

    Pteriodophytes have a longer evolutionary history than any other vascular land plant and, therefore, have endured greater loss of phylogenetically informative information. This factor has resulted in substantial disagreements in evaluating characters and, thus, controversy in establishing a stable classification. To compare competing classifications, we obtained DNA sequences of a chloroplast gene. The sequence of 1206 nt of the large subunit of the ribulose-bisphosphate carboxylase gene (rbc...

  19. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    Directory of Open Access Journals (Sweden)

    Cherubini Marcello

    2010-10-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs are a source of simple sequence repeats (SSRs that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut. Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283 were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak

  20. AcEST: CL1889Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL1889Contig1 491 2 Adiantum capillus-veneris contig: CL1889contig1 sequence. Link ...apillus-veneris contig: CL1889contig1 sequence. Link to clone list Link to clone list Clone ID BP919609 BP91

  1. Javanese Character Feature Extraction Based on Shape Energy

    Directory of Open Access Journals (Sweden)

    Galih Hendra Wibowo

    2017-07-01

    Full Text Available Javanese character is one of Indonesia's noble culture, especially in Java. However, the number of Javanese people who are able to read the letter has decreased so that there need to be conservation efforts in the form of a system that is able to recognize the characters. One solution to these problem lies in Optical Character Recognition (OCR studies, where one of its heaviest points lies in feature extraction which is to distinguish each character. Shape Energy is one of feature extraction method with the basic idea of how the character can be distinguished simply through its skeleton. Based on the basic idea, then the development of feature extraction is done based on its components to produce an angular histogram with various variations of multiples angle. Furthermore, the performance test of this method and its basic method is performed in Javanese character dataset, which has been obtained from various images, is 240 data with 19 labels by using K-Nearest Neighbors as its classification method. Performance values were obtained based on the accuracy which is generated through the Cross-Validation process of 80.83% in the angular histogram with an angle of 20 degrees, 23% better than Shape Energy. In addition, other test results show that this method is able to recognize rotated character with the lowest performance value of 86% at 180-degree rotation and the highest performance value of 96.97% at 90-degree rotation. It can be concluded that this method is able to improve the performance of Shape Energy in the form of recognition of Javanese characters as well as robust to the rotation.

  2. Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

    Directory of Open Access Journals (Sweden)

    Christian M. Tobias

    2008-11-01

    Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

  3. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Cronn Richard

    2009-12-01

    Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

  4. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

    Science.gov (United States)

    Awasthi, Praveen; Singh, Ashish; Sheikh, Gulfam; Mahajan, Vidushi; Gupta, Ajai Prakash; Gupta, Suphla; Bedi, Yashbir S; Gandhi, Sumit G

    2017-10-01

    Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

  5. The Inaccuracy of National Character Stereotypes

    Science.gov (United States)

    McCrae, Robert R.; Chan, Wayne; Jussim, Lee; De Fruyt, Filip; Löckenhoff, Corinna E.; De Bolle, Marleen; Costa, Paul T.; Hřebíčková, Martina; Graf, Sylvie; Realo, Anu; Allik, Jüri; Nakazato, Katsuharu; Shimonaka, Yoshiko; Yik, Michelle; Ficková, Emília; Brunner-Sciarra, Marina; Reátigui, Norma; de Figueora, Nora Leibovich; Schmidt, Vanina; Ahn, Chang-kyu; Ahn, Hyun-nie; Aguilar-Vafaie, Maria E.; Siuta, Jerzy; Szmigielska, Barbara; Cain, Thomas R.; Crawford, Jarret T.; Mastor, Khairul Anwar; Rolland, Jean-Pierre; Nansubuga, Florence; Miramontez, Daniel R.; Benet-Martínez, Veronica; Rossier, Jérôme; Bratko, Denis; Marušić, Iris; Halberstadt, Jamin; Yamaguchi, Mami; Knežević, Goran; Purić, Danka; Martin, Thomas A.; Gheorghiu, Mirona; Smith, Peter B.; Barbaranelli, Claudio; Wang, Lei; Shakespeare-Finch, Jane; Lima, Margarida P.; Klinkosz, Waldemar; Sekowski, Andrzej; Alcalay, Lidia; Simonetti, Franco; Avdeyeva, Tatyana V.; Pramila, V. S.; Terracciano, Antonio

    2013-01-01

    Consensual stereotypes of some groups are relatively accurate, whereas others are not. Previous work suggesting that national character stereotypes are inaccurate has been criticized on several grounds. In this article we (a) provide arguments for the validity of assessed national mean trait levels as criteria for evaluating stereotype accuracy; and (b) report new data on national character in 26 cultures from descriptions (N=3,323) of the typical male or female adolescent, adult, or old person in each. The average ratings were internally consistent and converged with independent stereotypes of the typical culture member, but were weakly related to objective assessments of personality. We argue that this conclusion is consistent with the broader literature on the inaccuracy of national character stereotypes. PMID:24187394

  6. Transliterating non-ASCII characters with Python

    Directory of Open Access Journals (Sweden)

    Seth Bernstein

    2013-10-01

    Full Text Available This lesson shows how to use Python to transliterate automatically a list of words from a language with a non-Latin alphabet to a standardized format using the American Standard Code for Information Interchange (ASCII characters. It builds on readers’ understanding of Python from the lessons “Viewing HTML Files,” “Working with Web Pages,” “From HTML to List of Words (part 1” and “Intro to Beautiful Soup.” At the end of the lesson, we will use the transliteration dictionary to convert the names from a database of the Russian organization Memorial from Cyrillic into Latin characters. Although the example uses Cyrillic characters, the technique can be reproduced with other alphabets using Unicode.

  7. Animated Character Analysis and Costume Design with Structured Analysis

    OpenAIRE

    Yıldırım Artaç, Berna; Ağaç, Saliha

    2016-01-01

    In various genres, costumes complement fictional characters and not onlyconstitute the external appearance of the fictional character, but are alsoused for purposes of fun or style by fans who dress up as the character andinternalize that character’s state of mind. This phenomenon is calledcosplay. A literature review of the field has revealed no study made previouslyon the cosplay costume design process according to character analysis. Thepresent study emphasizes the link between an...

  8. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    Energy Technology Data Exchange (ETDEWEB)

    Catfish Genome Consortium; Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-03-23

    Background-Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results-A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35percent of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions-This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  9. About Chinese Characters

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    It is perhaps a facet of human nature that makes a person want to beking, and to control others. The character "王" was originally"王",symbolizing the emerald prayer beads worn exclusively by the king. Inthe course of this character’s evolution, however, new connotations were

  10. The genetic and environmental structure of the character sub-scales of the temperament and character inventory in adolescence.

    Science.gov (United States)

    Lester, Nigel; Garcia, Danilo; Lundström, Sebastian; Brändström, Sven; Råstam, Maria; Kerekes, Nóra; Nilsson, Thomas; Cloninger, C Robert; Anckarsäter, Henrik

    2016-01-01

    The character higher order scales (self-directedness, cooperativeness, and self-transcendence) in the temperament and character inventory are important general measures of health and well-being [Mens Sana Monograph 11:16-24 (2013)]. Recent research has found suggestive evidence of common environmental influence on the development of these character traits during adolescence. The present article expands earlier research by focusing on the internal consistency and the etiology of traits measured by the lower order sub-scales of the character traits in adolescence. The twin modeling analysis of 423 monozygotic pairs and 408 same sex dizygotic pairs estimated additive genetics (A), common environmental (C), and non-shared environmental (E) influences on twin resemblance. All twins were part of the on-going longitudinal Child and Adolescent Twin Study in Sweden (CATSS). The twin modeling analysis suggested a common environmental contribution for two out of five self-directedness sub-scales (0.14 and 0.23), for three out of five cooperativeness sub-scales (0.07-0.17), and for all three self-transcendence sub-scales (0.10-0.12). The genetic structure at the level of the character lower order sub-scales in adolescents shows that the proportion of the shared environmental component varies in the trait of self-directedness and in the trait of cooperativeness, while it is relatively stable across the components of self-transcendence. The presence of this unique shared environmental effect in adolescence has implications for understanding the relative importance of interventions and treatment strategies aimed at promoting overall maturation of character, mental health, and well-being during this period of the life span.

  11. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    Science.gov (United States)

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  12. How jurors use and misuse character evidence.

    Science.gov (United States)

    Hunt, Jennifer S; Budesheim, Thomas Lee

    2004-04-01

    The Federal Rules of Evidence allow defendants to offer testimony about their good character, but that testimony can be impeached with cross-examination or a rebuttal witness. It is assumed that jurors use the defense's character evidence (CE) to form guilt and conviction judgments but use impeachment evidence only to assess the character witness's credibility. Two experiments tested these assumptions by presenting mock jurors with various forms of CE and impeachment. Participants made trait ratings for the character witness and defendant and guilt and conviction judgments. Positive CE did not affect guilt or conviction judgments, but cross-examination caused a backlash in which judgments were harsher than when no CE was given. Using path analysis, the authors tested a model of the process by which CE and impeachment affect defendant and witness impressions and guilt and conviction judgments. Implications for juror decision making are discussed.

  13. Introducing Character Animation with Blender

    CERN Document Server

    Mullen, Tony

    2011-01-01

    Introducing Character Animation with Blender, 2nd Edition is written in a friendly but professional tone, with clear descriptions and numerous illustrative screenshots. Throughout the book, tutorials focus on how to accomplish actual animation goals, while illustrating the necessary technical methods along the way. These are reinforced by clear descriptions of how each specific aspect of Blender works and fits together with the rest of the package. By following all the tutorials, the reader will gain all the skills necessary to build and animate a well-modeled, fully-rigged character of their

  14. AcEST: DK953406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK953406 CL390Contig1 Show DK953406 Clone id TST39A01NGRL0017_K24 Library TST39 Length 5...83 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0017_K24. 5' end sequence. Accession DK953406...), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK953406...ids Res. 25:3389-3402. Query= DK953406|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0017_K24, 5' (583

  15. AcEST: DK948019 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK948019 CL3Contig1 Show DK948019 Clone id TST38A01NGRL0002_D04 Library TST38 Length 716... Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_D04. 5' end sequence. Accession DK948019...of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK94801...database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948019|Adiantum capillus-veneris mRNA, c...th = 396 Score = 313 bits (801), Expect = 9e-84 Identities = 166/213 (77%), Posit

  16. AcEST: DK944801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK944801 - Show DK944801 Clone id YMU02A01NGRL0007_D21 Library YMU02 Length 485 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0007_D21. 5' end sequence. Accession DK944801 Tissue t... 25:3389-3402. Query= DK944801|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL0007_D21, 5' (472 letters)...lfolobus solfata... 32 1.8 sp|O13801|YE04_SCHPO Uncharacterized RNA-binding prote...DDPKDTSDYTIDHGLEELEELRKQVFGNDKIVLLGHSYGGALAIAYALKY 129 >sp|O13801|YE04_SCHPO Uncharacterized RNA-binding pro

  17. AcEST: DK949801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 0. 5' end sequence. DK949801 - Show DK949801 Clone id TST38A01NGRL0006_P10 Library TST38 Length 596 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0006_P10. 5' end sequence. Accession DK949801 Tissue t... Acids Res. 25:3389-3402. Query= DK949801|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0006_P10, 5' (5...25:3389-3402. Query= DK949801|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0006_P10, 5' (533 letters)

  18. AcEST: DK946801 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK946801 CL2328Contig1 Show DK946801 Clone id YMU02A01NGRL0013_M16 Library YMU02 Length ...299 Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0013_M16. 5' end sequence. Accession DK946801... Nucleic Acids Res. 25:3389-3402. Query= DK946801|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL0013_M1... 25:3389-3402. Query= DK946801|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL0013_M16, 5' (270 letters)

  19. AcEST: DK958018 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK958018 CL9Contig1 Show DK958018 Clone id TST39A01NGRL0029_O11 Library TST39 Length 673... Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O11. 5' end sequence. Accession DK958018...e search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958018|Adiantum capi...tabase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958018|Adiantum...TST39A01NGRL0029_O11 673 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O1

  20. Benchmark for license plate character segmentation

    Science.gov (United States)

    Gonçalves, Gabriel Resende; da Silva, Sirlene Pio Gomes; Menotti, David; Shwartz, William Robson

    2016-09-01

    Automatic license plate recognition (ALPR) has been the focus of many researches in the past years. In general, ALPR is divided into the following problems: detection of on-track vehicles, license plate detection, segmentation of license plate characters, and optical character recognition (OCR). Even though commercial solutions are available for controlled acquisition conditions, e.g., the entrance of a parking lot, ALPR is still an open problem when dealing with data acquired from uncontrolled environments, such as roads and highways when relying only on imaging sensors. Due to the multiple orientations and scales of the license plates captured by the camera, a very challenging task of the ALPR is the license plate character segmentation (LPCS) step, because its effectiveness is required to be (near) optimal to achieve a high recognition rate by the OCR. To tackle the LPCS problem, this work proposes a benchmark composed of a dataset designed to focus specifically on the character segmentation step of the ALPR within an evaluation protocol. Furthermore, we propose the Jaccard-centroid coefficient, an evaluation measure more suitable than the Jaccard coefficient regarding the location of the bounding box within the ground-truth annotation. The dataset is composed of 2000 Brazilian license plates consisting of 14000 alphanumeric symbols and their corresponding bounding box annotations. We also present a straightforward approach to perform LPCS efficiently. Finally, we provide an experimental evaluation for the dataset based on five LPCS approaches and demonstrate the importance of character segmentation for achieving an accurate OCR.

  1. Technical guide for monitoring selected conditions related to wilderness character

    Science.gov (United States)

    Peter Landres; Steve Boutcher; Liese Dean; Troy Hall; Tamara Blett; Terry Carlson; Ann Mebane; Carol Hardy; Susan Rinehart; Linda Merigliano; David N. Cole; Andy Leach; Pam Wright; Deb Bumpus

    2009-01-01

    The purpose of monitoring wilderness character is to improve wilderness stewardship by providing managers a tool to assess how selected actions and conditions related to wilderness character are changing over time. Wilderness character monitoring provides information to help answer two key questions about wilderness character and wilderness stewardship: 1. How is...

  2. A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

    Directory of Open Access Journals (Sweden)

    Alamar Santiago

    2009-09-01

    Full Text Available Abstract Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new

  3. A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

    Science.gov (United States)

    Marques, M Carmen; Alonso-Cantabrana, Hugo; Forment, Javier; Arribas, Raquel; Alamar, Santiago; Conejero, Vicente; Perez-Amador, Miguel A

    2009-01-01

    Background Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation. Results We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis. Conclusion The new EST collection denotes an

  4. Caracteres moleculares para la determinación taxonómica de tres especies de Lutzomyia (Diptera: Psychodidae, vectores potenciales de Leishmania presentes en el valle de Aburrá, Colombia Molecular characters for the taxonomic determination of three species of Lutzomyia (Diptera: Psychodidae, potential Leishmania vectors found in the Aburrá valley, Colombia

    Directory of Open Access Journals (Sweden)

    Alveiro Pérez-Doria

    2008-12-01

    Full Text Available En Colombia están registradas 143 especies de Lutzomyia França, pero menos del 7% de éstas se encuentran incriminadas como vectores de Leishmania spp. Debido a la alta semejanza morfológica de algunas especies vectoras con otras no vectoras, se necesitan caracteres taxonómicos alternativos para identificar correctamente los flebotomíneos de cada zona geográfica del país. Con este objetivo, en el presente trabajo se secuenció el extremo 3' del gen mitocondrial que codifica para la proteína citocromo b en tres vectores potenciales de Leishmania presentes en el valle de Aburrá, Colombia, Lutzomyia hartmanni (Fairchild y Hertig, L. columbiana (Ristorcelli y Van Ty y L. tihuiliensis Le Pont, Torrez-Espejo y Dujardin. A partir del alineamiento múltiple de nucleótidos se determinaron los sitios polimórficos, las distancias genéticas pareadas netas (p y la entropía. Las secuencias de nucleótidos fueron trasladadas a aminoácidos para estimar el número de sustituciones sinónimas y no sinónimas. En el alineamiento múltiple de 321 nucleótidos del gen citocromo b de L. columbiana, L. hartmanni y L. tihuiliensis se detectaron 83 sustituciones. En la secuencia parcial de la proteína se encontraron 18 reemplazos de aminoácidos. Las distancias genéticas interespecíficas fluctuaron en un rango mínimo de 0,137 entre L. tihuiliensis y L. columbiana, y un máximo de 0,215 entre L. columbiana y L. hartmanni. Los polimorfismos detectados en la secuencia de nucleótidos del gen y de aminoácidos de la proteína constituyen caracteres moleculares potencialmente útiles para la determinación taxonómica de estas especies de flebotomíneos.To date, 143 species of Lutzomyia França are recorded in Colombia, but less than 7% is incriminated in the transmission of Leishmania spp. Alternative taxonomic characters are necessary to correctly identify the particular sand fly fauna in each Colombian region, and the separation of morphologically

  5. Effect of refractive error on temperament and character properties

    Institute of Scientific and Technical Information of China (English)

    Emine; Kalkan; Akcay; Fatih; Canan; Huseyin; Simavli; Derya; Dal; Hacer; Yalniz; Nagihan; Ugurlu; Omer; Gecici; Nurullah; Cagil

    2015-01-01

    AIM: To determine the effect of refractive error on temperament and character properties using Cloninger’s psychobiological model of personality.METHODS: Using the Temperament and Character Inventory(TCI), the temperament and character profiles of 41 participants with refractive errors(17 with myopia,12 with hyperopia, and 12 with myopic astigmatism) were compared to those of 30 healthy control participants.Here, temperament comprised the traits of novelty seeking, harm-avoidance, and reward dependence, while character comprised traits of self-directedness,cooperativeness, and self-transcendence.RESULTS: Participants with refractive error showed significantly lower scores on purposefulness,cooperativeness, empathy, helpfulness, and compassion(P <0.05, P <0.01, P <0.05, P <0.05, and P <0.01,respectively).CONCLUSION: Refractive error might have a negative influence on some character traits, and different types of refractive error might have different temperament and character properties. These personality traits may be implicated in the onset and/or perpetuation of refractive errors and may be a productive focus for psychotherapy.

  6. Glyph Identification and Character Recognition for Sindhi OCR

    Directory of Open Access Journals (Sweden)

    NISAR AHMEDMEMON

    2017-10-01

    Full Text Available A computer can read and write multiple languages and today?s computers are capable of understanding various human languages. A computer can be given instructions through various input methods but OCR (Optical Character Recognition and handwritten character recognition are the input methods in which a scanned page containing text is converted into written or editable text. The change in language text available on scanned page demands different algorithm to recognize text because every language and script pose varying number of challenges to recognize text. The Latin language recognition pose less difficulties compared to Arabic script and languages that use Arabic script for writing and OCR systems for these Latin languages are near to perfection. Very little work has been done on regional languages of Pakistan. In this paper the Sindhi glyphs are identified and the number of characters and connected components are identified for this regional language of Pakistan. A graphical user interface has been created to perform identification task for glyphs and characters of Sindhi language. The glyphs of characters are successfully identified from scanned page and this information can be used to recognize characters. The language glyph identification can be used to apply suitable algorithm to identify language as well as to achieve a higher recognition rate.

  7. Character, Social-Emotional, and Academic Outcomes among Underachieving Elementary School Students

    Science.gov (United States)

    Grier, Leslie K.

    2012-01-01

    One purpose of this research was to examine the psychometric properties of a character assessment scale (the Character Assessment for School Age Children; CASAC) based on 6 pillars of character (Josephson Institute, 2009). Many youth development and character education programs utilize some, if not all, of the pillars of character explicitly or…

  8. A Japanese logographic character frequency list for cognitive science research.

    Science.gov (United States)

    Chikamatsu, N; Yokoyama, S; Nozaki, H; Long, E; Fukuda, S

    2000-08-01

    This paper describes a Japanese logographic character (kanji) frequency list, which is based on an analysis of the largest recently available corpus of Japanese words and characters. This corpus comprised a full year of morning and evening editions of a major newspaper, containing more than 23 million kanji characters and more than 4,000 different kanji characters. This paper lists the 3,000 most frequent kanji characters, as well as an analysis of kanji usage and correlations between the present list and previous Japanese frequency lists. The authors believe that the present list will help researchers more accurately and efficiently control the selection of kanji characters in cognitive science research and interpret related psycholinguistic data.

  9. A database application for wilderness character monitoring

    Science.gov (United States)

    Ashley Adams; Peter Landres; Simon Kingston

    2012-01-01

    The National Park Service (NPS) Wilderness Stewardship Division, in collaboration with the Aldo Leopold Wilderness Research Institute and the NPS Inventory and Monitoring Program, developed a database application to facilitate tracking and trend reporting in wilderness character. The Wilderness Character Monitoring Database allows consistent, scientifically based...

  10. On character amenability of semigroup algebras | Maepa ...

    African Journals Online (AJOL)

    We study the character amenability of semigroup algebras. We work on general semigroups and certain semigroups such as inverse semigroups with a nite number of idempotents, inverse semigroups with uniformly locally nite idempotent set, Brandt and Rees semigroup and study the character amenability of the ...

  11. The Strategies for Character Building through Sports Participation

    OpenAIRE

    M.S. Omar-Fauzee; Mohd Nizam Nazarudin; Yudha M. Saputra; Nina Sutresna; Duangkrai Taweesuk; Wipoj Chansem; Rozita Abd. Latif; Soh Kim Geok

    2012-01-01

    The sport participation has been a major part of our life in the societies. Studies on sports participation have found that sports have both positive and negative influence on character buildings. It has been on-going debate on whether ‘sports build character’ but through literature analysis, author had found that ‘with the intention, sports do build character.’ Therefore, strategies of building character through sports are suggested in this paper.

  12. Total Moral Quality: A New Approach for Character Education in Pesantren

    Directory of Open Access Journals (Sweden)

    Hasan Baharun

    2017-06-01

    Full Text Available This paper presents the concept of character education in pesantren which gives valuable contributions to the success of moral development for students. It also offers a different paradigm in developing the concept of character building in educational institution. This article is inspired by the lack of effective character learning in a variety of formal educational institutions. Hence, the schools which succeed in instilling character education can be used as a reference to develop character education. This study focuses on character education model developed by pesantren and offers an alternative perspective of the development of character education in Indonesia. This study adopts a qualitative research approach and uses a case study design. The study shows that the model of character education in pesantren is carried out through a multi-disciplinary approach so as to provide maximum results for the development of character education. This study suggests that the Total Moral Quality (TMQ is the further development of Thomas Lickona’s concept of character education of moral modeling, moral knowing, moral feeling and moral habituation and is applicable in the school.

  13. Character context: a shape descriptor for Arabic handwriting recognition

    Science.gov (United States)

    Mudhsh, Mohammed; Almodfer, Rolla; Duan, Pengfei; Xiong, Shengwu

    2017-11-01

    In the handwriting recognition field, designing good descriptors are substantial to obtain rich information of the data. However, the handwriting recognition research of a good descriptor is still an open issue due to unlimited variation in human handwriting. We introduce a "character context descriptor" that efficiently dealt with the structural characteristics of Arabic handwritten characters. First, the character image is smoothed and normalized, then the character context descriptor of 32 feature bins is built based on the proposed "distance function." Finally, a multilayer perceptron with regularization is used as a classifier. On experimentation with a handwritten Arabic characters database, the proposed method achieved a state-of-the-art performance with recognition rate equal to 98.93% and 99.06% for the 66 and 24 classes, respectively.

  14. Video Game Characters. Theory and Analysis

    OpenAIRE

    Felix Schröter; Jan-Noël Thon

    2014-01-01

    This essay develops a method for the analysis of video game characters based on a theoretical understanding of their medium-specific representation and the mental processes involved in their intersubjective construction by video game players. We propose to distinguish, first, between narration, simulation, and communication as three modes of representation particularly salient for contemporary video games and the characters they represent, second, between narrative, ludic, and social experien...

  15. AcEST: DK943939 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU02A01NGRL0004_H07 354 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_H0...7. 5' end sequence. DK943939 - Show DK943939 Clone id YMU02A01NGRL0004_H07 Library YMU02 Length 354 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_H07. 5' end sequence. Accession DK943939 Tissue t... of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK943939|Adiantum capillus-ven... CYA LHPRAVNCRKK CGH+N+LRP KK++ Sbjct: 1 IIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK 52 TrEMBL (release 39

  16. AcEST: DK951212 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST38A01NGRL0010_M18 620 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0010_M1...8. 5' end sequence. DK951212 CL3520Contig1 Show DK951212 Clone id TST38A01NGRL0010_M18 Library TST38 Length ...620 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0010_M18. 5' end sequence. Accession DK951212...rotein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK951212|Adiantum capillus-veneris ...mRNA, clone: TST38A01NGRL0010_M18, 5' (620 letters) Database: uniprot_sprot.fasta 412

  17. AcEST: DK959999 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0006_D09 669 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0006_D0...9. 5' end sequence. DK959999 - Show DK959999 Clone id TST39A01NGRL0006_D09 Library TST39 Length 669 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0006_D09. 5' end sequence. Accession DK959999 Tissue t...nce: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller,...s, Nucleic Acids Res. 25:3389-3402. Query= DK959999|Adiantum capillus-veneris mRN

  18. AcEST: DK949999 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST38A01NGRL0007_H20 715 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0007_H2...0. 5' end sequence. DK949999 CL70Contig1 Show DK949999 Clone id TST38A01NGRL0007_H20 Library TST38 Length 71...5 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0007_H20. 5' end sequence. Accession DK949999...haffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a n...ew generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK949999

  19. AcEST: DK962014 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK962014 CL62Contig1 Show DK962014 Clone id TST39A01NGRL0011_L13 Library TST39 Length 67...5 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0011_L13. 5' end sequence. Accession DK962014...rams, Nucleic Acids Res. 25:3389-3402. Query= DK962014|Adiantum capillus-veneris ... search programs, Nucleic Acids Res. 25:3389-3402. Query= DK962014|Adiantum capillus-veneris mRNA, clone: TS...TST39A01NGRL0011_L13 675 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0011_L1

  20. AcEST: DK952014 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK952014 CL132Contig1 Show DK952014 Clone id TST38A01NGRL0012_P06 Library TST38 Length 6...73 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0012_P06. 5' end sequence. Accession DK952014...Acids Res. 25:3389-3402. Query= DK952014|Adiantum capillus-veneris mRNA, clone: T...protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK952014|Adiantum capillus-veneris...TST38A01NGRL0012_P06 673 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0012_P0

  1. AcEST: DK954069 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 9. 5' end sequence. DK954069 CL33Contig1 Show DK954069 Clone id TST39A01NGRL0019_H09 Library TST39 Length 58...8 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H09. 5' end sequence. Accession DK95406...f protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK954069|Adiantum capillus-vener...T: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95406...TST39A01NGRL0019_H09 588 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H0

  2. AcEST: DK956406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK956406 CL111Contig1 Show DK956406 Clone id TST39A01NGRL0025_K13 Library TST39 Length 5...91 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0025_K13. 5' end sequence. Accession DK956406...LAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK956406...tr... 231 2e-60 sp|P53445|ALF1_LAMJA Fructose-bisphosphate aldolase, muscle type... 229 6e-60 sp|Q40677|ALFC...ew generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK956406

  3. AcEST: DK946406 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK946406 - Show DK946406 Clone id YMU02A01NGRL0012_I08 Library YMU02 Length 540 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0012_I08. 5' end sequence. Accession DK946406 Tissue t... protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK946406|Adiantum capillus-veneri...chizosacch... 121 2e-27 sp|O14062|RS12A_SCHPO 40S ribosomal protein S12-A OS=Schizosacch... 121 2e-27 sp|Q54... new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK946406

  4. AcEST: DK944064 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK944064 CL53Contig1 Show DK944064 Clone id YMU02A01NGRL0004_N23 Library YMU02 Length 49...9 Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N23. 5' end sequence. Accession DK94406...ion of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944064|Adiantum capillus-...ration of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944064|Adiantum capill...YMU02A01NGRL0004_N23 499 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N2

  5. AcEST: DK944062 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 0. 5' end sequence. DK944062 CL98Contig1 Show DK944062 Clone id YMU02A01NGRL0004_N20 Library YMU02 Length 42...5 Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N20. 5' end sequence. Accession DK94406... programs, Nucleic Acids Res. 25:3389-3402. Query= DK944062|Adiantum capillus-ven...ion of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944062|Adiantum capillus-...YMU02A01NGRL0004_N20 425 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N2

  6. AcEST: DK962099 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK962099 CL3534Contig1 Show DK962099 Clone id TST39A01NGRL0011_P06 Library TST39 Length ...641 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0011_P06. 5' end sequence. Accession DK962099... a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK962099...97), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25...TST39A01NGRL0011_P06 641 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0011_P0

  7. AcEST: DK958014 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 7. 5' end sequence. DK958014 CL177Contig1 Show DK958014 Clone id TST39A01NGRL0029_O07 Library TST39 Length 6...74 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O07. 5' end sequence. Accession DK95801...ein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958014|Ad...binding protein 1 OS=Drosophila melanogaster GN=CG8801 PE=2 SV=1 Length = 652 Sco...ds Res. 25:3389-3402. Query= DK958014|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0029_O07, 5' (674 l

  8. AcEST: DK958016 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 9. 5' end sequence. DK958016 - Show DK958016 Clone id TST39A01NGRL0029_O09 Library TST39 Length 624 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O09. 5' end sequence. Accession DK958016 Tissue t...a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958016|Adian... a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958016|Adia...TST39A01NGRL0029_O09 624 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O0

  9. AcEST: DK958013 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 6. 5' end sequence. DK958013 - Show DK958013 Clone id TST39A01NGRL0029_O06 Library TST39 Length 670 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O06. 5' end sequence. Accession DK958013 Tissue t...7), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95801...n database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958013|Adia...TST39A01NGRL0029_O06 670 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O0

  10. AcEST: DK948011 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 0. 5' end sequence. DK948011 CL3356Contig1 Show DK948011 Clone id TST38A01NGRL0002_C20 Library TST38 Length ...682 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C20. 5' end sequence. Accession DK94801...cleic Acids Res. 25:3389-3402. Query= DK948011|Adiantum capillus-veneris mRNA, cl...eration of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948011|Adiantum capil...TST38A01NGRL0002_C20 682 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C2

  11. AcEST: DK958011 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK958011 - Show DK958011 Clone id TST39A01NGRL0029_O04 Library TST39 Length 670 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O04. 5' end sequence. Accession DK958011 Tissue t... programs, Nucleic Acids Res. 25:3389-3402. Query= DK958011|Adiantum capillus-ven...ation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958011|Adiantum capillu...TST39A01NGRL0029_O04 670 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O0

  12. AcEST: DK948016 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK948016 CL5Contig2 Show DK948016 Clone id TST38A01NGRL0002_D01 Library TST38 Length 698... Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_D01. 5' end sequence. Accession DK948016... 25:3389-3402. Query= DK948016|Adiantum capillus-veneris mRNA, clone: TST38A01NGR...grams, Nucleic Acids Res. 25:3389-3402. Query= DK948016|Adiantum capillus-veneris...TST38A01NGRL0002_D01 698 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_D0

  13. CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION

    Directory of Open Access Journals (Sweden)

    Nikolaos Alachiotis

    2013-03-01

    Full Text Available Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG, an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

  14. Computational Design of Animated Mechanical Characters

    Science.gov (United States)

    Coros, Stelian; Thomaszewski, Bernhard; DRZ Team Team

    2014-03-01

    A factor key to the appeal of modern CG movies and video-games is that the virtual worlds they portray place no bounds on what can be imagined. Rapid manufacturing devices hold the promise of bringing this type of freedom to our own world, by enabling the fabrication of physical objects whose appearance, deformation behaviors and motions can be precisely specified. In order to unleash the full potential of this technology however, computational design methods that create digital content suitable for fabrication need to be developed. In recent work, we presented a computational design system that allows casual users to create animated mechanical characters. Given an articulated character as input, the user designs the animated character by sketching motion curves indicating how they should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices.

  15. Optical Character Recognition.

    Science.gov (United States)

    Converso, L.; Hocek, S.

    1990-01-01

    This paper describes computer-based optical character recognition (OCR) systems, focusing on their components (the computer, the scanner, the OCR, and the output device); how the systems work; and features to consider in selecting a system. A list of 26 questions to ask to evaluate systems for potential purchase is included. (JDD)

  16. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

    Directory of Open Access Journals (Sweden)

    Weis Patrick

    2010-01-01

    Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

  17. Developing Individual and Team Character in Sport

    Science.gov (United States)

    Gaines, Stacey A.

    2012-01-01

    The idea that participation in sport builds character is a long-standing one. Advocates of sport participation believe that sport provides an appropriate context for the learning of social skills such as cooperation and the development of prosocial behavior (Weiss, Smith, & Stuntz, 2008). Research in sport regarding character development has…

  18. Personality, temperament and character in Erich Fromm's theory

    Directory of Open Access Journals (Sweden)

    Redžić Saduša F.

    2012-01-01

    Full Text Available The character of the man is the substitute for instincts that animals have. In reality characters are not found in pure form, as specified orientation, but as a mixture of types. The social character of Fromm has an ethical and heuristic importance. Human passions are rooted in character and are a way to give meaning to existence, to respond to the human existential situation. If we are not able to respond through the love, then, in the absence of, we turn to destructiveness. According to Fromm, the most important goal of society should be human development. He lays down a rational belief in critical thought coupled with love of life. Although the development of personality is largely determined by social structure, Fromm concludes it is not entirely passive, that a man has the opportunity, space and power to use his mind to react to the alienation and inhumane living conditions. Through analysis of the social character From is giving a kind of critique of modern, market-oriented society, based on the principles of humanistic ethics. .

  19. Membangun Karakter Anak Usia Dini melalui Pembelajaran Math Character

    Directory of Open Access Journals (Sweden)

    Titin Faridatun Nisa’

    2016-09-01

    Full Text Available Penelitian ini bertujuan untuk mengetahui penerapan pembelajaran math character untuk membangun karakter Anak Usia Dini (AUD dan kesulitan-kesulitan yang dialami guru dalam penerapan pembelajaran math character. Target penelitian ini adalah terbentuknya karakter anak usia dini melalui pembelajaran math character. Jenis penelitian ini adalah penelitian deskriptif dengan metode penelitian kualitatif. Teknik pengumpulan informasi penelitian ini dengan metode observasi dan wawancara. Analisis data penelitian ini menggunakan analisis deskriptif. Hasil penelitian menunjukkan bahwa penerapan pembelajaran math character dapat membangun delapan belas nilai-nilai karakter AUD. Kesulitan-kesulitan yang dialami guru dalam pembentukan karakter AUD melalui pembelajaran math character meliputi tema yang digunakan termasuk tema baru, siswa belum terbiasa dengan pembelajaran berbasis sentra, usia siswa bervariasi, dan adanya ikut campur wali siswa dalam kegiatan pembelajaran di kelas sehingga siswa menjadi kurang mandiri.

  20. Chinese character recognition based on Gabor feature extraction and CNN

    Science.gov (United States)

    Xiong, Yudian; Lu, Tongwei; Jiang, Yongyuan

    2018-03-01

    As an important application in the field of text line recognition and office automation, Chinese character recognition has become an important subject of pattern recognition. However, due to the large number of Chinese characters and the complexity of its structure, there is a great difficulty in the Chinese character recognition. In order to solve this problem, this paper proposes a method of printed Chinese character recognition based on Gabor feature extraction and Convolution Neural Network(CNN). The main steps are preprocessing, feature extraction, training classification. First, the gray-scale Chinese character image is binarized and normalized to reduce the redundancy of the image data. Second, each image is convoluted with Gabor filter with different orientations, and the feature map of the eight orientations of Chinese characters is extracted. Third, the feature map through Gabor filters and the original image are convoluted with learning kernels, and the results of the convolution is the input of pooling layer. Finally, the feature vector is used to classify and recognition. In addition, the generalization capacity of the network is improved by Dropout technology. The experimental results show that this method can effectively extract the characteristics of Chinese characters and recognize Chinese characters.

  1. Characterization of expressed sequence tag-derived simple sequence repeat markers for Aspergillus flavus: emphasis on variability of isolates from the southern United States.

    Science.gov (United States)

    Wang, Xinwang; Wadl, Phillip A; Wood-Jones, Alicia; Windham, Gary; Trigiano, Robert N; Scruggs, Mary; Pilgrim, Candace; Baird, Richard

    2012-12-01

    Simple sequence repeat (SSR) markers were developed from Aspergillus flavus expressed sequence tag (EST) database to conduct an analysis of genetic relationships of Aspergillus isolates from numerous host species and geographical regions, but primarily from the United States. Twenty-nine primers were designed from 362 tri-nucleotide EST-SSR sequences. Eighteen polymorphic loci were used to genotype 96 Aspergillus species isolates. The number of alleles detected per locus ranged from 2 to 24 with a mean of 8.2 alleles. Haploid diversity ranged from 0.28 to 0.91. Genetic distance matrix was used to perform principal coordinates analysis (PCA) and to generate dendrograms using unweighted pair group method with arithmetic mean (UPGMA). Two principal coordinates explained more than 75 % of the total variation among the isolates. One clade was identified for A. flavus isolates (n = 87) with the other Aspergillus species (n = 7) using PCA, but five distinct clusters were present when the others taxa were excluded from the analysis. Six groups were noted when the EST-SSR data were compared using UPGMA. However, the latter PCA or UPGMA comparison resulted in no direct associations with host species, geographical region or aflatoxin production. Furthermore, there was no direct correlation to visible morphological features such as sclerotial types. The isolates from Mississippi Delta region, which contained the largest percentage of isolates, did not show any unusual clustering except for isolates K32, K55, and 199. Further studies of these three isolates are warranted to evaluate their pathogenicity, aflatoxin production potential, additional gene sequences (e.g., RPB2), and morphological comparisons.

  2. Studies on Dasyaceae. 3. Towards a phylogeny of the Dasyaceae (Ceramiales, Rhodophyta), based on comparative rbcL gene sequences and morphology

    NARCIS (Netherlands)

    de Jong, Y.S D M; van der Wurff, A.W G; Stam, W.T.; Olsen, J.L.

    Phylogenetic analyses of the Dasyaceae based on sequence analysis of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and 42 morphological characters are presented. Comparative sequence analysis confirms the general view of the Ceramiaceae as a primitive, paraphyletic

  3. A Chinese character teaching system using structure theory and morphing technology.

    Science.gov (United States)

    Sun, Linjia; Liu, Min; Hu, Jiajia; Liang, Xiaohui

    2014-01-01

    This paper proposes a Chinese character teaching system by using the Chinese character structure theory and the 2D contour morphing technology. This system, including the offline phase and the online phase, automatically generates animation for the same Chinese character from different writing stages to intuitively show the evolution of shape and topology in the process of Chinese characters teaching. The offline phase builds the component models database for the same script and the components correspondence database for different scripts. Given two or several different scripts of the same Chinese character, the online phase firstly divides the Chinese characters into components by using the process of Chinese character parsing, and then generates the evolution animation by using the process of Chinese character morphing. Finally, two writing stages of Chinese characters, i.e., seal script and clerical script, are used in experiment to show the ability of the system. The result of the user experience study shows that the system can successfully guide students to improve the learning of Chinese characters. And the users agree that the system is interesting and can motivate them to learn.

  4. A Chinese character teaching system using structure theory and morphing technology.

    Directory of Open Access Journals (Sweden)

    Linjia Sun

    Full Text Available This paper proposes a Chinese character teaching system by using the Chinese character structure theory and the 2D contour morphing technology. This system, including the offline phase and the online phase, automatically generates animation for the same Chinese character from different writing stages to intuitively show the evolution of shape and topology in the process of Chinese characters teaching. The offline phase builds the component models database for the same script and the components correspondence database for different scripts. Given two or several different scripts of the same Chinese character, the online phase firstly divides the Chinese characters into components by using the process of Chinese character parsing, and then generates the evolution animation by using the process of Chinese character morphing. Finally, two writing stages of Chinese characters, i.e., seal script and clerical script, are used in experiment to show the ability of the system. The result of the user experience study shows that the system can successfully guide students to improve the learning of Chinese characters. And the users agree that the system is interesting and can motivate them to learn.

  5. Character Education of the Most Developed Countries in ASEAN

    Science.gov (United States)

    Istiningsih

    2016-01-01

    Character education into an international issue, especially in developing countries. More specifically in Indonesia, character education is a major issue in the 2012's to the present. What kind of education that may build character? To be able to answer this question, we need a broad and deep research. Research simpler related to character…

  6. Character Education in Three Schools: Catholic, Quaker and Public

    Science.gov (United States)

    Meidl, Christopher; Meidl, Tynisha

    2013-01-01

    Character education has always played a role in the purpose of schools. Most US states have a statement about character education as a part of the mission of the schools. This research studied how character education was perceived by participants in regards to school mission statements/philosophies, school atmosphere and curriculum in a Catholic…

  7. An expressed sequence tag (EST) data mining strategy succeeding in the discovery of new G-protein coupled receptors.

    Science.gov (United States)

    Wittenberger, T; Schaller, H C; Hellebrand, S

    2001-03-30

    We have developed a comprehensive expressed sequence tag database search method and used it for the identification of new members of the G-protein coupled receptor superfamily. Our approach proved to be especially useful for the detection of expressed sequence tag sequences that do not encode conserved parts of a protein, making it an ideal tool for the identification of members of divergent protein families or of protein parts without conserved domain structures in the expressed sequence tag database. At least 14 of the expressed sequence tags found with this strategy are promising candidates for new putative G-protein coupled receptors. Here, we describe the sequence and expression analysis of five new members of this receptor superfamily, namely GPR84, GPR86, GPR87, GPR90 and GPR91. We also studied the genomic structure and chromosomal localization of the respective genes applying in silico methods. A cluster of six closely related G-protein coupled receptors was found on the human chromosome 3q24-3q25. It consists of four orphan receptors (GPR86, GPR87, GPR91, and H963), the purinergic receptor P2Y1, and the uridine 5'-diphosphoglucose receptor KIAA0001. It seems likely that these receptors evolved from a common ancestor and therefore might have related ligands. In conclusion, we describe a data mining procedure that proved to be useful for the identification and first characterization of new genes and is well applicable for other gene families. Copyright 2001 Academic Press.

  8. AcEST: DK953939 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0019_B19 645 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_B1...9. 5' end sequence. DK953939 CL12Contig1 Show DK953939 Clone id TST39A01NGRL0019_B19 Library TST39 Length 64...5 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_B19. 5' end sequence. Accession DK953939...ase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK953939|Adiantum ca...pillus-veneris mRNA, clone: TST39A01NGRL0019_B19, 5' (645 letters) Database: uniprot_sprot.fasta 412,525 seq

  9. AcEST: DK943636 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU02A01NGRL0003_H12 321 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0003_H1...2. 5' end sequence. DK943636 CL16Contig1 Show DK943636 Clone id YMU02A01NGRL0003_H12 Library YMU02 Length 32...1 Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0003_H12. 5' end sequence. Accession DK943636...f protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK943636|Adiantum capillus-vener...T and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK943636

  10. AcEST: DK953636 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0018_E20 327 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0018_E2...0. 5' end sequence. DK953636 - Show DK953636 Clone id TST39A01NGRL0018_E20 Library TST39 Length 327 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0018_E20. 5' end sequence. Accession DK953636 Tissue t...d BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK953636... generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK953636|Adiantum c

  11. AcEST: DK961212 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0009_I01 591 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0009_I0...1. 5' end sequence. DK961212 - Show DK961212 Clone id TST39A01NGRL0009_I01 Library TST39 Length 591 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0009_I01. 5' end sequence. Accession DK961212 Tissue t...eration of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK961212|Adiantum capil...lus-veneris mRNA, clone: TST39A01NGRL0009_I01, 5' (591 letters) Database: uniprot_sprot.fasta 412

  12. AcEST: DK944060 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK944060 CL1Contig3 Show DK944060 Clone id YMU02A01NGRL0004_N18 Library YMU02 Length 496... Definition Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N18. 5' end sequence. Accession DK944060...tabase search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944060|Adiantum capillus-veneris mRNA, clo... 25:3389-3402. Query= DK944060|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL0004_N18, 5' (466 letters)...YMU02A01NGRL0004_N18 496 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0004_N1

  13. AcEST: DK954061 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK954061 - Show DK954061 Clone id TST39A01NGRL0019_H01 Library TST39 Length 594 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H01. 5' end sequence. Accession DK954061 Tissue t...w generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK954061|Adiantum ...T and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95406...TST39A01NGRL0019_H01 594 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H0

  14. AcEST: DK954064 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK954064 CL947Contig1 Show DK954064 Clone id TST39A01NGRL0019_H04 Library TST39 Length 7...69 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H04. 5' end sequence. Accession DK95406... of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK954064|Adiantum capillus-ven...cleic Acids Res. 25:3389-3402. Query= DK954064|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0019_H04, ...TST39A01NGRL0019_H04 769 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H0

  15. AcEST: DK954060 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK954060 CL412Contig1 Show DK954060 Clone id TST39A01NGRL0019_G24 Library TST39 Length 6...26 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_G24. 5' end sequence. Accession DK95406...s Res. 25:3389-3402. Query= DK954060|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0019_G24, 5' (626 le...generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK954060|Adiantum ca...TST39A01NGRL0019_G24 626 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_G2

  16. AcEST: DK954065 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 5. 5' end sequence. DK954065 CL168Contig1 Show DK954065 Clone id TST39A01NGRL0019_H05 Library TST39 Length 6...25 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H05. 5' end sequence. Accession DK95406... PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95406...ids Res. 25:3389-3402. Query= DK954065|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0019_H05, 5' (625 ...TST39A01NGRL0019_H05 625 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0019_H0

  17. AcEST: DK961000 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK961000 - Show DK961000 Clone id TST39A01NGRL0008_O23 Library TST39 Length 653 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0008_O23. 5' end sequence. Accession DK961000 Tissue t... BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK961000...eic Acids Res. 25:3389-3402. Query= DK961000|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0008_O23, 5'...TST39A01NGRL0008_O23 653 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0008_O2

  18. AcEST: DK951000 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK951000 CL11Contig1 Show DK951000 Clone id TST38A01NGRL0010_D14 Library TST38 Length 63...5 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0010_D14. 5' end sequence. Accession DK951000... of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK951000|Adiantum capillus-ven...25:3389-3402. Query= DK951000|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0010_D14, 5' (635 letters) ...TST38A01NGRL0010_D14 635 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0010_D1

  19. AcEST: DK944200 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK944200 - Show DK944200 Clone id YMU02A01NGRL0005_E18 Library YMU02 Length 232 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0005_E18. 5' end sequence. Accession DK944200 Tissue t...ams, Nucleic Acids Res. 25:3389-3402. Query= DK944200|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL000...database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK944200|Adiantum capillus-veneris mRNA, c...YMU02A01NGRL0005_E18 232 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0005_E1

  20. AcEST: DK952099 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK952099 CL720Contig1 Show DK952099 Clone id TST38A01NGRL0013_C22 Library TST38 Length 5...79 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0013_C22. 5' end sequence. Accession DK952099..., Nucleic Acids Res. 25:3389-3402. Query= DK952099|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0013_C...n database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK952099|Adiantum capillus-veneris mRNA,...TST38A01NGRL0013_C22 579 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0013_C2

  1. AcEST: DK948012 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1. 5' end sequence. DK948012 CL61Contig1 Show DK948012 Clone id TST38A01NGRL0002_C21 Library TST38 Length 63...2 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C21. 5' end sequence. Accession DK94801...eneration of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948012|Adiantum cap...ST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK948012|A...TST38A01NGRL0002_C21 632 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C2

  2. AcEST: DK948013 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK948013 - Show DK948013 Clone id TST38A01NGRL0002_C22 Library TST38 Length 680 Definiti...on Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C22. 5' end sequence. Accession DK948013 Tissue t...-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK94801...ms, Nucleic Acids Res. 25:3389-3402. Query= DK948013|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0002...TST38A01NGRL0002_C22 680 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C2

  3. AcEST: DK958019 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK958019 - Show DK958019 Clone id TST39A01NGRL0029_O12 Library TST39 Length 641 Definiti...on Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O12. 5' end sequence. Accession DK958019 Tissue t...AST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95801...a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958019|Adian...TST39A01NGRL0029_O12 641 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O1

  4. AcEST: DK948015 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4. 5' end sequence. DK948015 CL1717Contig1 Show DK948015 Clone id TST38A01NGRL0002_C24 Library TST38 Length ...543 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C24. 5' end sequence. Accession DK94801...ids Res. 25:3389-3402. Query= DK948015|Adiantum capillus-veneris mRNA, clone: TST38A01NGRL0002_C24, 5' (486 ...TST38A01NGRL0002_C24 543 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_C2...997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 2

  5. AcEST: DK948017 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 2. 5' end sequence. DK948017 CL1579Contig1 Show DK948017 Clone id TST38A01NGRL0002_D02 Library TST38 Length ...638 Definition Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_D02. 5' end sequence. Accession DK94801...BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK94801...rch programs, Nucleic Acids Res. 25:3389-3402. Query= DK948017|Adiantum capillus-veneris mRNA, clone: TST38A...TST38A01NGRL0002_D02 638 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0002_D0

  6. AcEST: DK958010 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3. 5' end sequence. DK958010 CL175Contig1 Show DK958010 Clone id TST39A01NGRL0029_O03 Library TST39 Length 6...65 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O03. 5' end sequence. Accession DK95801...of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95801...c Acids Res. 25:3389-3402. Query= DK958010|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0029_O03, 5' (...tive uncharacterized protein OS=Picea... 115 3e-24 tr|A8Y801|A8Y801_ZANAE Rieske iron-sulphur protein OS=Zan

  7. AcEST: DK958017 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 0. 5' end sequence. DK958017 CL232Contig1 Show DK958017 Clone id TST39A01NGRL0029_O10 Library TST39 Length 6...34 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O10. 5' end sequence. Accession DK95801...eic Acids Res. 25:3389-3402. Query= DK958017|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0029_O10, 5'...ew generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK958017|Adiantum...TST39A01NGRL0029_O10 634 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O1

  8. AcEST: DK947373 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU02A01NGRL0015_K22 477 Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0015_K2...2. 5' end sequence. DK947373 - Show DK947373 Clone id YMU02A01NGRL0015_K22 Library YMU02 Length 477 Definiti...on Adiantum capillus-veneris mRNA. clone: YMU02A01NGRL0015_K22. 5' end sequence. Accession DK947373 Tissue t...t (release 56.9) Link to BlastX Result : Swiss-Prot sp_hit_id P17673 Definition sp|P17673...ams, Nucleic Acids Res. 25:3389-3402. Query= DK947373|Adiantum capillus-veneris mRNA, clone: YMU02A01NGRL001

  9. AcEST: DK957373 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0028_D04 652 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0028_D0...4. 5' end sequence. DK957373 CL831Contig1 Show DK957373 Clone id TST39A01NGRL0028_D04 Library TST39 Length 6...52 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0028_D04. 5' end sequence. Accession DK957373...ams, Nucleic Acids Res. 25:3389-3402. Query= DK957373|Adiantum capillus-veneris m...reus (... 59 2e-08 sp|Q818F0|DNAJ_BACCR Chaperone protein dnaJ OS=Bacillus cereus (... 59 2e-08 sp|Q73

  10. Relationships between Character Education and School Climate

    Science.gov (United States)

    Karaburk, Hasan

    2017-01-01

    The purpose of this study was to explore the relationships between character education and school climate based on the lived experiences and beliefs of teachers. The research was conducted in a public middle school to explore understandings and beliefs of teachers about character education and its perceived impact on school climate. Social…

  11. "It Could Affect You as a Person, Character-Wise": Promoting Character Development and Preventing Sexual Violence at West Point

    Science.gov (United States)

    Arbeit, Miriam R.

    2017-01-01

    The United States Military Academy at West Point develops cadets into "leaders of character" who will become Army officers. This focus on character presents an opportunity for the prevention of sexual violence through an emphasis on military values. Using constructivist grounded theory, this study examined how cadets experience their own…

  12. Integrating Character Education In Teaching Speaking For Business Administration Students

    OpenAIRE

    Woro Prastiwi, Chyntia Heru

    2016-01-01

    Globalization along with the advancement of information and communication technology has brought tremendous effects on students' character. Education field as a place of community has to contribute in developing students' character traits. Integrating character education in curriculum is the key for qualified education. This research aimed to describe the way to integrate character education in teaching speaking for Business Administration students. The data was obtained from teaching and lea...

  13. Distribution of DNA repair-related ESTs in sugarcane

    Directory of Open Access Journals (Sweden)

    W.C. Lima

    2001-12-01

    Full Text Available DNA repair pathways are necessary to maintain the proper genomic stability and ensure the survival of the organism, protecting it against the damaging effects of endogenous and exogenous agents. In this work, we made an analysis of the expression patterns of DNA repair-related genes in sugarcane, by determining the EST (expressed sequence tags distribution in the different cDNA libraries of the SUCEST transcriptome project. Three different pathways - photoreactivation, base excision repair and nucleotide excision repair - were investigated by employing known DNA repair proteins as probes to identify homologous ESTs in sugarcane, by means of computer similarity search. The results showed that DNA repair genes may have differential expressions in tissues, depending on the pathway studied. These in silico data provide important clues on the potential variation of gene expression, to be confirmed by direct biochemical analysis.As vias de reparo de DNA são requeridas para manter a necessária estabilidade genômica e garantir a sobrevivência do organismo, frente aos efeitos deletérios causados por fatores endógenos e exógenos. Neste trabalho, realizamos a análise dos padrões de expressão dos genes de reparo de DNA encontrados na cana-de-açúcar, pela determinação da distribuição de ESTs nas diferentes bibliotecas de cDNA no projeto de transcriptoma SUCEST. Três vias de reparo - fotorreativação, reparo por excisão de bases e reparo por excisão de nucleotídeos - foram estudadas através do uso de proteínas de reparo como sondas para identificação de ESTs homólogos em cana-de-açúcar, com base na procura computacional de similaridade. Os resultados indicam que os genes de reparo de DNA possuem uma expressão diferencial nos tecidos, dependendo da via de reparo analisada. Esses dados in silico fornecem importantes indícios da expressão diferencial, a qual deve ser confirmada por análises bioquímicas diretas.

  14. ECONOMIC ETHICS: APPLIED AND PROFESSIONAL CHARACTER

    Directory of Open Access Journals (Sweden)

    Ella Gordova

    2012-01-01

    Full Text Available In given article economic ethics are considered as set of norms of behavior of the businessman, the requirements shown by a cultural society to its style of work, to character of dialogue between participants of business, to their social shape. The conclusion becomes that economic ethics have applied character in relation to theoretical, to obschenormativnoy ethics, hence, represent section of applied ethics. On the other hand, the specific standard maintenance characterizes economic ethics as ethics professional.

  15. Googling DNA sequences on the World Wide Web.

    Science.gov (United States)

    Hajibabaei, Mehrdad; Singer, Gregory A C

    2009-11-10

    New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

  16. Diradical character of some fluoranthenes

    Directory of Open Access Journals (Sweden)

    SVETLANA MARKOVIĆ

    2010-09-01

    Full Text Available It is shown that some Kekuléan fluoranthenes are diradicals and that their ground state is a triplet. In the energetically less favorable singlet state, these hydrocarbons also exhibit pronounced diradical character. The diradical character y of the compounds under investigation was estimated using the unrestricted symmetry-broken (yPUHF and complete active space (yNOON methods. It was found that the yPUHF values better reproduce the diradical character of the investigated hydrocarbons. It was shown that singly occupied molecular orbital (SOMO and SOMO-1 of a diradical structure occupy different parts of space with a small shared region, resulting in a spin density distribution over the entire molecule. The spatial diradical distribution in the singlet diradical structures was examined by inspecting the HOMOs and LUMOs for a and b spin electrons. It was shown that the a-HOMO and the b-LUMO (as well as the b-HOMO and the a-LUMO occupy practically the same part of space. In this way, there are no unpaired electrons in a singlet diradical structure, yet two of them occupy different parts of space, thus allowing the p-electrons to delocalize.

  17. Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides.

    Science.gov (United States)

    Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

    2015-09-01

    Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

  18. A novel handwritten character recognition system using gradient ...

    Indian Academy of Sciences (India)

    The issues faced by the handwritten character recognition systems are the similarity. ∗ ... tical/structural features have also been successfully used in character ..... The coordinates (xc, yc) of centroid are calculated by equations (4) and (5). xc =.

  19. AcEST: DK958012 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 5. 5' end sequence. DK958012 CL314Contig1 Show DK958012 Clone id TST39A01NGRL0029_O05 Library TST39 Length 6...84 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O05. 5' end sequence. Accession DK95801...s. 25:3389-3402. Query= DK958012|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0029_O05, 5' (684 letter..., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95801...TST39A01NGRL0029_O05 684 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O0

  20. AcEST: DK958015 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 8. 5' end sequence. DK958015 CL1173Contig1 Show DK958015 Clone id TST39A01NGRL0029_O08 Library TST39 Length ...239 Definition Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O08. 5' end sequence. Accession DK95801... Nucleic Acids Res. 25:3389-3402. Query= DK958015|Adiantum capillus-veneris mRNA, clone: TST39A01NGRL0029_O0...d BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= DK95801...TST39A01NGRL0029_O08 239 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0029_O0

  1. Peter as character in the Gospel of Matthew: complexity and inversion

    Directory of Open Access Journals (Sweden)

    João Leonel

    2014-03-01

    Full Text Available This article focuses on the apostle Peter as a character in the Gospel of Matthew.  It aims at identifying the nuances and changes of the character Peter in the Gospel. For this purpose, I take as a starting point that the gospel belongs to the literary genre of ancient Greco-Roman Biography, which presents Jesus Christ as the protagonist. The other characters are developed in relationship with him. The same is true with the Apostle Peter. The article unfolds from narrative theory, in particular the categorization of characters. I categorize, based on Erich Auerbach and Robert Alter, the features of biblical characters, developing comparisons with theories of the character in the modern novel. The analysis of the main texts from the Gospel of Matthew that portray the character Peter leads to the conclusion that its main features are complexity and inversion. They produce an overview of the involution of the character in the narrative of the Gospel of Matthew.

  2. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

  3. Automated Degradation Diagnosis in Character Recognition System Subject to Camera Vibration

    Directory of Open Access Journals (Sweden)

    Chunmei Liu

    2014-01-01

    Full Text Available Degradation diagnosis plays an important role for degraded character processing, which can tell the recognition difficulty of a given degraded character. In this paper, we present a framework for automated degraded character recognition system by statistical syntactic approach using 3D primitive symbol, which is integrated by degradation diagnosis to provide accurate and reliable recognition results. Our contribution is to design the framework to build the character recognition submodels corresponding to degradation subject to camera vibration or out of focus. In each character recognition submodel, statistical syntactic approach using 3D primitive symbol is proposed to improve degraded character recognition performance. In the experiments, we show attractive experimental results, highlighting the system efficiency and recognition performance by statistical syntactic approach using 3D primitive symbol on the degraded character dataset.

  4. Distributional Similarity for Chinese: Exploiting Characters and Radicals

    Directory of Open Access Journals (Sweden)

    Peng Jin

    2012-01-01

    Full Text Available Distributional Similarity has attracted considerable attention in the field of natural language processing as an automatic means of countering the ubiquitous problem of sparse data. As a logographic language, Chinese words consist of characters and each of them is composed of one or more radicals. The meanings of characters are usually highly related to the words which contain them. Likewise, radicals often make a predictable contribution to the meaning of a character: characters that have the same components tend to have similar or related meanings. In this paper, we utilize these properties of the Chinese language to improve Chinese word similarity computation. Given a content word, we first extract similar words based on a large corpus and a similarity score for ranking. This rank is then adjusted according to the characters and components shared between the similar word and the target word. Experiments on two gold standard datasets show that the adjusted rank is superior and closer to human judgments than the original rank. In addition to quantitative evaluation, we examine the reasons behind errors drawing on linguistic phenomena for our explanations.

  5. AcEST: BP915821 [AcEST

    Lifescience Database Archive (English)

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  6. AcEST: DK945353 [AcEST

    Lifescience Database Archive (English)

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  8. AcEST: BP920666 [AcEST

    Lifescience Database Archive (English)

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  9. Meeting Characters in Caldecotts: What Does This Mean for Today's Readers?

    Science.gov (United States)

    Koss, Melanie D.; Martinez, Miriam; Johnson, Nancy J.

    2016-01-01

    We examined representations of main characters in Caldecott Award winner and honor books over the past 25 years. Each book containing a human main character was coded for the following features: culture/ethnicity, gender, age, place where character lives, time period in which the character lives, disability, religion, socioeconomic status, and…

  10. AcEST: BP920339 [AcEST

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

    Full Text Available blast op. Sequence too short.) sp_hit_id - Definition - Align length - Score (bit) - E-value - Report - TrE...t.) tr_hit_id - Definition - Align length - Score (bit) - E-value - Report - ...

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    Lifescience Database Archive (English)

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  14. AcEST: BP917667 [AcEST

    Lifescience Database Archive (English)

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  15. Larval development of Notolopas brasiliensis Miers, 1886 (Brachyura: Majoidea: Pisidae described from laboratory reared material and a reappraisal of the characters of Pisidae

    Directory of Open Access Journals (Sweden)

    William Santana

    2006-01-01

    Full Text Available The complete larval stages of Notolopas brasiliensis are described from laboratory reared material, with emphasis on the external morphological features of Majoidea, and compare the morphology of N. brasiliensis with other genera of Pisidae. Larval development of N. brasiliensis consists of two zoeal stages and one megalopa. The duration mean of each zoeal stage was 4.2 ± 1.0 days for Zoea I and 3.8 ± 0.7 days for Zoea II, the megalopa instar appearing 8.1 ± 0.4 days after hatching. The characters previously used to define larval forms of Pisidae are either symplesiomorphic or potentially highly homoplastic. As well, was observed that there are no common sets of larval characters that would define Pisidae nowadays. However, was showed that only a combination of characters could differentiate Notolopas from other pisid genera.O completo desenvolvimento larval de Notolopas brasiliensis é descrito, a partir de material criado em laboratório, com ênfase na morfologia externa de Majoidea e comparado aos demais gêneros de Pisidae. O desenvolvimento larval de N. brasiliensis consiste em dois estágios de zoea e um de megalopa. A duração media de cada estágio foi de 4.2 ± 1.0 dias para a Zoea I e 3.8 ± 0.7 dias para a Zoea II, a megalopa aparece entre 8.1 ± 0.4 dias após a eclosão. Os caracteres previamente utilizados para definir as formas larvais de Pisidae ou são simplesiomórficos ou altamente homoplásticos. Foi observado que não existe um conjunto de caracteres capazes de definir Pisidae até o presente.Contudo foi mostrado que uma combinação de caracteres pode ser utilizada para diferenciar Notolopas dos demais gêneros da família.

  16. Playing MMORPGs: connections between addiction and identifying with a character.

    Science.gov (United States)

    Smahel, David; Blinka, Lukas; Ledabyl, Ondrej

    2008-12-01

    Addiction to online role-playing games is one of the most discussed aspects of recent cyberpsychology, mainly for its potentially negative impact on the social lives of young people. In our study, we focus on some aspects of youth and adolescent addiction to MMORPGs. We investigated connections between players and their game characters and examined if, and in what ways, player relationship to their character affected potential addiction. Players attitude to their characters seems to play a specific role, since players who tend to be addicted view their characters as being superior and more often wish to be like their characters in their real lives. Our research also confirmed that younger players are generally more prone to addiction.

  17. Genus-two characters of the Ising model

    International Nuclear Information System (INIS)

    Choi, J.H.; Koh, I.G.

    1989-01-01

    As a first step in studying conformal theories on a higher-genus Riemann surface, we construct genus-two characters of the Ising model from their behavior in zero- and nonzero-homology pinching limits, the Goddard-Kent-Oliveco set-space construction, and the branching coefficients in the level-two A 1 /sup (1)/ Kac-Moody characters on the higher-genus Riemann surface

  18. AcEST: BP917893 [AcEST

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