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Sample records for sage transcriptome database

  1. The Mouse SAGE Site: database of public mouse SAGE libraries

    Czech Academy of Sciences Publication Activity Database

    Divina, Petr; Forejt, Jiří

    2004-01-01

    Roč. 32, - (2004), s. D482-D483 ISSN 0305-1048 R&D Projects: GA MŠk LN00A079; GA ČR GV204/98/K015 Grant - others:HHMI(US) 555000306 Institutional research plan: CEZ:AV0Z5052915 Keywords : mouse SAGE libraries * web -based database Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.260, year: 2004

  2. Defining the Human Macula Transcriptome and Candidate Retinal Disease Genes UsingEyeSAGE

    Science.gov (United States)

    Rickman, Catherine Bowes; Ebright, Jessica N.; Zavodni, Zachary J.; Yu, Ling; Wang, Tianyuan; Daiger, Stephen P.; Wistow, Graeme; Boon, Kathy; Hauser, Michael A.

    2009-01-01

    Purpose To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). Methods Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. Results Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. Conclusions The EyeSAGE database, combining three different gene-profiling platforms including the authors’ multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions. PMID:16723438

  3. A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity.

    Science.gov (United States)

    Sengoelge, Guerkan; Winnicki, Wolfgang; Kupczok, Anne; von Haeseler, Arndt; Schuster, Michael; Pfaller, Walter; Jennings, Paul; Weltermann, Ansgar; Blake, Sophia; Sunder-Plassmann, Gere

    2014-08-27

    Large scale transcript analysis of human glomerular microvascular endothelial cells (HGMEC) has never been accomplished. We designed this study to define the transcriptome of HGMEC and facilitate a better characterization of these endothelial cells with unique features. Serial analysis of gene expression (SAGE) was used for its unbiased approach to quantitative acquisition of transcripts. We generated a HGMEC SAGE library consisting of 68,987 transcript tags. Then taking advantage of large public databases and advanced bioinformatics we compared the HGMEC SAGE library with a SAGE library of non-cultured ex vivo human glomeruli (44,334 tags) which contained endothelial cells. The 823 tags common to both which would have the potential to be expressed in vivo were subsequently checked against 822,008 tags from 16 non-glomerular endothelial SAGE libraries. This resulted in 268 transcript tags differentially overexpressed in HGMEC compared to non-glomerular endothelia. These tags were filtered using a set of criteria: never before shown in kidney or any type of endothelial cell, absent in all nephron regions except the glomerulus, more highly expressed than statistically expected in HGMEC. Neurogranin, a direct target of thyroid hormone action which had been thought to be brain specific and never shown in endothelial cells before, fulfilled these criteria. Its expression in glomerular endothelium in vitro and in vivo was then verified by real-time-PCR, sequencing and immunohistochemistry. Our results represent an extensive molecular characterization of HGMEC beyond a mere database, underline the endothelial heterogeneity, and propose neurogranin as a potential link in the kidney-thyroid axis.

  4. Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS

    Directory of Open Access Journals (Sweden)

    Davis Simon J

    2007-09-01

    Full Text Available Abstract Background Deep transcriptome analysis will underpin a large fraction of post-genomic biology. 'Closed' technologies, such as microarray analysis, only detect the set of transcripts chosen for analysis, whereas 'open' e.g. tag-based technologies are capable of identifying all possible transcripts, including those that were previously uncharacterized. Although new technologies are now emerging, at present the major resources for open-type analysis are the many publicly available SAGE (serial analysis of gene expression and MPSS (massively parallel signature sequencing libraries. These technologies have never been compared for their utility in the context of deep transcriptome mining. Results We used a single LongSAGE library of 503,431 tags and a "classic" MPSS library of 1,744,173 tags, both prepared from the same T cell-derived RNA sample, to compare the ability of each method to probe, at considerable depth, a human cellular transcriptome. We show that even though LongSAGE is more error-prone than MPSS, our LongSAGE library nevertheless generated 6.3-fold more genome-matching (and therefore likely error-free tags than the MPSS library. An analysis of a set of 8,132 known genes detectable by both methods, and for which there is no ambiguity about tag matching, shows that MPSS detects only half (54% the number of transcripts identified by SAGE (3,617 versus 1,955. Analysis of two additional MPSS libraries shows that each library samples a different subset of transcripts, and that in combination the three MPSS libraries (4,274,992 tags in total still only detect 73% of the genes identified in our test set using SAGE. The fraction of transcripts detected by MPSS is likely to be even lower for uncharacterized transcripts, which tend to be more weakly expressed. The source of the loss of complexity in MPSS libraries compared to SAGE is unclear, but its effects become more severe with each sequencing cycle (i.e. as MPSS tag length increases

  5. A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity

    DEFF Research Database (Denmark)

    Stein, Wilfred D; Litman, Thomas; Fojo, Tito

    2004-01-01

    are their corresponding solid tumors. We used the Serial Analysis of Gene Expression (SAGE) database to identify differences between solid tumors and cell lines, hoping to detect genes that could potentially explain differences in drug sensitivity. SAGE libraries were available for both solid tumors and cell lines from...

  6. The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

    Directory of Open Access Journals (Sweden)

    Steinhauer Diana

    2011-02-01

    Full Text Available Abstract Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.. While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. Results We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold under salt stress in both organs, witnessing a differential organ-specific response to stress. Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 Uni

  7. A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

    Directory of Open Access Journals (Sweden)

    Scoté-Blachon Céline

    2008-09-01

    Full Text Available Abstract Background "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression, LongSAGE and MPSS (Massively Parallel Signature Sequencing are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. Results In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. Conclusion We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.

  8. Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.).

    Science.gov (United States)

    Barrios, Abel; Caminero, Constantino; García, Pedro; Krezdorn, Nicolas; Hoffmeier, Klaus; Winter, Peter; Pérez de la Vega, Marcelino

    2017-06-30

    Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation. To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between -3 to -15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the

  9. Lathyrus sativus transcriptome resistance response to Ascochyta lathyri investigated by deepSuperSAGE analysis

    Science.gov (United States)

    Almeida, Nuno F.; Krezdorn, Nicolas; Rotter, Björn; Winter, Peter; Rubiales, Diego; Vaz Patto, Maria C.

    2015-01-01

    Lathyrus sativus (grass pea) is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. It is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. Nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. To elucidate the pathways differentially regulated during ascochyta-grass pea interaction and to identify resistance candidate genes, we compared the early response of the leaf gene expression profile of a resistant L. sativus genotype to Ascochyta lathyri infection with a non-inoculated control sample from the same genotype employing deepSuperSAGE. This analysis generated 14.387 UniTags of which 95.7% mapped to a reference grass pea/rust interaction transcriptome. From the total mapped UniTags, 738 were significantly differentially expressed between control and inoculated leaves. The results indicate that several gene classes acting in different phases of the plant/pathogen interaction are involved in the L. sativus response to A. lathyri infection. Most notably a clear up-regulation of defense-related genes involved in and/or regulated by the ethylene pathway was observed. There was also evidence of alterations in cell wall metabolism indicated by overexpression of cellulose synthase and lignin biosynthesis genes. This first genome-wide overview of the gene expression profile of the L. sativus response to ascochyta infection delivered a valuable set of candidate resistance genes for future use in precision breeding. PMID:25852725

  10. Lathyrus sativus transcriptome resistance response to Ascochyta lathyri as reviewed by deepSuperSAGE analysis

    Directory of Open Access Journals (Sweden)

    Nuno Felipe Almeida

    2015-03-01

    Full Text Available Lathyrus sativus (grass pea is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. It is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. Nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. To elucidate the pathways differentially regulated during ascochyta-grass pea interaction and to identify resistance candidate genes, we compared the early response of the leaf gene expression profile of a resistant L. sativus genotype to Ascochyta lathyri infection with a non-inoculated control sample from the same genotype employing deepSuperSAGE. This analysis generated 14.387 UniTags of which 95.7% mapped to a reference grass pea/rust interaction transcriptome. From the total mapped UniTags, 738 were significantly differentially expressed between control and inoculated leaves. The results indicate that several gene classes acting in different phases of the plant/pathogen interaction are involved in the L. sativus response to A. lathyri infection. Most notably a clear up-regulation of defense-related genes involved in and/or regulated by the ethylene pathway was observed. There was also evidence of alterations in cell wall metabolism indicated by overexpression of cellulose synthase and lignin biosynthesis genes. This first genome-wide overview of the gene expression profile of the L. sativus response to ascochyta infection delivered a valuable set of candidate resistance genes for future use in precision breeding.

  11. SAGE ANALYSIS OF TRANSCRIPTOME RESPONSES IN ARABIDOPSIS ROOTS EXPOSED TO 2,4,6-TRINITROTOLUENE

    Science.gov (United States)

    Serial Analysis of Gene Expression (SAGE) was used to profile transcript levels in Arabidopsis thaliana roots and assess their responses to 2,4,6-trinitrotoluene (TNT) exposure. SAGE libraries representing control and TNT-exposed seedling root transcripts were constructed, and ea...

  12. Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE).

    Science.gov (United States)

    Taft, A S; Vermeire, J J; Bernier, J; Birkeland, S R; Cipriano, M J; Papa, A R; McArthur, A G; Yoshino, T P

    2009-04-01

    Infection of the snail, Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke, Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of the S. mansoni miracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia and in vitro cultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of the B. glabrata embryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to the S. mansoni gene predictions (v4.0e) either by estimating theoretical 3' UTR lengths or using existing 3' EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

  13. TRAM (Transcriptome Mapper: database-driven creation and analysis of transcriptome maps from multiple sources

    Directory of Open Access Journals (Sweden)

    Danieli Gian

    2011-02-01

    Full Text Available Abstract Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays, implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile, useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene

  14. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

    Science.gov (United States)

    Yang, Cheng-Hong; Chuang, Li-Yeh; Shih, Tsung-Mu; Chang, Hsueh-Wei

    2010-12-17

    SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM) and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

  15. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

    Directory of Open Access Journals (Sweden)

    Cheng-Hong Yang

    Full Text Available BACKGROUND: SAGE (serial analysis of gene expression is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. METHODOLOGY/PRINCIPAL FINDINGS: To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. CONCLUSIONS/SIGNIFICANCE: The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

  16. CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

    OpenAIRE

    Verma, Mohit; Kumar, Vinay; Patel, Ravi K.; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database fea...

  17. A SAGE based approach to human glomerular endothelium : defining the transcriptome, finding a novel molecule and highlighting endothelial diversity

    NARCIS (Netherlands)

    Sengoelge, Guerkan; Winnicki, Wolfgang; Kupczok, Anne; von Haeseler, Arndt; Schuster, Michael; Pfaller, Walter; Jennings, Paul; Weltermann, Ansgar; Blake, Sophia; Sunder-Plassmann, Gere

    2014-01-01

    BACKGROUND: Large scale transcript analysis of human glomerular microvascular endothelial cells (HGMEC) has never been accomplished. We designed this study to define the transcriptome of HGMEC and facilitate a better characterization of these endothelial cells with unique features. Serial analysis

  18. The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis

    DEFF Research Database (Denmark)

    Gyetvai, Gabor; Sønderkær, Mads; Göbel, Ulrike

    2012-01-01

    of the compatible and incompatible interaction were captured by DeepSAGE analysis of 44 biological samples comprising five genotypes, differing only by the presence or absence of the R1 transgene, three infection time points and three biological replicates. 30.859 unique 21 base pair sequence tags were obtained......Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). Understanding the molecular basis of resistance and susceptibility to late blight is therefore highly relevant for developing resistant cultivars, either by marker...... interactions over the infection time course and between compatible and incompatible genotypes. Transcriptional changes were more numerous in compatible than in incompatible interactions. In contrast to incompatible interactions, transcriptional changes in the compatible interaction were observed predominantly...

  19. Transcriptome

    Science.gov (United States)

    ... Also: Talking Glossary of Genetic Terms Definitions for genetic terms used on this page En Español: Transcriptoma Transcriptome What is a transcriptome? What can a transcriptome tell us? How can transcriptome data be used to explore gene function? What is ...

  20. Contributions: SAGE

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Contributions: SAGE. Space Alternating Generalized Expectation (SAGE) Maximization algorithm provides an iterative approach to parameter estimation when direct maximization of the likelihood function may be infeasible. Complexity is less in those applications ...

  1. Sage grouse

    Science.gov (United States)

    Zimmerman, Shawna; Timmer, Jennifer M.; Aldridge, Cameron L.; Oyler-McCance, Sara J.; Braun, Clait E.; Young, Jessica R.

    2017-01-01

    Sage grouse are a group of chicken-sized birds with a unique breeding behavior and dependence on sagebrush shrubs (genus Artemisia) for food and shelter throughout their life cycle. In the last century, human population expansion throughout western North America has reduced the amount of sagebrush and degraded and fragmented the remaining areas. Vanishing sagebrush has resulted in sage grouse (genus Centrocercus) population declines and elevated conservation concern. Western Colorado is home to both species of sage grouse: greater sage grouse (Centrocercus urophasianus) and Gunnison sage grouse (Centrocercus minimus). Populations in the state, and throughout their range, have declined sufficiently to warrant consideration for federal protection for both species under the Endangered Species Act.

  2. CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics.

    Directory of Open Access Journals (Sweden)

    Mohit Verma

    Full Text Available Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB, which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology search and comparative gene expression analysis. The current release of CTDB (v2.0 hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database to facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms between different chickpea types. We anticipate that integrated information content of this database will accelerate the functional and applied genomic research for improvement of chickpea. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.

  3. Transcriptome database resource and gene expression atlas for the rose

    Science.gov (United States)

    2012-01-01

    Background For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Results Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. Conclusions The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy. PMID:23164410

  4. The Co-regulation Data Harvester: Automating gene annotation starting from a transcriptome database

    Science.gov (United States)

    Tsypin, Lev M.; Turkewitz, Aaron P.

    Identifying co-regulated genes provides a useful approach for defining pathway-specific machinery in an organism. To be efficient, this approach relies on thorough genome annotation, a process much slower than genome sequencing per se. Tetrahymena thermophila, a unicellular eukaryote, has been a useful model organism and has a fully sequenced but sparsely annotated genome. One important resource for studying this organism has been an online transcriptomic database. We have developed an automated approach to gene annotation in the context of transcriptome data in T. thermophila, called the Co-regulation Data Harvester (CDH). Beginning with a gene of interest, the CDH identifies co-regulated genes by accessing the Tetrahymena transcriptome database. It then identifies their closely related genes (orthologs) in other organisms by using reciprocal BLAST searches. Finally, it collates the annotations of those orthologs' functions, which provides the user with information to help predict the cellular role of the initial query. The CDH, which is freely available, represents a powerful new tool for analyzing cell biological pathways in Tetrahymena. Moreover, to the extent that genes and pathways are conserved between organisms, the inferences obtained via the CDH should be relevant, and can be explored, in many other systems.

  5. KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba.

    Directory of Open Access Journals (Sweden)

    Gabriele Sales

    Full Text Available Antarctic krill (Euphausia superba is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2 is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans. The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1 the full list of assembled genes and transcripts; 2 their level of similarity to transcripts and proteins from other species; 3 the predicted protein domains contained within each transcript; 4 their predicted GO terms; 5 the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

  6. KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.

    Science.gov (United States)

    Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

    2013-07-09

    The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM). KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers. KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with

  7. 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

  8. SAGE results

    International Nuclear Information System (INIS)

    Gavrin, V.N.

    1996-01-01

    The Russian-American Gallium solar neutrino Experiment (SAGE) is described. The solar neutrino flux measured by 31 extractions through October, 1993 is presented. The result of 69+/-10(stat)+5/-7(syst) SNU is to be compared with a Standard Solar Model prediction of 132 SNU. The initial results of a measurement of experimental efficiencies are also discussed by exposing the gallium target to neutrinos from an artificial source. The capture rate of neutrinos from this source is very close to that which is expected. The result can be expressed as a ratio of the measured capture rate to the anticipated rate from the source activity. This ratio is 0.93+0.15, -0.17 where the systematic and statistical errors have been combined. To first order the experimental efficiencies are in agreement with those determined during solar neutrino measurements and in previous auxiliary measurements. One must conclude that the discrepancy between the measured solar neutrino flux and that predicted by the solar models can not arise from an experimental artifact. (author)

  9. SAGE IV Pathfinder

    Data.gov (United States)

    National Aeronautics and Space Administration — Utilizing a unique, new occultation technique involving imaging, the SAGE IV concept will meet or exceed the quality of previous SAGE measurements at a small...

  10. SQUAT: A web tool to mine human, murine and avian SAGE data

    Directory of Open Access Journals (Sweden)

    Besson Jérémy

    2008-09-01

    Full Text Available Abstract Background There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns. Description We have developed an application called SQUAT (SAGE Querying and Analysis Tools which is available at: http://bsmc.insa-lyon.fr/squat/. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken. This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: ≪what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?≫. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated. Conclusion SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.

  11. Transcriptome data - Initial stage of dough fermentation - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us DGBY Transcriptome data - Initial stage of dough fermentation Data detail Data name Transcri...ptome data - Initial stage of dough fermentation DOI 10.18908/lsdba.nbdc00953-002 Description of data conten...ts Gene expression profiles of baker's yeast during initial dough-fermentation were investigated using liquid fermentation...aptation mechanisms of baker's yeast. Results showed the onset of fermentation caused drastic changes in gen...f baker's yeast during dough-fermentation, and will thus help clarify genomic res

  12. Results from SAGE II

    International Nuclear Information System (INIS)

    Nico, J.S.

    1994-01-01

    The Russian-American Gallium solar neutrino Experiment (SAGE) began the second phase of operation (SAGE II) in September of 1992. Monthly measurements of the integral flux of solar neutrinos have been made with 55 tonnes of gallium. The K-peak results of the first nine runs of SAGE II give a capture rate of 66 -13 +18 (stat) -7 +5 (sys) SNU. Combined with the SAGE I result of 73 -16 +18 (stat) -7 5 (sys) SNU, the capture rate is 69 -11 +11 (stat) -7 +5 (sys) SNU. This represents only 52%--56% of the capture rate predicted by different Standard Solar Models

  13. KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella

    OpenAIRE

    Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

    2013-01-01

    Background The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to fa...

  14. 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

  15. 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

  16. 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

  17. 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

  18. GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

    Directory of Open Access Journals (Sweden)

    Raquel L. Costa

    2017-07-01

    Full Text Available There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were

  19. The SAGE spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Pakarinen, J.; Papadakis, P. [University of Liverpool, Department of Physics, Oliver Lodge Laboratory, Liverpool (United Kingdom); University of Jyvaeskylae, Department of Physics, Jyvaeskylae (Finland); Sorri, J.; Greenlees, P.T.; Jones, P.; Julin, R.; Konki, J.; Rahkila, P.; Sandzelius, M. [University of Jyvaeskylae, Department of Physics, Jyvaeskylae (Finland); Herzberg, R.D.; Butler, P.A.; Cox, D.M.; Cresswell, J.R.; Mistry, A.; Page, R.D.; Parr, E.; Sampson, J.; Seddon, D.A.; Thornhill, J.; Wells, D. [University of Liverpool, Department of Physics, Oliver Lodge Laboratory, Liverpool (United Kingdom); Coleman-Smith, P.J.; Lazarus, I.H.; Letts, S.C.; Pucknell, V.F.E.; Simpson, J. [STFC Daresbury Laboratory, Warrington (United Kingdom)

    2014-03-15

    The SAGE spectrometer has been constructed for in-beam nuclear structure studies. SAGE combines a Ge-detector array and an electron spectrometer for detection of γ-rays and internal conversion electrons, respectively, and allows simultaneous observation of both electrons and γ-rays emitted from excited nuclei. SAGE is set up in the Accelerator Laboratory of the University of Jyvaeskylae and works in conjunction with the RITU gas-filled recoil separator and the GREAT focal-plane spectrometer allowing the use of the recoil-decay tagging method. (orig.)

  20. The SAGE spectrometer

    International Nuclear Information System (INIS)

    Pakarinen, J.; Papadakis, P.; Sorri, J.; Greenlees, P.T.; Jones, P.; Julin, R.; Konki, J.; Rahkila, P.; Sandzelius, M.; Herzberg, R.D.; Butler, P.A.; Cox, D.M.; Cresswell, J.R.; Mistry, A.; Page, R.D.; Parr, E.; Sampson, J.; Seddon, D.A.; Thornhill, J.; Wells, D.; Coleman-Smith, P.J.; Lazarus, I.H.; Letts, S.C.; Pucknell, V.F.E.; Simpson, J.

    2014-01-01

    The SAGE spectrometer has been constructed for in-beam nuclear structure studies. SAGE combines a Ge-detector array and an electron spectrometer for detection of γ-rays and internal conversion electrons, respectively, and allows simultaneous observation of both electrons and γ-rays emitted from excited nuclei. SAGE is set up in the Accelerator Laboratory of the University of Jyvaeskylae and works in conjunction with the RITU gas-filled recoil separator and the GREAT focal-plane spectrometer allowing the use of the recoil-decay tagging method. (orig.)

  1. Results from SAGE

    International Nuclear Information System (INIS)

    Abdurashitov, J.N.; Gavrin, V.N.; Girin, S.V.

    1996-01-01

    The Russian-American Gallium Solar Neutrino Experiment (SAGE) is described. Beginning in September 1992, SAGE II data were taken with 55 tons of Ga and with significantly reduced backgrounds. The solar neutrino flux measured by 31 extractions through October 1993 is presented. The result of 69 ± 10 +5/-7 SNU is to be compared with a Standard Solar Model prediction of 132 SNU

  2. 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.

  3. CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

    Science.gov (United States)

    Hernandez-Prieto, Miguel A; Futschik, Matthias E

    2012-01-01

    Synechocystis sp. PCC6803 is one of the best studied cyanobacteria and an important model organism for our understanding of photosynthesis. The early availability of its complete genome sequence initiated numerous transcriptome studies, which have generated a wealth of expression data. Analysis of the accumulated data can be a powerful tool to study transcription in a comprehensive manner and to reveal underlying regulatory mechanisms, as well as to annotate genes whose functions are yet unknown. However, use of divergent microarray platforms, as well as distributed data storage make meta-analyses of Synechocystis expression data highly challenging, especially for researchers with limited bioinformatic expertise and resources. To facilitate utilisation of the accumulated expression data for a wider research community, we have developed CyanoEXpress, a web database for interactive exploration and visualisation of transcriptional response patterns in Synechocystis. CyanoEXpress currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in 31 independent studies. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis and can be freely accessed. The database is available for free at http://cyanoexpress.sysbiolab.eu.

  4. Numerical analysis using Sage

    CERN Document Server

    Anastassiou, George A

    2015-01-01

    This is the first numerical analysis text to use Sage for the implementation of algorithms and can be used in a one-semester course for undergraduates in mathematics, math education, computer science/information technology, engineering, and physical sciences. The primary aim of this text is to simplify understanding of the theories and ideas from a numerical analysis/numerical methods course via a modern programming language like Sage. Aside from the presentation of fundamental theoretical notions of numerical analysis throughout the text, each chapter concludes with several exercises that are oriented to real-world application.  Answers may be verified using Sage.  The presented code, written in core components of Sage, are backward compatible, i.e., easily applicable to other software systems such as Mathematica®.  Sage is  open source software and uses Python-like syntax. Previous Python programming experience is not a requirement for the reader, though familiarity with any programming language is a p...

  5. BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

    Science.gov (United States)

    Meyer, Michael J; Geske, Philip; Yu, Haiyuan

    2016-05-15

    Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Sage for undergraduates

    CERN Document Server

    Bard, Gregory V

    2015-01-01

    Professor Bard has provided a valuable service by carefully explaining everything an undergraduate student of mathematics, or a teacher of these topics, needs to get started with Sage quickly and easily. It will also be useful for any student or teacher of another STEM discipline. There is an excellent mix of the most frequently used commands, along with warnings about common pitfalls or caveats. I highly recommend it for anyone new to Sage, or who desires an overview of the system's impressive capabilities. -Robert A. Beezer, University of Puget Sound This book is a sort of "Missing Manual"

  7. Solar neutrino results from SAGE

    International Nuclear Information System (INIS)

    Gavrin, V.N.

    1999-01-01

    We report the status of the Russian-American Gallium solar neutrino Experiment (SAGE). The solar neutrino result for SAGE III, 20 runs during the measuring period May 1995 through December 1997, is 56.7 +9.3/-8.7(stat.)+4.6/-4.8(syst.) SNU. The combined result for 57 measurements from 1990 through 1997 (SAGE I+II+III) is 66.9 +7.1/-6.8 (stat) +5.4/-5.7 (syst) SNU. The final result of the SAGE 51 Cr experiment to check the response of SAGE to low energy neutrinos is also presented

  8. Gene expression profiling of human breast tissue samples using SAGE-Seq.

    Science.gov (United States)

    Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

    2010-12-01

    We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

  9. Technology evaluation: SAGE, Genzyme molecular oncology.

    Science.gov (United States)

    Bartlett, J

    2001-02-01

    collection of gene expression profiles utilizing all methods including high-density microarrays [315329]. Ontogeny (now Curis Inc) and GMO have entered into a collaboration to study genes for the potential discovery of therapeutic products. GMO will use its SAGE technology to produce libraries of RNA supplied by Ontogeny. The libraries will be put through Ontogeny's screening program [279417]. Under an agreement made in August 1998, Bayer will use SAGE technology to identify genes and thus potential therapeutics [317452]. GMO and Hexagen signed an agreement in March 1998 on the use of SAGE technology in Hexagen's disease gene discovery programs. The first phase of the collaboration will focus on the use of SAGE in studies within Hexagen's type II diabetes gene discovery program. Hexagen has designed these studies to discover susceptibility genes for diabetes and to provide gene expression information for genes associated with type II diabetes [280012]. GMO signed a five-year agreement with Johns Hopkins University School of Medicine (JHU) in July 1997 for research leading to the identification of cancer-related genes. Under the terms of the agreement, JHU researchers will use the SAGE technology to identify and analyze gene expression in cancer. The power of SAGE in finding rare genes was confirmed in a study of gastrointestinal cancer by JHU researchers published in the May 27, 1997 issue of Science. The study showed that of almost 50,000 genes expressed in normal gastrointestinal cells and gastrointestinal tumor cells, 86% of the genes were present at five or fewer copies per cell. Only 51% of those low-abundancy genes were recorded in the GenBank database of known genes in the human genome [257128].

  10. SAGE Version 7.0 Algorithm: Application to SAGE II

    Science.gov (United States)

    Damadeo, R. P; Zawodny, J. M.; Thomason, L. W.; Iyer, N.

    2013-01-01

    This paper details the Stratospheric Aerosol and Gas Experiments (SAGE) version 7.0 algorithm and how it is applied to SAGE II. Changes made between the previous (v6.2) and current (v7.0) versions are described and their impacts on the data products explained for both coincident event comparisons and time-series analysis. Users of the data will notice a general improvement in all of the SAGE II data products, which are now in better agreement with more modern data sets (e.g. SAGE III) and more robust for use with trend studies.

  11. First results from SAGE II

    International Nuclear Information System (INIS)

    Abdurashitov, J.N.; Faizov, E.L.; Gavrin, V.N.

    1994-01-01

    The Russian-American Gallium solar neutrino Experiment (SAGE) began the second phase of operation (SAGE II) in September of 1992. Monthly measurements of the integral flux of solar neutrinos have been made with 55 tonnes of gallium. The K-peak results of the first five runs of SAGE II give a capture rate of 76 -18 +21 (stat) -7 +5 (sys) SNU. combined with the SAGE I result, the capture rate is 74 -12 +13 (stat) -7 +5 (sys) SNU. This represents only 56%--60% of the capture rate predicted by different Standard Solar Models

  12. First results from SAGE II

    International Nuclear Information System (INIS)

    Aburashitov, J.N.; Faizov, E.L.; Gavrin, V.N.; Gusev, A.O.; Kalikhov, A.V.; Knodel, T.V.; Knyshenko, I.I.; Kornoukhov, V.N.; Mirmov, I.N.; Pshukov, A.M.; Shalagin, A.M.; Shikhin, A.A.; Timofeyev, P.V.; Veretenkin, E.P.; Vermul, V.M.; Zatsepin, G.T.; Bowles, T.J.; Nico, J.S.; Teasdale, W.A.; Wark, D.L.; Wilkerson, J.F.; Cleveland, B.T.; Daily, T.; Davis, R. Jr.; Lande, K.; Lee, C.K.; Wildenhain, P.W.; Elliott, S.R.; Cherry, M.L.

    1995-01-01

    The Russian-American Gallium solar neutrino Experiment (SAGE) began the second phase of operation (SAGE II) in September of 1992. Monthly measurements of the integral flux of solar neutrinos have been made with 55 tonnes of gallium. The K-peak results of the first five runs of SAGE II give a capture rate of 76 +21 -18 (stat) +5 -7 (sys) SNU. Combined with the SAGE I result, the capture rate is 74 +13 -12 (stat) +5 -7 (sys) SNU. This represents only 56%--60% of the capture rate predicted by different Standard Solar Models. copyright 1995 American Institute of Physics

  13. Serial analysis of gene expression (SAGE)

    NARCIS (Netherlands)

    van Ruissen, Fred; Baas, Frank

    2007-01-01

    In 1995, serial analysis of gene expression (SAGE) was developed as a versatile tool for gene expression studies. SAGE technology does not require pre-existing knowledge of the genome that is being examined and therefore SAGE can be applied to many different model systems. In this chapter, the SAGE

  14. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

    Directory of Open Access Journals (Sweden)

    Raherison Elie

    2012-08-01

    Full Text Available Abstract Background Conifers have very large genomes (13 to 30 Gigabases that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

  15. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  16. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  17. Simulation of the SAGE spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Cox, D.M.; Herzberg, R.D. [University of Liverpool, Department of Physics, Oliver Lodge Laboratory, Liverpool (United Kingdom); Konki, J.; Greenlees, P.T.; Pakarinen, J.; Papadakis, P.; Rahkila, P.; Sandzelius, M.; Sorri, J. [University of Jyvaeskylae, Department of Physics, Jyvaeskylae (Finland); Hauschild, K. [Universite Paris-Sud, CSNSM-IN2P3-CNRS, Orsay (France)

    2015-06-15

    The SAGE spectrometer combines a Ge-detector array with a Si detector to allow simultaneous detection of γ-rays and electrons. A comprehensive GEANT4 simulation package of the SAGE spectrometer has been developed with the ability to simulate the expected datasets based on user input files. The measured performance of the spectrometer is compared to the results obtained from the simulations. (orig.)

  18. Simulation of the SAGE spectrometer

    International Nuclear Information System (INIS)

    Cox, D.M.; Herzberg, R.D.; Konki, J.; Greenlees, P.T.; Pakarinen, J.; Papadakis, P.; Rahkila, P.; Sandzelius, M.; Sorri, J.; Hauschild, K.

    2015-01-01

    The SAGE spectrometer combines a Ge-detector array with a Si detector to allow simultaneous detection of γ-rays and electrons. A comprehensive GEANT4 simulation package of the SAGE spectrometer has been developed with the ability to simulate the expected datasets based on user input files. The measured performance of the spectrometer is compared to the results obtained from the simulations. (orig.)

  19. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

    Directory of Open Access Journals (Sweden)

    Wincker Patrick

    2010-06-01

    Full Text Available Abstract Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center, the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR and to the Gene Ontology (GO protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred

  20. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes.

    Science.gov (United States)

    Macagno, Eduardo R; Gaasterland, Terry; Edsall, Lee; Bafna, Vineet; Soares, Marcelo B; Scheetz, Todd; Casavant, Thomas; Da Silva, Corinne; Wincker, Patrick; Tasiemski, Aurélie; Salzet, Michel

    2010-06-25

    The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. A total of approximately 133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences

  1. USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression

    NARCIS (Netherlands)

    van Kampen, A. H.; van Schaik, B. D.; Pauws, E.; Michiels, E. M.; Ruijter, J. M.; Caron, H. N.; Versteeg, R.; Heisterkamp, S. H.; Leunissen, J. A.; Baas, F.; van der Mee, M.

    2000-01-01

    MOTIVATION: SAGE enables the determination of genome-wide mRNA expression profiles. A comprehensive analysis of SAGE data requires software, which integrates (statistical) data analysis methods with a database system. Furthermore, to facilitate data sharing between users, the application should

  2. Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach.

    Science.gov (United States)

    Pascale, Raffaella; Grossi, Gerarda; Cruciani, Gabriele; Mecca, Giansalvatore; Santoro, Donatello; Sarli Calace, Renzo; Falabella, Patrizia; Bianco, Giuliana

    Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.

  3. SAGE 1 data user's guide

    International Nuclear Information System (INIS)

    Mcmaster, L.R.; Chu, W.P.; Rowland, M.W.

    1992-08-01

    A guide for using the data products from the Stratospheric Aerosol and Gas Experiment 1 (SAGE 1) for scientific investigations of stratospheric chemistry related to aerosol, ozone, nitrogen dioxide, dynamics, and climate change is presented. A detailed description of the aerosol profile tape, the ozone profile tape, and the nitrogen dioxide profile tape is included. These tapes are the SAGE 1 data products containing aerosol extinction data and ozone and nitrogen dioxide concentration data for use in the different scientific investigations. Brief descriptions of the instrument operation, data collection, processing, and validation, and some of the scientific analyses that were conducted are also included

  4. Serial analysis of gene expression (SAGE in bovine trypanotolerance: preliminary results

    Directory of Open Access Journals (Sweden)

    David Berthier

    2003-06-01

    Full Text Available Abstract In Africa, trypanosomosis is a tsetse-transmitted disease which represents the most important constraint to livestock production. Several indigenous West African taurine (Bos taurus breeds, such as the Longhorn (N'Dama cattle are well known to control trypanosome infections. This genetic ability named "trypanotolerance" results from various biological mechanisms under multigenic control. The methodologies used so far have not succeeded in identifying the complete pool of genes involved in trypanotolerance. New post genomic biotechnologies such as transcriptome analyses are efficient in characterising the pool of genes involved in the expression of specific biological functions. We used the serial analysis of gene expression (SAGE technique to construct, from Peripheral Blood Mononuclear Cells of an N'Dama cow, 2 total mRNA transcript libraries, at day 0 of a Trypanosoma congolense experimental infection and at day 10 post-infection, corresponding to the peak of parasitaemia. Bioinformatic comparisons in the bovine genomic databases allowed the identification of 187 up- and down- regulated genes, EST and unknown functional genes. Identification of the genes involved in trypanotolerance will allow to set up specific microarray sets for further metabolic and pharmacological studies and to design field marker-assisted selection by introgression programmes.

  5. Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania

    Directory of Open Access Journals (Sweden)

    Smandi Sondos

    2012-01-01

    Full Text Available Abstract Background Leishmaniasis are widespread parasitic-diseases with an urgent need for more active and less toxic drugs and for effective vaccines. Understanding the biology of the parasite especially in the context of host parasite interaction is a crucial step towards such improvements in therapy and control. Several experimental approaches including SAGE (Serial analysis of gene expression have been developed in order to investigate the parasite transcriptome organisation and plasticity. Usual SAGE tag-to-gene mapping techniques are inadequate because almost all tags are normally located in the 3'-UTR outside the CDS, whereas most information available for Leishmania transcripts is restricted to the CDS predictions. The aim of this work is to optimize a SAGE libraries tag-to-gene mapping technique and to show how this development improves the understanding of Leishmania transcriptome. Findings The in silico method implemented herein was based on mapping the tags to Leishmania genome using BLAST then mapping the tags to their gene using a data-driven probability distribution. This optimized tag-to-gene mappings improved the knowledge of Leishmania genome structure and transcription. It allowed analyzing the expression of a maximal number of Leishmania genes, the delimitation of the 3' UTR of 478 genes and the identification of biological processes that are differentially modulated during the promastigote to amastigote differentiation. Conclusion The developed method optimizes the assignment of SAGE tags in trypanosomatidae genomes as well as in any genome having polycistronic transcription and small intergenic regions.

  6. Arabidopsis Gene Family Profiler (aGFP) - user-oriented transcriptomic database with easy-to-use graphic interface

    Czech Academy of Sciences Publication Activity Database

    Dupľáková, Nikoleta; Reňák, David; Hovanec, P.; Honysová, Barbora; Twell, D.; Honys, David

    2007-01-01

    Roč. 7, - (2007), Article Number: 39 ISSN 1471-2229 R&D Projects: GA MŠk(CZ) LC06004; GA ČR GA522/06/0896 Institutional research plan: CEZ:AV0Z50380511 Source of funding: V - iné verejné zdroje ; V - iné verejné zdroje Keywords : STANFORD MICROARRAY DATABASE * EXPRESSION ANALYSIS * DNA MICROARRAYS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.232, year: 2007

  7. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

    Science.gov (United States)

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-04

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub

    Directory of Open Access Journals (Sweden)

    Hukam C. Rawal

    2017-11-01

    Full Text Available Clusterbean (Cyamopsis tetragonoloba L. Taub, is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ unigenes. We annotated 79% unigenes against Plant Genes from the National Center for Biotechnology Information (NCBI, Swiss-Prot, Pfam, gene ontology (GO and KEGG databases. Among the annotated unigenes, 30,020 were assigned with 116,964 GO terms, 9984 with EC and 6111 with 137 KEGG pathways. At different fragments per kilobase of transcript per millions fragments sequenced (FPKM levels, genes were found expressed higher in flower tissue followed by shoot and leaf. Additionally, we identified 8687 potential simple sequence repeats (SSRs with an average frequency of one SSR per 8.75 kb. A total of 28 amplified SSRs in 21 clusterbean genotypes resulted in polymorphism in 13 markers with average polymorphic information content (PIC of 0.21. We also constructed a database named ‘ClustergeneDB’ for easy retrieval of unigenes and the microsatellite markers. The tissue specific genes identified and the molecular marker resources developed in this study is expected to aid in genetic improvement of clusterbean for its end use.

  9. Technology Tips: Building Interactive Demonstrations with Sage

    Science.gov (United States)

    Murray, Maura

    2013-01-01

    Sage is an open-source software package that can be used in many different areas of mathematics, ranging from algebra to calculus and beyond. One of the most exciting pedagogical features of Sage (http://www.sagemath.org) is its ability to create interacts--interactive examples that can be used in a classroom demonstration or by students in a…

  10. Solar neutrino results from SAGE

    International Nuclear Information System (INIS)

    Gavrin, V.N.

    2001-01-01

    The results of ten years of solar neutrino observation by the Russian-American gallium solar neutrino experiment (SAGE) are reported. The overall result of 70 runs during the measurement period from January 1990 to October 1999 is 75.4 -6.8 +7.0 (stat.) -3.0 +3.5 (syst) SNU. This represents only slightly more than half of the predicted standard solar model rate of 129 SNU. The individual results on each run, and the results of combined analysis of all runs during each year, as well as the results of combined analysis of all runs during monthly and bimonthly periods are presented

  11. Solar neutrino results from SAGE

    International Nuclear Information System (INIS)

    Gavrin, V.N.

    2000-01-01

    We report the results of ten years of solar neutrino observation by the Russian-American Gallium solar neutrino Experiment (SAGE). The overall result of 70 runs during the measurement period January 1990 to October 1999 is 75.4 + 7.0/-6.8 (stat.) +3.5/-3.0 (syst.) SNU. This represents only slightly more than half of the predicted standard solar model rate of 129 SNU. The individual results of each run, and the results of combined analysis of all runs during each year, as well as the results of combined analysis of all runs during monthly and bimonthly periods are presented

  12. Spatial heterogeneity in response of male greater sage-grouse lek attendance to energy development.

    Directory of Open Access Journals (Sweden)

    Andrew J Gregory

    Full Text Available Landscape modification due to rapidly expanding energy development, in particular oil and gas, in the westernUSA, have prompted concerns over how such developments may impact wildlife. One species of conservation concern across much of the Intermountain West is the greater sage-grouse (Centrocercusurophasianus. Sage-grouse have been petitioned for listing under provisions of the Endangered Species Act 7 times and the state of Wyoming alone represents 64% of the extant sage-grouse population in the eastern portion of their range. Consequently, the relationship between sage-grouse populations and oil and gas development in Wyoming is an important component to managing the long-term viability of this species. We used 814 leks from the Wyoming Game and Fish Department's lek survey database and well pad data from the Wyoming Oil and Gas Conservation Commission to evaluate changes in sage-grouse lek counts as a function of oil and gas development since 1991.From 1991-2011 we found that oil and gas well-pad density increased 3.6-fold across the state and was associated with a 24% decline in the number of male sage-grouse. Using a spatial and temporally structured analysis via Geographically Weighted Regression, we found a 1-to-4 year time lag between development density and lek decline. Sage-grouse also responded to development densities at multiple spatial neighborhoods surrounding leks, including broad scales of 10 km. However, sage-grouse lek counts do not always decline as a result of oil and gas development. We found similar development densities resulting in different sage-grouse lek count responses, suggesting that development density alone is insufficient to predict the impacts that oil and gas development have on sage-grouse. Finally, our analysis suggests a maximum development density of 1 well-pad within 2 km of leks to avoid measurable impacts within 1 year, and <6 well-pads within 10 km of leks to avoid delayed impacts.

  13. Characterization of the global profile of genes expressed in cervical epithelium by Serial Analysis of Gene Expression (SAGE

    Directory of Open Access Journals (Sweden)

    Piña-Sanchez Patricia

    2005-09-01

    Full Text Available Abstract Background Serial Analysis of Gene Expression (SAGE is a new technique that allows a detailed and profound quantitative and qualitative knowledge of gene expression profile, without previous knowledge of sequence of analyzed genes. We carried out a modification of SAGE methodology (microSAGE, useful for the analysis of limited quantities of tissue samples, on normal human cervical tissue obtained from a donor without histopathological lesions. Cervical epithelium is constituted mainly by cervical keratinocytes which are the targets of human papilloma virus (HPV, where persistent HPV infection of cervical epithelium is associated with an increase risk for developing cervical carcinomas (CC. Results We report here a transcriptome analysis of cervical tissue by SAGE, derived from 30,418 sequenced tags that provide a wealth of information about the gene products involved in normal cervical epithelium physiology, as well as genes not previously found in uterine cervix tissue involved in the process of epidermal differentiation. Conclusion This first comprehensive and profound analysis of uterine cervix transcriptome, should be useful for the identification of genes involved in normal cervix uterine function, and candidate genes associated with cervical carcinoma.

  14. Sage

    Science.gov (United States)

    ... oil is considered a toxic dose. Keep in Mind Tell all your health care providers about any ... Privacy and Policies Accessibility en Español FOIA Site Map Contact Us U.S. Department of Health & Human Services , ...

  15. The radon influence of SAGE results

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.; Mirmov, I.N.

    2002-01-01

    The method for evaluating systematic errors, connected with radon, is described in the experiment on determining the SAGE solar neutrino flux. The systematic error by the measured neutrino capture rate in the gallium 75 SNU target does not exceed 0.3 SNU. The obtained value (0.3 SNU) is the upper limit of the radon systematic error. Its low value means, that radon does not contribute significantly to the SAGE result [ru

  16. The transcriptome of Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Roos David S

    2005-12-01

    Full Text Available Abstract Background Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. Results We have used serial analysis of gene expression (SAGE to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. Conclusion This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and

  17. SAGE: String-overlap Assembly of GEnomes.

    Science.gov (United States)

    Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

    2014-09-15

    De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

  18. Probability of lek collapse is lower inside sage-grouse Core Areas: Effectiveness of conservation policy for a landscape species.

    Directory of Open Access Journals (Sweden)

    Emma Suzuki Spence

    Full Text Available Greater sage-grouse (Centrocercus urophasianus occupy sagebrush (Artemisia spp. habitats in 11 western states and 2 Canadian provinces. In September 2015, the U.S. Fish and Wildlife Service announced the listing status for sage-grouse had changed from warranted but precluded to not warranted. The primary reason cited for this change of status was that the enactment of new regulatory mechanisms was sufficient to protect sage-grouse populations. One such plan is the 2008, Wyoming Sage Grouse Executive Order (SGEO, enacted by Governor Freudenthal. The SGEO identifies "Core Areas" that are to be protected by keeping them relatively free from further energy development and limiting other forms of anthropogenic disturbances near active sage-grouse leks. Using the Wyoming Game and Fish Department's sage-grouse lek count database and the Wyoming Oil and Gas Conservation Commission database of oil and gas well locations, we investigated the effectiveness of Wyoming's Core Areas, specifically: 1 how well Core Areas encompass the distribution of sage-grouse in Wyoming, 2 whether Core Area leks have a reduced probability of lek collapse, and 3 what, if any, edge effects intensification of oil and gas development adjacent to Core Areas may be having on Core Area populations. Core Areas contained 77% of male sage-grouse attending leks and 64% of active leks. Using Bayesian binomial probability analysis, we found an average 10.9% probability of lek collapse in Core Areas and an average 20.4% probability of lek collapse outside Core Areas. Using linear regression, we found development density outside Core Areas was related to the probability of lek collapse inside Core Areas. Specifically, probability of collapse among leks >4.83 km from inside Core Area boundaries was significantly related to well density within 1.61 km (1-mi and 4.83 km (3-mi outside of Core Area boundaries. Collectively, these data suggest that the Wyoming Core Area Strategy has benefited

  19. Probability of lek collapse is lower inside sage-grouse Core Areas: Effectiveness of conservation policy for a landscape species.

    Science.gov (United States)

    Spence, Emma Suzuki; Beck, Jeffrey L; Gregory, Andrew J

    2017-01-01

    Greater sage-grouse (Centrocercus urophasianus) occupy sagebrush (Artemisia spp.) habitats in 11 western states and 2 Canadian provinces. In September 2015, the U.S. Fish and Wildlife Service announced the listing status for sage-grouse had changed from warranted but precluded to not warranted. The primary reason cited for this change of status was that the enactment of new regulatory mechanisms was sufficient to protect sage-grouse populations. One such plan is the 2008, Wyoming Sage Grouse Executive Order (SGEO), enacted by Governor Freudenthal. The SGEO identifies "Core Areas" that are to be protected by keeping them relatively free from further energy development and limiting other forms of anthropogenic disturbances near active sage-grouse leks. Using the Wyoming Game and Fish Department's sage-grouse lek count database and the Wyoming Oil and Gas Conservation Commission database of oil and gas well locations, we investigated the effectiveness of Wyoming's Core Areas, specifically: 1) how well Core Areas encompass the distribution of sage-grouse in Wyoming, 2) whether Core Area leks have a reduced probability of lek collapse, and 3) what, if any, edge effects intensification of oil and gas development adjacent to Core Areas may be having on Core Area populations. Core Areas contained 77% of male sage-grouse attending leks and 64% of active leks. Using Bayesian binomial probability analysis, we found an average 10.9% probability of lek collapse in Core Areas and an average 20.4% probability of lek collapse outside Core Areas. Using linear regression, we found development density outside Core Areas was related to the probability of lek collapse inside Core Areas. Specifically, probability of collapse among leks >4.83 km from inside Core Area boundaries was significantly related to well density within 1.61 km (1-mi) and 4.83 km (3-mi) outside of Core Area boundaries. Collectively, these data suggest that the Wyoming Core Area Strategy has benefited sage

  20. SAGE as a Source for Undergraduate Research Projects

    Science.gov (United States)

    Hutz, Benjamin

    2017-01-01

    This article examines the use of the computer algebra system SAGE for undergraduate student research projects. After reading this article, the reader should understand the benefits of using SAGE as a source of research projects and how to commence working with SAGE. The author proposes a tiered working group model to allow maximum benefit to the…

  1. TCW: transcriptome computational workbench.

    Science.gov (United States)

    Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

    2013-01-01

    The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

  2. The SAGE Model of Social Psychological Research.

    Science.gov (United States)

    Power, Séamus A; Velez, Gabriel; Qadafi, Ahmad; Tennant, Joseph

    2018-05-01

    We propose a SAGE model for social psychological research. Encapsulated in our acronym is a proposal to have a synthetic approach to social psychological research, in which qualitative methods are augmentative to quantitative ones, qualitative methods can be generative of new experimental hypotheses, and qualitative methods can capture experiences that evade experimental reductionism. We remind social psychological researchers that psychology was founded in multiple methods of investigation at multiple levels of analysis. We discuss historical examples and our own research as contemporary examples of how a SAGE model can operate in part or as an integrated whole. The implications of our model are discussed.

  3. Validation of SAGE II ozone measurements

    Science.gov (United States)

    Cunnold, D. M.; Chu, W. P.; Mccormick, M. P.; Veiga, R. E.; Barnes, R. A.

    1989-01-01

    Five ozone profiles from the Stratospheric Aerosol and Gas Experiment (SAGE) II are compared with coincident ozonesonde measurements obtained at Natal, Brazil, and Wallops Island, Virginia. It is shown that the mean difference between all of the measurements is about 1 percent and that the agreement is within 7 percent at altitudes between 20 and 53 km. Good agreement is also found for ozone mixing ratios on pressure surfaces. It is concluded that the SAGE II profiles provide useful ozone information up to about 60 km altitude.

  4. The SAGE Model of Social Psychological Research

    Science.gov (United States)

    Power, Séamus A.; Velez, Gabriel; Qadafi, Ahmad; Tennant, Joseph

    2018-01-01

    We propose a SAGE model for social psychological research. Encapsulated in our acronym is a proposal to have a synthetic approach to social psychological research, in which qualitative methods are augmentative to quantitative ones, qualitative methods can be generative of new experimental hypotheses, and qualitative methods can capture experiences that evade experimental reductionism. We remind social psychological researchers that psychology was founded in multiple methods of investigation at multiple levels of analysis. We discuss historical examples and our own research as contemporary examples of how a SAGE model can operate in part or as an integrated whole. The implications of our model are discussed. PMID:29361241

  5. Unexpected observations after mapping LongSAGE tags to the human genome

    Directory of Open Access Journals (Sweden)

    Duret Laurent

    2007-05-01

    Full Text Available Abstract Background SAGE has been used widely to study the expression of known transcripts, but much less to annotate new transcribed regions. LongSAGE produces tags that are sufficiently long to be reliably mapped to a whole-genome sequence. Here we used this property to study the position of human LongSAGE tags obtained from all public libraries. We focused mainly on tags that do not map to known transcripts. Results Using a published error rate in SAGE libraries, we first removed the tags likely to result from sequencing errors. We then observed that an unexpectedly large number of the remaining tags still did not match the genome sequence. Some of these correspond to parts of human mRNAs, such as polyA tails, junctions between two exons and polymorphic regions of transcripts. Another non-negligible proportion can be attributed to contamination by murine transcripts and to residual sequencing errors. After filtering out our data with these screens to ensure that our dataset is highly reliable, we studied the tags that map once to the genome. 31% of these tags correspond to unannotated transcripts. The others map to known transcribed regions, but many of them (nearly half are located either in antisense or in new variants of these known transcripts. Conclusion We performed a comprehensive study of all publicly available human LongSAGE tags, and carefully verified the reliability of these data. We found the potential origin of many tags that did not match the human genome sequence. The properties of the remaining tags imply that the level of sequencing error may have been under-estimated. The frequency of tags matching once the genome sequence but not in an annotated exon suggests that the human transcriptome is much more complex than shown by the current human genome annotations, with many new splicing variants and antisense transcripts. SAGE data is appropriate to map new transcripts to the genome, as demonstrated by the high rate of cross

  6. SAGES Guidelines: Prevention and management of gastro ...

    African Journals Online (AJOL)

    SAGES Guidelines: Prevention and management of gastro-oesophageal varices and variceal haemorrhage in cirrhosis. J F Botha. Abstract. No Abstract South African Gastroenterology Review Vol. 6 (1) 2008: pp. 23-25. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT.

  7. Effect of radon on SAGE results

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.; Mirmov, I.N.

    2002-01-01

    A method for estimating the systematic uncertainty associated with radon in the SAGE experiment aimed at observing the solar-neutrino flux is described. For the gallium target used in this experiment, the systematic uncertainty in the measured neutrino-capture rate of 75 SNU is below 0.3 SNU

  8. Lessons learned with the SAGE spectrometer

    International Nuclear Information System (INIS)

    Sorri, J; Greenlees, P T; Jones, P; Julin, R; Konki, J; Pakarinen, J; Rahkila, P; Sandzelius, M; Uusitalo, J; Papadakis, P; Cox, D M; Herzberg, R D

    2012-01-01

    The SAGE spectrometer combines a high-efficiency γ-ray detection system with an electron spectrometer. Some of the design features have been known to be problematic and surprises have come up during the early implementation of the spectrometer. Tests related to bismuth germanate Compton-suppression shields, electron detection efficiency and an improved cooling system are discussed in the paper. (paper)

  9. Sage grouse on the Idaho National Environmental Research Park

    International Nuclear Information System (INIS)

    Connelly, J.W.; Ball, I.J.

    1983-01-01

    A comprehensive study of sage grouse (Centrocercus urophasianus) ecology was conducted on the Idaho National Engineering Laboratory (INEL) site between June 1977 and May 1981. Sage grouse used lawns surrounding INEL facilities for feeding and loafing throughot the summer. Mean summer home range was 406 ha for adult female sage grouse and 94 ha for juveniles. Radionuclide concentrations in grouse summering near a liquid radioactive waste disposal area (N = 29) were significantly higher than those in grouse summering near a solid radioactive waste disposal area (N = 14) or control areas (N = 20). Sage grouse moved from 2 to 83 km during seasonal migration. Fall movements from INEL facilities to winter range were slow and meandering. Spring movements of females from leks to summer range were also slow and meandering but male movements appeared rapid and direct. Sage grouse remained in segregated flocks during early summer but the number of mixed sex flocks increased in late summer. Sage grouse occurred in segregated flocks throughout the winter. Both flock type and habitat influenced winter sage grouse flock size. Mean flock size remained relatively constant as winter weather became more severe. Agricultural aras were an important component of sage grouse summer range and were preferred by all sage grouse sex and age classes. Sage grouse winter range was generally characterized by sagebrush stands with 11 to 30% canopy coverage

  10. 78 FR 59368 - Notice of Public Meeting: Northeast California Resource Advisory Council Sage Grouse Conservation...

    Science.gov (United States)

    2013-09-26

    ... Public Meeting: Northeast California Resource Advisory Council Sage Grouse Conservation Subcommittee and...) Northeast California Resource Advisory Council's sage grouse conservation subcommittee and the full Resource... conservation of sage grouse habitat. On November 12, the subcommittee will develop a recommendation for...

  11. Shaping asteroid models using genetic evolution (SAGE)

    Science.gov (United States)

    Bartczak, P.; Dudziński, G.

    2018-02-01

    In this work, we present SAGE (shaping asteroid models using genetic evolution), an asteroid modelling algorithm based solely on photometric lightcurve data. It produces non-convex shapes, orientations of the rotation axes and rotational periods of asteroids. The main concept behind a genetic evolution algorithm is to produce random populations of shapes and spin-axis orientations by mutating a seed shape and iterating the process until it converges to a stable global minimum. We tested SAGE on five artificial shapes. We also modelled asteroids 433 Eros and 9 Metis, since ground truth observations for them exist, allowing us to validate the models. We compared the derived shape of Eros with the NEAR Shoemaker model and that of Metis with adaptive optics and stellar occultation observations since other models from various inversion methods were available for Metis.

  12. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

    Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

  13. Update regarding the society of American Gastrointestinal and Endoscopic Surgeons (SAGES) grant distribution and impact on recipient's academic career.

    Science.gov (United States)

    DuCoin, Christopher; Petersen, Rebecca P; Urbach, David; Aggarwal, Rajesh; Madan, Atul K; Pryor, Aurora D

    2018-07-01

    Small seed grants strongly impact academic careers, result in future funding, and lead to increased involvement in surgical societies. We hypothesize that, in accordance with the SAGES Research and Career Development committee mission, there has been a shift in grant support from senior faculty to residents and junior faculty. We hypothesize that these junior physician-researchers are subsequently remaining involved with SAGES and advancing within their academic institutions. All current and previous SAGES grant recipients were surveyed through Survey Monkey™. Questions included current academic status and status at time of grant, ensuing funding, publication and presentation of grant, and impact on career. Results were verified through a Medline query. SAGES database was examined for involvement within the society. Respondent data were compared to 2009 data. One hundred and ninety four grants were awarded to 167 recipients. Of those, 75 investigators responded for a response rate 44.9%. 32% were trainees, 43% assistant professors, 16% associate professors, 3% full professors, 3% professors with tenure, and 3% in private practice. This is a shift from 2009 data with a considerable increase in funding of trainees by 19% and assistant professors by 10% and a decrease in funding of associate professors by 5% and professors by 10%. 41% of responders who were awarded the grant as assistant or associate professors had advanced to full professor and 99% were currently in academic medicine. Eighty-two percent indicated that they had completed their project and 93% believed that the award helped their career. All responders remained active in SAGES. SAGES has chosen to reallocate an increased percentage of grant money to more junior faculty members and residents. It appears that these grants may play a role in keeping recipients interested in the academic surgical realm and involved in the society while simultaneously helping them advance in faculty rank.

  14. 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.

  15. SAGE 2.1: SOLVENT ALTERNATIVES GUIDE: USER'S GUIDE

    Science.gov (United States)

    The guide provides instruction for using the SAGE (Solvent Alternatives GuidE) software system, version 2.1. SAGE recommends solvent replacements in cleaning and degreasing operations. It leads the user through a question-and-answer session. The user's responses allow the system ...

  16. Ecology of greater sage-grouse in the Dakotas

    Science.gov (United States)

    Christopher C. Swanson

    2009-01-01

    Greater sage-grouse (Centrocercus urophasianus) populations and the sagebrush (Artemisia spp.) communities that they rely on have dramatically declined from historic levels. Moreover, information regarding sage-grouse annual life-history requirements at the eastern-most extension of sagebrush steppe communities is lacking....

  17. Statistical evaluation of SAGE libraries: consequences for experimental design

    NARCIS (Netherlands)

    Ruijter, Jan M.; van Kampen, Antoine H. C.; Baas, Frank

    2002-01-01

    Since the introduction of serial analysis of gene expression (SAGE) as a method to quantitatively analyze the differential expression of genes, several statistical tests have been published for the pairwise comparison of SAGE libraries. Testing the difference between the number of specific tags

  18. A Geant4 simulation package for the SAGE spectrometer

    International Nuclear Information System (INIS)

    Papadakis, P; Cox, D M; Butler, P A; Herzberg, R-D; Pakarinen, J; Konki, J; Greenlees, P T; Hauschild, K; Rahkila, P; Sandzelius, M; Sorri, J

    2012-01-01

    A comprehensive Geant4 simulation was built for the SAGE spectrometer. The simulation package includes the silicon and germanium detectors, the mechanical structure and the electromagnetic fields present in SAGE. This simulation can be used for making predictions through simulating experiments and for comparing simulated and experimental data to better understand the underlying physics.

  19. Molecular insights into the biology of Greater Sage-Grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Quinn, Thomas W.

    2011-01-01

    Recent research on Greater Sage-Grouse (Centrocercus urophasianus) genetics has revealed some important findings. First, multiple paternity in broods is more prevalent than previously thought, and leks do not comprise kin groups. Second, the Greater Sage-Grouse is genetically distinct from the congeneric Gunnison sage-grouse (C. minimus). Third, the Lyon-Mono population in the Mono Basin, spanning the border between Nevada and California, has unique genetic characteristics. Fourth, the previous delineation of western (C. u. phaios) and eastern Greater Sage-Grouse (C. u. urophasianus) is not supported genetically. Fifth, two isolated populations in Washington show indications that genetic diversity has been lost due to population declines and isolation. This chapter examines the use of molecular genetics to understand the biology of Greater Sage-Grouse for the conservation and management of this species and put it into the context of avian ecology based on selected molecular studies.

  20. Supporting Adolescents with Guidance and Employment (SAGE).

    Science.gov (United States)

    Ringwalt, C L; Graham, L A; Paschall, M J; Flewelling, R L; Browne, D C

    1996-01-01

    Supporting Adolescents with Guidance and Employment (SAGE) is a multifaceted, community-based violence-prevention program. Its target is African-American male adolescents in Durham, North Carolina. Public health professionals, county government officials, and local businessmen collaborated in its development and implementation. The program is based on the paradigm of risk and protective factors, in which various risk factors for youth violence are buffered by modifiable, protective psychosocial processes. SAGE includes an eight-month African-American Rites of Passage program (adult mentoring, African-American culture and history lessons, and manhood and conflict-resolution training), a six-week summer employment component, and a 12-week entrepreneurial experience. Of the 260 youth recruited, 88 were randomly assigned to receive all three program components, 85 were assigned to the summer employment and entrepreneurial components only, and 87 were assigned to a delayed program or control condition. We compared these three groups' psychosocial and behavioral outcomes using survey data and archival records. Program implementation data include attendance records; mentor-youth activity logs pre- and postprogram focus group discussions; and telephone interviews with parents, program staff, and participants. The mean age of the adolescents recruited into the program was 14. Half reported receiving free lunches at school; half were not living with a father; and one quarter reported that their mothers had not completed high school. During the previous year, many had engaged in various violence-related behaviors, including fighting (49%) and carrying a gun (22%). Youths in each program condition were similar with respect to key demographic and behavioral characteristics. The key components of the SAGE program represent increasingly popular but untested approaches. Preliminary results reveal that these youths are involved in violent behavior both as perpetrators and as

  1. The Soviet-American gallium experiment (SAGE)

    International Nuclear Information System (INIS)

    Garvey, G.T.

    1989-01-01

    The Soviet-American Gallium Experiment (SAGE) undertaking is a multi-institutional collaboration among scientists from the Institute for Nuclear Research, Moscow (INR), Los Alamos National Laboratory (LANL), and several US universities. It's purpose is to measure the number of low-energy electron neutrinos emitted from the Sun that arrive at this planet. As such, it is an extremely important experiment, touching on fundamental physics issues as well as solar dynamics. In contrast to the strategic overviews, plans, and hopes for intentional collaboration presented earlier today, SAGE is an ongoing working effort with high hopes of producing the first measurement of the Sun's low-energy flux. There are several international physics collaborations involving US and Soviet scientists at the large accelerator installations throughout the world. As the scale of research gets ever larger, requiring ever more resources and then larger collaborations. Much physics research lies solely in the realm of basic research so that governments feel easier about collaborations. Contacts between the US and USSR scientists interested in nuclear and particle physics goes back to the nineteen fifties and have continued with only minor interruptions since then. Over the past two decades the principal oversight of these activities has been through the Joint Coordinating Committee on the Fundamental Properties of Matter, supported by the DOE in the US and the State Committee for Atomic Energy in the USSR. The Academies of Science of both countries have been very helpful and supportive. Each venture has some distinguishing features; in the case of SAGE, the unique aspects are the collaboration between Soviet scientists and scientists at a DOE weapons laboratory and the fact that the experiment is carried out in a remote region of the USSR. The particular problems caused are discussed. 3 refs., 3 figs

  2. SAGE II measurements of early Pinatubo aerosols

    Science.gov (United States)

    Mccormick, M. P.; Veiga, R. E.

    1992-01-01

    SAGE II satellite measurements of the Mt. Pinatubo eruption cloud in the stratosphere during June, July, and early August 1991 show that aerosols in the tropics reached as high as 29 km altitude with most of the cloud between 20 and 25 km. The most optically thick portions of the cloud covered latitudes from 10 deg S to 30 deg N during the early part of this period. By late July, high stratospheric optical depths were observed to at least 70 deg N, with the high values north of about 30 deg N from layers below 20 km. High pressure systems in both hemispheres were observed to be correlated with the movement of volcanic material at 21 km into the westerly jet stream at high southern latitudes and similarly to high northern latitudes at 16 km. By August, the entire Southern Hemisphere had experienced a 10-fold increase in optical depth relative to early July due to layers above 20 km. Initial mass calculations using SAGE II data place the aerosol produced from this eruption at 20 to 30 megatons, well above the 12 megatons produced by El Chichon.

  3. Automatic Deduction in Dynamic Geometry using Sage

    Directory of Open Access Journals (Sweden)

    Francisco Botana

    2012-02-01

    Full Text Available We present a symbolic tool that provides robust algebraic methods to handle automatic deduction tasks for a dynamic geometry construction. The main prototype has been developed as two different worksheets for the open source computer algebra system Sage, corresponding to two different ways of coding a geometric construction. In one worksheet, diagrams constructed with the open source dynamic geometry system GeoGebra are accepted. In this worksheet, Groebner bases are used to either compute the equation of a geometric locus in the case of a locus construction or to determine the truth of a general geometric statement included in the GeoGebra construction as a boolean variable. In the second worksheet, locus constructions coded using the common file format for dynamic geometry developed by the Intergeo project are accepted for computation. The prototype and several examples are provided for testing. Moreover, a third Sage worksheet is presented in which a novel algorithm to eliminate extraneous parts in symbolically computed loci has been implemented. The algorithm, based on a recent work on the Groebner cover of parametric systems, identifies degenerate components and extraneous adherence points in loci, both natural byproducts of general polynomial algebraic methods. Detailed examples are discussed.

  4. Monoterpene synthases from common sage (Salvia officinalis)

    Energy Technology Data Exchange (ETDEWEB)

    Croteau, Rodney Bruce (Pullman, WA); Wise, Mitchell Lynn (Pullman, WA); Katahira, Eva Joy (Pullman, WA); Savage, Thomas Jonathan (Christchurch 5, NZ)

    1999-01-01

    cDNAs encoding (+)-bornyl diphosphate synthase, 1,8-cineole synthase and (+)-sabinene synthase from common sage (Salvia officinalis) have been isolated and sequenced, and the corresponding amino acid sequences has been determined. Accordingly, isolated DNA sequences (SEQ ID No:1; SEQ ID No:3 and SEQ ID No:5) are provided which code for the expression of (+)-bornyl diphosphate synthase (SEQ ID No:2), 1,8-cineole synthase (SEQ ID No:4) and (+)-sabinene synthase SEQ ID No:6), respectively, from sage (Salvia officinalis). In other aspects, replicable recombinant cloning vehicles are provided which code for (+)-bornyl diphosphate synthase, 1,8-cineole synthase or (+)-sabinene synthase, or for a base sequence sufficiently complementary to at least a portion of (+)-bornyl diphosphate synthase, 1,8-cineole synthase or (+)-sabinene synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding (+)-bornyl diphosphate synthase, 1,8-cineole synthase or (+)-sabinene synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant monoterpene synthases that may be used to facilitate their production, isolation and purification in significant amounts. Recombinant (+)-bornyl diphosphate synthase, 1,8-cineole synthase and (+)-sabinene synthase may be used to obtain expression or enhanced expression of (+)-bornyl diphosphate synthase, 1,8-cineole synthase and (+)-sabinene synthase in plants in order to enhance the production of monoterpenoids, or may be otherwise employed for the regulation or expression of (+)-bornyl diphosphate synthase, 1,8-cineole synthase and (+)-sabinene synthase, or the production of their products.

  5. The Russian-American Gallium solar neutrino Experiment (SAGE)

    International Nuclear Information System (INIS)

    Bowles, T.J.

    1994-01-01

    The Russian-American Gallium Experiment (SAGE) began measurements of the integral flux of solar neutrinos using 30 tons of metallic gallium as the target in January 1990. The mass of the gallium was increased to 57 tons in September 1991 and SAGE began to count the decay of 71 Ge using both the K and L peaks in September 1992. The results indicate a deficit of about 40% of the flux predicted by the Standard Solar Model. The chemical extraction and counting techniques used by SAGE are presented, with particular attention on backgrounds. The present status, results, and future plans of SAGE are presented, along with a discussion of the possible physics implications

  6. Long SAGE analysis of genes differentially expressed in the midgut ...

    African Journals Online (AJOL)

    Long SAGE analysis of genes differentially expressed in the midgut and silk gland between the sexes of the silkwormBombyx mori. Liping Gan, Ying Wang, Jian Xi, Yanshan Niu, Hongyou Qin, Yanghu Sima, Shiqing Xu ...

  7. SAGE - MULTIDIMENSIONAL SELF-ADAPTIVE GRID CODE

    Science.gov (United States)

    Davies, C. B.

    1994-01-01

    SAGE, Self Adaptive Grid codE, is a flexible tool for adapting and restructuring both 2D and 3D grids. Solution-adaptive grid methods are useful tools for efficient and accurate flow predictions. In supersonic and hypersonic flows, strong gradient regions such as shocks, contact discontinuities, shear layers, etc., require careful distribution of grid points to minimize grid error and produce accurate flow-field predictions. SAGE helps the user obtain more accurate solutions by intelligently redistributing (i.e. adapting) the original grid points based on an initial or interim flow-field solution. The user then computes a new solution using the adapted grid as input to the flow solver. The adaptive-grid methodology poses the problem in an algebraic, unidirectional manner for multi-dimensional adaptations. The procedure is analogous to applying tension and torsion spring forces proportional to the local flow gradient at every grid point and finding the equilibrium position of the resulting system of grid points. The multi-dimensional problem of grid adaption is split into a series of one-dimensional problems along the computational coordinate lines. The reduced one dimensional problem then requires a tridiagonal solver to find the location of grid points along a coordinate line. Multi-directional adaption is achieved by the sequential application of the method in each coordinate direction. The tension forces direct the redistribution of points to the strong gradient region. To maintain smoothness and a measure of orthogonality of grid lines, torsional forces are introduced that relate information between the family of lines adjacent to one another. The smoothness and orthogonality constraints are direction-dependent, since they relate only the coordinate lines that are being adapted to the neighboring lines that have already been adapted. Therefore the solutions are non-unique and depend on the order and direction of adaption. Non-uniqueness of the adapted grid is

  8. Sage-grouse habitat selection during winter in Alberta

    Science.gov (United States)

    Carpenter, Jennifer L.; Aldridge, Cameron L.; Boyce, Mark S.

    2010-01-01

    Greater sage-grouse (Centrocercus urophasianus) are dependent on sagebrush (Artemisia spp.) for food and shelter during winter, yet few studies have assessed winter habitat selection, particularly at scales applicable to conservation planning. Small changes to availability of winter habitats have caused drastic reductions in some sage-grouse populations. We modeled winter habitat selection by sage-grouse in Alberta, Canada, by using a resource selection function. Our purpose was to 1) generate a robust winter habitat-selection model for Alberta sage-grouse; 2) spatially depict habitat suitability in a Geographic Information System to identify areas with a high probability of selection and thus, conservation importance; and 3) assess the relative influence of human development, including oil and gas wells, in landscape models of winter habitat selection. Terrain and vegetation characteristics, sagebrush cover, anthropogenic landscape features, and energy development were important in top Akaike's Information Criterionselected models. During winter, sage-grouse selected dense sagebrush cover and homogenous less rugged areas, and avoided energy development and 2-track truck trails. Sage-grouse avoidance of energy development highlights the need for comprehensive management strategies that maintain suitable habitats across all seasons. ?? 2010 The Wildlife Society.

  9. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

    Science.gov (United States)

    Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

    2015-07-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Greater Sage-Grouse (Centrocercus Urophasianus) Hen Survival: Effects of Raptors, Anthropogenic and Landscape Features, and Hen Behavior

    OpenAIRE

    Dinkins, Jonathan B.; Conover, Michael R.; Kirol, Christopher P.; Beck, Jeffrey L.; Frey, S. Nicole

    2014-01-01

    Survival of breeding-age hens has been identified as the demographic rate with the greatest potential to influence population growth of Greater Sage-Grouse (Centrocercus urophasianus (Bonaparte, 1827); hereafter “Sage-Grouse”). During 2008–2011, we collected summer survival data from 427 Sage-Grouse hens in southern Wyoming, USA. We assessed the effects of raptor densities, anthropogenic features, landscape features, and Sage-Grouse hen behavior on Sage-Grouse hen survival. Survival of Sage-G...

  11. A comparative Analysis by SAGE of Gene Expression Profiles of Esophageal Adenocarcinoma and Esophageal Squamous Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Jantine W. P. M. van Baal

    2008-01-01

    Full Text Available Esophageal adenocarcinoma (EA and esophageal squamous cell carcinoma (ESCC are the two main types of esophageal cancer. Despite extensive research the exact molecular basis of these cancers is unclear. Therefore we evaluated the transcriptome of EA in comparison to non-dysplastic Barrett’s esophagus (BE, the metaplastic epithelium that predisposes for EA, and compared the transcriptome of ESCC to normal esophageal squamous epithelium. For obtaining the transcriptomes tissue biopsies were used and serial analysis of gene expression (SAGE was applied. Validation of results by RT-PCR and immunoblotting was performed using tissues of an additional 23 EA and ESCC patients. Over 58,000 tags were sequenced. Between EA and BE 1013, and between ESCC and normal squamous epithelium 1235 tags were significantly differentially expressed (p < 0.05. The most up-regulated genes in EA compared to BE were SRY-box 4 and Lipocalin2, whereas the most down-regulated genes in EA were Trefoil factors and Annexin A10. The most up-regulated genes in ESCC compared to normal squamous epithelium were BMP4, E-Cadherin and TFF3. The results could suggest that the BE expression profile is closer related to normal squamous esophagus then to EA. In addition, several uniquely expressed genes are identified.

  12. Bias correction and Bayesian analysis of aggregate counts in SAGE libraries

    Directory of Open Access Journals (Sweden)

    Briggs William M

    2010-02-01

    Full Text Available Abstract Background Tag-based techniques, such as SAGE, are commonly used to sample the mRNA pool of an organism's transcriptome. Incomplete digestion during the tag formation process may allow for multiple tags to be generated from a given mRNA transcript. The probability of forming a tag varies with its relative location. As a result, the observed tag counts represent a biased sample of the actual transcript pool. In SAGE this bias can be avoided by ignoring all but the 3' most tag but will discard a large fraction of the observed data. Taking this bias into account should allow more of the available data to be used leading to increased statistical power. Results Three new hierarchical models, which directly embed a model for the variation in tag formation probability, are proposed and their associated Bayesian inference algorithms are developed. These models may be applied to libraries at both the tag and aggregate level. Simulation experiments and analysis of real data are used to contrast the accuracy of the various methods. The consequences of tag formation bias are discussed in the context of testing differential expression. A description is given as to how these algorithms can be applied in that context. Conclusions Several Bayesian inference algorithms that account for tag formation effects are compared with the DPB algorithm providing clear evidence of superior performance. The accuracy of inferences when using a particular non-informative prior is found to depend on the expression level of a given gene. The multivariate nature of the approach easily allows both univariate and joint tests of differential expression. Calculations demonstrate the potential for false positive and negative findings due to variation in tag formation probabilities across samples when testing for differential expression.

  13. Measurement of fast neutron background in SAGE

    CERN Document Server

    Abdurashitov, J N; Kalikhov, A V; Matushko, V L; Shikhin, A A; Yants, V E; Zaborskaia, O S

    2002-01-01

    The spectrometer intended for direct measurements of ultra low fluxes of fast neutrons is described. It is sensitive to neutron fluxes of 10 sup - sup 7 cm sup - sup 2 s sup - sup 1 and lower. The detection efficiency of fast neutrons with simultaneous energy measurement was determined from Monte-Carlo simulation to be equal to 0.11 +- 0.01. The background counting rate in the detector corresponds to a neutron flux of (6.5 +- 2.1) x 10 sup - sup 7 cm sup - sup 2 s sup - sup 1 in the range 1.0-11.0 MeV. The natural neutron flux from the surrounding mine rock at the depth of 4700 meters of water equivalent was measured to be (7.3 +- 2.4) x 10 sup - sup 7 cm sup - sup 2 s sup - sup 1 in the range 1.0-11.0 MeV. The flux of fast neutrons in the SAGE main room was measured to be < 2.3 x 10 sup - sup 7 cm sup - sup 2 s sup - sup 1 in 1.0-11.0 MeV energy range.

  14. Measurement of fast neutron background in SAGE

    International Nuclear Information System (INIS)

    Abdurashitov, J.N.; Gavrin, V.N.; Kalikhov, A.V.; Matushko, V.L.; Shikhin, A.A.; Yants, V.E.; Zaborskaia, O.S.

    2002-01-01

    The spectrometer intended for direct measurements of ultra low fluxes of fast neutrons is described. It is sensitive to neutron fluxes of 10 -7 cm -2 s -1 and lower. The detection efficiency of fast neutrons with simultaneous energy measurement was determined from Monte-Carlo simulation to be equal to 0.11 ± 0.01. The background counting rate in the detector corresponds to a neutron flux of (6.5 ± 2.1) x 10 -7 cm -2 s -1 in the range 1.0-11.0 MeV. The natural neutron flux from the surrounding mine rock at the depth of 4700 meters of water equivalent was measured to be (7.3 ± 2.4) x 10 -7 cm -2 s -1 in the range 1.0-11.0 MeV. The flux of fast neutrons in the SAGE main room was measured to be -7 cm -2 s -1 in 1.0-11.0 MeV energy range

  15. Stratospheric ozone profile and total ozone trends derived from the SAGE I and SAGE II data

    Science.gov (United States)

    Mccormick, M. P.; Veiga, Robert E.; Chu, William P.

    1992-01-01

    Global trends in both stratospheric column ozone and as a function of altitude are derived on the basis of SAGE I/II ozone data from the period 1979-1991. A statistical model containing quasi-biennial, seasonal, and semiannual oscillations, a linear component, and a first-order autoregressive noise process was fit to the time series of SAGE I/II monthly zonal mean data. The linear trend in column ozone above 17-km altitude, averaged between 65 deg S and 65 deg N, is -0.30 +/-0.19 percent/yr, or -3.6 percent over the time period February 1979 through April 1991. The data show that the column trend above 17 km is nearly zero in the tropics and increases towards the high latitudes with values of -0.6 percent/yr at 60 deg S and -0.35 percent/yr at 60 deg N. Both these results are in agreement with the recent TOMS results. The profile trend analyses show that the column ozone losses are occurring below 25 km, with most of the loss coming from the region between 17 and 20 km. Negative trend values on the order of -2 percent/yr are found at 17 km in midlatitudes.

  16. Four Intoxication Cases Related to the Misuse of Sage Oil

    Directory of Open Access Journals (Sweden)

    Suzan Gündüz

    2016-06-01

    Full Text Available Infantile colic is excessive crying of infants younger than 4 months. Families of children suffering from infantile colic attend to the emergency department frequently and the etiology is not well-known. However many families of chil­dren suffering from infantile colic try pharmacologic and non-pharmacologic treatment, they are sleepless and ex­hausted and are affected negatively. Sage oil is in volatile form and it is recommended to apply 1-2 drops on plantar and tummy region of the body by massage for the treat­ment of infantile colic. Most of drugs used for infantile colic are drops and used orally. Families who do not learn detailed usage information may use it orally or may pre­sumed another drug while suffering from sleepless and drowsiness. Herein we reported 4 cases of sage oil intoxi­cation because of wrong information of wrong application of sage oil. We aimed to reduce the prescribing of sage oil in the treatment of infantile colic and emphasize to give more information about proper use of sage oil.

  17. Nesting success and resource selection of Greater Sage-Grouse [chapter 8

    Science.gov (United States)

    Nicholas W. Kaczor; Kent C. Jensen; Robert W. Klaver; Mark A. Rumble; Katie M. Herman-Brunson; Christopher C. Swanson

    2011-01-01

    Declines of Greater Sage-Grouse (Centrocercus urophasianus) in South Dakota are a concern because further population declines may lead to isolation from populations in Wyoming and Montana. Furthermore, little information exists about reproductive ecology and resource selection of sage grouse on the eastern edge of their distribution. We investigated Greater Sage-Grouse...

  18. 78 FR 65936 - Endangered and Threatened Wildlife and Plants; Proposed Endangered Status for Gunnison Sage...

    Science.gov (United States)

    2013-11-04

    ... and Plants; Proposed Endangered Status for Gunnison Sage-Grouse and Proposed Designation of Critical Habitat for Gunnison Sage-Grouse AGENCY: Fish and Wildlife Service, Interior. ACTION: Proposed rule... rules to list the Gunnison sage-grouse (Centrocercus minimus) as endangered and to designate critical...

  19. 78 FR 2539 - Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for Gunnison Sage...

    Science.gov (United States)

    2013-01-11

    ... Gunnison Sage-Grouse; Proposed Rule #0;#0;Federal Register / Vol. 78 , No. 8 / Friday, January 11, 2013...; Designation of Critical Habitat for Gunnison Sage-Grouse AGENCY: Fish and Wildlife Service, Interior. ACTION... the Gunnison sage-grouse (Centrocercus minimus) under the Endangered Species Act of 1973, as amended...

  20. Lek ecology of male greater sage-grouse in Carbon County, Wyoming

    Science.gov (United States)

    Aleshia Lynn Fremgen

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus, hereafter "sage-grouse") have experienced range-wide population declines for several decades, and as a result they were considered warranted for listing under the Endangered Species Act in 2010. Therefore, wildlife managers need to understand how sage-grouse breeding behavior influences long-term reproductive...

  1. Resource selection during brood-rearing by Greater Sage-Grouse [chapter 12

    Science.gov (United States)

    Nicholas W. Kaczor; Katie M. Herman-Brunson; Kent C. Jensen; Mark A. Rumble; Robert W. Klaver; Christopher C. Swanson

    2011-01-01

    Understanding population dynamics and resource selection is crucial in developing wildlife resource management plans for sensitive species such as Greater Sage-Grouse (Centrocercus urophasianus). Little is known about sage grouse habitats on the eastern edge of their range. We investigated resource selection of Greater Sage-Grouse during brood- rearing in North and...

  2. An overview af SAGE I and II ozone measurements

    Science.gov (United States)

    Mccormick, M. P.; Zawodny, J. M.; Veiga, R. E.; Larsen, J. C.; Wang, P. H.

    1989-01-01

    The stratospheric Aerosol and Gas Experiments (SAGE) I and II measure Mie, Rayleigh, and gaseous extinction profiles using the solar occultation technique. These global measurements yield ozone profiles with a vertical resolution of 1 km which have been routinely obtained for the periods from February 1979 to November 1981 (SAGE I) and October 1984 to the present (SAGE II). The long-term periodic behavior of the measured ozone is presented as well as case studies of the observed short-term spatial and temporal variability. A linear regression shows annual, semiannual, and quasi-biennial oscillation features at various altitudes and latitudes which, in general, agree with past work. Also, ozone, aerosol, and water vapor data are described for the Antarctic springtime, showing large variation relative to the vortex. Cross-sections in latitude and altitude and polar plots at various altitudes clearly delineate the ozone hole vertically and areally.

  3. The Escherichia coli transcriptome linked to growth fitness

    Directory of Open Access Journals (Sweden)

    Bei-Wen Ying

    2016-03-01

    Full Text Available A series of Escherichia coli strains with varied genomic sequences were subjected to high-density microarray analyses to elucidate the fitness-correlated transcriptomes. Fitness, which is commonly evaluated by the growth rate during the exponential phase, is not only determined by the genome but is also linked to growth conditions, e.g., temperature. We previously reported genetic and environmental contributions to E. coli transcriptomes and evolutionary transcriptome changes in thermal adaptation. Here, we describe experimental details on how to prepare microarray samples that truly represent the growth fitness of the E. coli cells. A step-by-step record of sample preparation procedures that correspond to growing cells and transcriptome data sets that are deposited at the GEO database (GSE33212, GSE52770, GSE61739 are also provided for reference. Keywords: Transcriptome, Growth fitness, Escherichia coli, Microarray

  4. How do SAGES members rate its guidelines?

    Science.gov (United States)

    Hope, William W; Richardson, William; Fanelli, Robert; Stefanidis, Dimitrios

    2014-04-01

    The development of practice guidelines should take into consideration the opinions of end users. The Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) has implemented several changes in its guideline development and dissemination process based on previous end-user input. An anonymous electronic survey was conducted via e-mail solicitation in September 2011. Respondents were asked to submit their feedback on the 26 guidelines produced by our society using a 32-item questionnaire and to suggest topics for new guideline development and areas of improvement. Responses from the survey were received by 494 people, of whom 474 (96 %) were clinicians; 373 (75 %) were general, laparoscopic, or bariatric surgeons; and 324 (65 %) held leadership roles within their institution. Most respondents were 35-44 years old (36 %), male (83 %), and had been in practice for over 10 years (54 %). A total of 383 (81 %) had used our guidelines, and, of those, 96 % agreed with their content. Guideline quality was rated 4.34; value 4.27; and ease of access 3.97 on a five-point Likert scale. The most commonly referenced guideline in the survey regarded surgical treatment of reflux (67 %), followed by laparoscopy during pregnancy (51 %). The three most common reasons guidelines were accessed were to update knowledge (68 %), to maximize patient care through evidence-based treatment (51 %), and to obtain a critical literature review. The majority of respondents indicated they greatly value and agree with our guidelines. These results indicate that recent efforts to improve our guidelines have succeeded.

  5. Web services for transcriptomics

    NARCIS (Netherlands)

    Neerincx, P.

    2009-01-01

    Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as

  6. SAGE 2.0 SOLVENT ALTERNATIVES GUIDE - USER'S GUIDE

    Science.gov (United States)

    The guide provides instruction for using the SAGE (Solvent Alternatives Guide) software system, version 2.O. It assumes that the user is familiar with the fundamentals of operating a personal computer under the Microsoft disk operating system (MS-DOS). AGE recommends solvent repl...

  7. Male greater sage-grouse detectability on leks

    Science.gov (United States)

    Aleshia L. Fremgen; Christopher P. Hansen; Mark A. Rumble; R. Scott Gamo; Joshua J. Millspaugh

    2016-01-01

    It is unlikely all male sage-grouse are detected during lek counts, which could complicate the use of lek counts as an index to population abundance. Understanding factors that influence detection probabilities will allow managers to more accurately estimate the number of males present on leks. We fitted 410 males with global positioning system and very high...

  8. USDA Forest Service Sage-Grouse Conservation Science Strategy

    Science.gov (United States)

    Deborah Finch; Douglas Boyce; Jeanne Chambers; Chris Colt; Clint McCarthy; Stanley Kitchen; Bryce Richardson; Mary Rowland; Mark Rumble; Michael Schwartz; Monica Tomosy; Michael Wisdom

    2015-01-01

    Numerous federal and state agencies, research institutions and stakeholders have undertaken tremendous conservation and research efforts across 11 States in the western United States to reduce threats to Greater Sage-Grouse (Centrocercus urophasianus) and sagebrush (Artemisia spp) habitats. In 2010, the U.S. Fish and Wildlife Service (USFWS) determined that the Greater...

  9. Inhibitory effect of aromatic herbs, lavender, sage and chamomile ...

    African Journals Online (AJOL)

    This study demonstrated anti-herpes simplex virus (HSV) activity of lavender, sage and chamomile extracts. Green monkey kidney cells were protected from HSV-2 infection by dichloromethane and methanol extract of lavender with therapeutic indices (TI) of 1.98 and 2.90, respectively when the cells were treated before ...

  10. Composition of the essential oil of White sage, Salvia apiana.

    Energy Technology Data Exchange (ETDEWEB)

    Hochrein, James Michael; Irwin, Adriane Nadine; Borek, Theodore Thaddeus, III

    2003-08-01

    The essential oil of white sage, Salvia apiana, was obtained by steam distillation and analysed by GC-MS. A total of 13 components were identified, accounting for >99.9% of the oil. The primary component was 1,8-cineole, accounting for 71.6% of the oil.

  11. Effect of sage extract ( Salvia officinalis ) on growth performance ...

    African Journals Online (AJOL)

    This study was performed to evaluate the effect of different doses of sage extract on the growth and blood parameters, oxidative stress and DNA damage in partridges. In total, 252 day-old partridges (Alectoris chukar) were used. The birds were divided into four groups: 0.1% flavomycin was included in the diet of the control ...

  12. Field Geophysics at SAGE: Strategies for Effective Education

    Science.gov (United States)

    Braile, L. W.; Baldridge, W. S.; Jiracek, G. R.; Biehler, S.; Ferguson, J. F.; Pellerin, L.; McPhee, D. K.; Bedrosian, P. A.; Snelson, C. M.; Hasterok, D. P.

    2011-12-01

    SAGE (Summer of Applied Geophysical Experience) is a unique program of education and research in geophysical field methods for undergraduate and graduate students from any university and for professionals. The core program is held for 4 weeks each summer in New Mexico and for an additional week in the following academic year in San Diego for U.S. undergraduates supported by the NSF Research Experience for Undergraduates (REU) program. Since SAGE was initiated in 1983, 730 students have participated in the program. NSF REU funding for SAGE began in 1990 and 319 REU students have completed SAGE through 2011. The primary objectives of SAGE are to teach the major geophysical exploration methods (seismic, gravity, magnetics, electromagnetics); apply these methods to the solution of specific problems (environmental, archaeological, hydrologic, geologic structure and stratigraphy); gain experience in processing, modeling and interpretation of geophysical data; and integrate the geophysical models and interpretations with geology. Additional objectives of SAGE include conducting research on the Rio Grande rift of northern New Mexico, and providing information on geophysics careers and professional development experiences to SAGE participants. Successful education, field and research strategies that we have implemented over the years include: 1. learn by doing; 2. mix lecture/discussion, field work, data processing and analysis, modeling and interpretation, and presentation of results; 3. a two-tier team approach - method/technique oriented teams and interpretation/integration teams (where each team includes persons representing different methods), provides focus, in-depth study, opportunity for innovation, and promotes teamwork and a multi-disciplinary approach; 4. emphasis on presentations/reports - each team (and all team members) make presentation, each student completes a written report; 5. experiment design discussion - students help design field program and consider

  13. SAGES climate survey: results and strategic planning for our future.

    Science.gov (United States)

    Telem, Dana A; Qureshi, Alia; Edwards, Michael; Jones, Daniel B

    2018-03-30

    While SAGES prides itself on diversity and inclusivity, we also recognize that as an organization we are not impervious to blind spots impacting equity within the membership. To address this, the We R Sages task force was formed to identify the barriers and facilitators to creating a diverse organization and develop a strategic plan for the implementation of programing and opportunities that promote diversity and inclusivity within our membership. As the first step in the process, a survey was administered to gauge the current organizational climate. In September of 2017, a validated climate survey was administered to 704 SAGES committee members via SurveyMonkey®. Climate was assessed on: overall SAGES experience, consideration of leaving the organization, mentorship within the organization, resources and opportunities within the organization, and attitudes and experiences within the organization. Additional free text responses were encouraged to generate qualitative themes. The survey response rate was 52.1% (n = 367). Respondent self-identified demographics were: male (73%), white (63%), heterosexual (95.5%), and non-disabled (98%). Average overall satisfaction was 8.1/10. 12.5% of respondents had considered leaving the organization and 74.4% had not identified a formal mentor within the organization. Average agreement with equitable distribution of resources and opportunities was 5.8/10. 93.6% of respondents had not experienced bias within the organization. Overall SAGES has a very positive climate; however, several key issues were identified from the quantitative survey as well as the free text responses. Strategic planning to address issues of membership recruitment, committee engagement, advancement transparency, diversity awareness, leadership development, and formal mentorship are being implemented.

  14. Development of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus)

    Science.gov (United States)

    Fike, Jennifer A.; Oyler-McCance, Sara J.; Zimmerman, Shawna J; Castoe, Todd A.

    2015-01-01

    Gunnison Sage-grouse are an obligate sagebrush species that has experienced significant population declines and has been proposed for listing under the U.S. Endangered Species Act. In order to examine levels of connectivity among Gunnison Sage-grouse leks, we identified 13 novel microsatellite loci though next-generation shotgun sequencing, and tested them on the closely related Greater Sage-grouse. The number of alleles per locus ranged from 2 to 12. No loci were found to be linked, although 2 loci revealed significant departures from Hardy–Weinberg equilibrium or evidence of null alleles. While these microsatellites were designed for Gunnison Sage-grouse, they also work well for Greater Sage-grouse and could be used for numerous genetic questions including landscape and population genetics.

  15. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

  16. Determination of absolute internal conversion coefficients using the SAGE spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Sorri, J., E-mail: juha.m.t.sorri@jyu.fi [University of Jyvaskyla, Department of Physics, P.O. Box 35, FI-40014 University of Jyvaskyla (Finland); Greenlees, P.T.; Papadakis, P.; Konki, J. [University of Jyvaskyla, Department of Physics, P.O. Box 35, FI-40014 University of Jyvaskyla (Finland); Cox, D.M. [University of Jyvaskyla, Department of Physics, P.O. Box 35, FI-40014 University of Jyvaskyla (Finland); Department of Physics, University of Liverpool, Oxford Street, Liverpool L69 7ZE (United Kingdom); Auranen, K.; Partanen, J.; Sandzelius, M.; Pakarinen, J.; Rahkila, P.; Uusitalo, J. [University of Jyvaskyla, Department of Physics, P.O. Box 35, FI-40014 University of Jyvaskyla (Finland); Herzberg, R.-D. [Department of Physics, University of Liverpool, Oxford Street, Liverpool L69 7ZE (United Kingdom); Smallcombe, J.; Davies, P.J.; Barton, C.J.; Jenkins, D.G. [Department of Physics, University of York, Heslington, York YO10 5DD (United Kingdom)

    2016-03-11

    A non-reference based method to determine internal conversion coefficients using the SAGE spectrometer is carried out for transitions in the nuclei of {sup 154}Sm, {sup 152}Sm and {sup 166}Yb. The Normalised-Peak-to-Gamma method is in general an efficient tool to extract internal conversion coefficients. However, in many cases the required well-known reference transitions are not available. The data analysis steps required to determine absolute internal conversion coefficients with the SAGE spectrometer are presented. In addition, several background suppression methods are introduced and an example of how ancillary detectors can be used to select specific reaction products is given. The results obtained for ground-state band E2 transitions show that the absolute internal conversion coefficients can be extracted using the methods described with a reasonable accuracy. In some cases of less intense transitions only an upper limit for the internal conversion coefficient could be given.

  17. Determination of absolute internal conversion coefficients using the SAGE spectrometer

    International Nuclear Information System (INIS)

    Sorri, J.; Greenlees, P.T.; Papadakis, P.; Konki, J.; Cox, D.M.; Auranen, K.; Partanen, J.; Sandzelius, M.; Pakarinen, J.; Rahkila, P.; Uusitalo, J.; Herzberg, R.-D.; Smallcombe, J.; Davies, P.J.; Barton, C.J.; Jenkins, D.G.

    2016-01-01

    A non-reference based method to determine internal conversion coefficients using the SAGE spectrometer is carried out for transitions in the nuclei of "1"5"4Sm, "1"5"2Sm and "1"6"6Yb. The Normalised-Peak-to-Gamma method is in general an efficient tool to extract internal conversion coefficients. However, in many cases the required well-known reference transitions are not available. The data analysis steps required to determine absolute internal conversion coefficients with the SAGE spectrometer are presented. In addition, several background suppression methods are introduced and an example of how ancillary detectors can be used to select specific reaction products is given. The results obtained for ground-state band E2 transitions show that the absolute internal conversion coefficients can be extracted using the methods described with a reasonable accuracy. In some cases of less intense transitions only an upper limit for the internal conversion coefficient could be given.

  18. Serial analysis of gene expression (SAGE) in rat liver regeneration

    International Nuclear Information System (INIS)

    Cimica, Velasco; Batusic, Danko; Haralanova-Ilieva, Borislava; Chen, Yonglong; Hollemann, Thomas; Pieler, Tomas; Ramadori, Giuliano

    2007-01-01

    We have applied serial analysis of gene expression for studying the molecular mechanism of the rat liver regeneration in the model of 70% partial hepatectomy. We generated three SAGE libraries from a normal control liver (NL library: 52,343 tags), from a sham control operated liver (Sham library: 51,028 tags), and from a regenerating liver (PH library: 53,061 tags). By SAGE bioinformatics analysis we identified 40 induced genes and 20 repressed genes during the liver regeneration. We verified temporal expression of such genes by real time PCR during the regeneration process and we characterized 13 induced genes and 3 repressed genes. We found connective tissue growth factor transcript and protein induced very early at 4 h after PH operation before hepatocytes proliferation is triggered. Our study suggests CTGF as a growth factor signaling mediator that could be involved directly in the mechanism of liver regeneration induction

  19. Sage-Grouse and Wind Energy: Biology, Habits, and Potential Effects from Development

    Energy Technology Data Exchange (ETDEWEB)

    Becker, James M.; Tagestad, Jerry D.; Duberstein, Corey A.; Downs, Janelle L.

    2009-07-15

    Proposed development of domestic energy resources, including wind energy, is expected to impact the sagebrush steppe ecosystem in the western United States. The greater sage-grouse relies on habitats within this ecosystem for survival, yet very little is known about how wind energy development may affect sage-grouse. The purpose of this report is to inform organizations of the impacts wind energy development could have on greater sage-grouse populations and identify information needed to fill gaps in knowledge.

  20. Smart and Green Energy (SAGE) for Base Camps Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Engels, Matthias; Boyd, Paul A.; Koehler, Theresa M.; Goel, Supriya; Sisk, Daniel R.; Hatley, Darrel D.; Mendon, Vrushali V.; Hail, John C.

    2014-02-11

    The U.S. Army Logistics Innovation Agency’s (LIA’s) Smart and Green Energy (SAGE) for Base Camps project was to investigate how base camps’ fuel consumption can be reduced by 30% to 60% using commercial off-the-shelf (COTS) technologies for power generation, renewables, and energy efficient building systems. Field tests and calibrated energy models successfully demonstrated that the fuel reductions are achievable.

  1. Interspecific nest parasitism by chukar on greater sage-grouse

    Science.gov (United States)

    Fearon, Michelle L.; Coates, Peter S.

    2014-01-01

    Nest parasitism occurs when a female bird lays eggs in the nest of another and the host incubates the eggs and may provide some form of parental care for the offspring (Lyon and Eadie 1991). Precocial birds (e.g., Galliformes and Anseriformes) are typically facultative nest parasites of both their own and other species (Lyon and Eadie 1991). This behavior increases a female’s reproductive success when she parasitizes other nests while simultaneously raising her own offspring. Both interspecific and conspecific nest parasitism have been well documented in several families of the order Galliformes, particularly the Phasianidae (Lyon and Eadie 1991, Geffen and Yom-Tov 2001, Krakauer and Kimball 2009). The Chukar (Alectoris chukar) has been widely introduced as a game bird to western North America from Eurasia and is now well established within the Great Basin from northeastern California east to Utah and north to Idaho and Oregon (Christensen 1996). Over much of this range the Chukar occurs with other phasianids, including the native Greater Sage-Grouse (Centrocercus urophasianus), within sagebrush (Artemisia spp.) steppe (Christensen 1996, Schroeder et al. 1999, Connelly et al. 2000). Chukar typically exploit a broader range of habitats than do sage-grouse, but both species use the same species of sagebrush and other shrubs for nesting cover (Christensen 1996, Schroeder et al. 1999). Chukar are known to parasitize nests of other individuals of their own species (Geffen and Yom-Tov 2001), but we are unaware of reported evidence that Chukar may parasitize nests of sage-grouse. Here we describe a case of a Chukar parasitizing a sage-grouse nest in the sagebrush steppe of western Nevada.

  2. The historical distribution of Gunnison Sage-Grouse in Colorado

    Science.gov (United States)

    Braun, Clait E.; Oyler-McCance, Sara J.; Nehring, Jennifer A.; Commons, Michelle L.; Young, Jessica R.; Potter, Kim M.

    2014-01-01

    The historical distribution of Gunnison Sage-Grouse (Centrocercus minimus) in Colorado is described based on published literature, observations, museum specimens, and the known distribution of sagebrush (Artemisia spp.). Historically, Gunnison Sage-Grouse were widely but patchily distributed in up to 22 counties in south-central and southwestern Colorado. The historical distribution of this species was south of the Colorado-Eagle river drainages primarily west of the Continental Divide. Potential contact areas with Greater Sage-Grouse (C. urophasianus) were along the Colorado-Eagle river system in Mesa, Garfield, and Eagle counties, west of the Continental Divide. Gunnison Sage-Grouse historically occupied habitats that were naturally highly fragmented by forested mountains and plateaus/mesas, intermountain basins without robust species of sagebrush, and river systems. This species adapted to use areas with more deciduous shrubs (i.e., Quercus spp., Amelanchier spp., Prunus spp.) in conjunction with sagebrush. Most areas historically occupied were small, linear, and patchily distributed within the overall landscape matrix. The exception was the large intermountain basin in Gunnison, Hinsdale, and Saguache counties. The documented distribution east of the Continental Divide within the large expanse of the San Luis Valley (Alamosa, Conejos, Costilla, and Rio Grande counties) was minimal and mostly on the eastern, northern, and southern fringes. Many formerly occupied habitat patches were vacant by the mid 1940s with extirpations continuing to the late 1990s. Counties from which populations were recently extirpated include Archuleta and Pitkin (1960s), and Eagle, Garfield, Montezuma, and Ouray (1990s).

  3. SAGES's advanced GI/MIS fellowship curriculum pilot project.

    Science.gov (United States)

    Weis, Joshua J; Goldblatt, Matthew; Pryor, Aurora; Dunkin, Brian J; Brunt, L Michael; Jones, Daniel B; Scott, Daniel J

    2018-06-01

    The American health care system faces deficits in quality and quantity of surgeons. SAGES is a major stakeholder in surgical fellowship training and is responsible for defining the curriculum for the Advanced GI/MIS fellowship. SAGES leadership is actively adapting this curriculum. The process of reform began in 2014 through a series of iterative meetings and discussions. A working group within the Resident and Fellow Training Committee reviewed case log data from 2012 to 2015. These data were used to propose new criteria designed to provide adequate exposure to core content. The working group also proposed using video assessment of an MIS case to provide objective assessment of competency. Case log data were available for 326 fellows with a total of 85,154 cases logged (median 227 per fellow). The working group proposed new criteria starting with minimum case volumes for five defined categories including foregut (20), bariatrics (25), inguinal hernia (10), ventral hernia (10), and solid organ/colon/thoracic (10). Fellows are expected to perform an additional 75 complex MIS cases of any category for a total of 150 required cases overall. The proposal also included a minimum volume of flexible endoscopy (50) and submission of an MIS foregut case for video assessment. The new criteria more clearly defined which surgeon roles count for major credit within individual categories. Fourteen fellowships volunteered to pilot these new criteria for the 2017-2018 academic year. The new SAGES Advanced GI/MIS fellowship has been crafted to better define the core content that should be contained in these fellowships, while still allowing sufficient heterogeneity so that individual learners can tailor their training to specific areas of interest. The criteria also introduce innovative, evidence-based methods for assessing competency. Pending the results of the pilot program, SAGES will consider broad implementation of the new fellowship criteria.

  4. Essential oil composition of wild growing Sage from R. Macedonia

    Directory of Open Access Journals (Sweden)

    Gjoshe Stefkov

    2012-03-01

    Full Text Available The main objective of this study was to analyze and identify the essential oil composition of S. officinalis populations growing in Republic of Macedonia and to evaluate these data according to different standards’ requirements for, commercially most utilized, Dalmatian sage. The essential oil yield, obtained after hydrodestilation from leaves, of three different populations of Salvia officinalis L. from Republic of Macedonia was determined, varying from 1.40 to 3.46%. The GC/FID/MS analysis of the composition of the essential oils revealed 63, 57 and 51 components in Galicica Mtn., Jablanica Mtn. and Karaorman Mtn. sage populations, respectively. The main components of the oil, in all three samples, were the terpene hydrocarbons, encompassing the monoterpenes: camphor (13.15 - 25.91%, α-thujone (19.25 - 26.33%, β-thujone (2.03 - 5.28%, 1,8-cineole (6.51 – 13.60%, α-pinene (0.93 – 1.47%, borneol (1.07 – 4.67%, then sesquiterpenes: trans (E-caryophyllene (1.72 – 5.33%, α-humulene (2.89 – 7.99%, viridiflorol (4.27 – 7.99%, and the diterpene manool (2.13 - 3.79%. Thus, our results for the essential oil composition of sage complied with the reference values specified in the DAC 86 monograph for Salvia essential oil.

  5. Transcriptome profiling of Elettaria cardamomum (L. Maton (small cardamom

    Directory of Open Access Journals (Sweden)

    F. Nadiya

    2017-03-01

    Full Text Available Elettaria cardamomum (L. Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base and 24,889,197 (75 base raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild and SRX1141276 (cultivars. The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

  6. The effect of sage, sodium erythorbate and a mixture of sage and sodium erythorbate on the quality of turkey meatballs stored under vacuum and modified atmosphere conditions.

    Science.gov (United States)

    Karpińska-Tymoszczyk, M

    2010-12-01

    1. The combined effect of sage (S), sodium erythorbate (SE), a mixture of sage and sodium erythorbate (MIX) and vacuum packaging (VP) and modified atmosphere packaging (MAP) on the quality of cooked turkey meatballs stored at 4°C was investigated. The physicochemical properties (colour, MDA, AV, pH, water activity), microbiological quality characteristics (counts of mesophilic and psychrotrophic bacteria, fungi, coliforms and Clostridium sp.) and flavour attributes of meatballs were determined. 2. The values of the colour parameters L*, a* and b* were affected by the additives and packaging method. The colour of meatballs was better protected by sodium erythorbate than by sage or a mixture of sage and sodium erythorbate. The additives effectively stabilised lipids against oxidation and slowed down hydrolytic changes in turkey meatballs. Sage and a mixture of sage and sodium erythorbate showed stronger antioxidant properties than sodium erythorbate added alone. Products with additives were characterised by better sensory quality than control samples. Sage and MIX prevented the growth of mesophilic and psychrotrophic bacteria. All additives inhibited the growth of coliforms. 3. MAP was more effective than VP in maintaining the microbial and sensory quality stability of cooked turkey meatballs. However, VP appears to be a better method as regards the maintaining of lipid stability in turkey meatballs.

  7. Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

    Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

  8. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression

    International Nuclear Information System (INIS)

    Abba, Martin C; Aldaz, C Marcelo; Drake, Jeffrey A; Hawkins, Kathleen A; Hu, Yuhui; Sun, Hongxia; Notcovich, Cintia; Gaddis, Sally; Sahin, Aysegul; Baggerly, Keith

    2004-01-01

    Genomic and transcriptomic alterations affecting key cellular processes such us cell proliferation, differentiation and genomic stability are considered crucial for the development and progression of cancer. Most invasive breast carcinomas are known to derive from precursor in situ lesions. It is proposed that major global expression abnormalities occur in the transition from normal to premalignant stages and further progression to invasive stages. Serial analysis of gene expression (SAGE) was employed to generate a comprehensive global gene expression profile of the major changes occurring during breast cancer malignant evolution. In the present study we combined various normal and tumor SAGE libraries available in the public domain with sets of breast cancer SAGE libraries recently generated and sequenced in our laboratory. A recently developed modified t test was used to detect the genes differentially expressed. We accumulated a total of approximately 1.7 million breast tissue-specific SAGE tags and monitored the behavior of more than 25,157 genes during early breast carcinogenesis. We detected 52 transcripts commonly deregulated across the board when comparing normal tissue with ductal carcinoma in situ, and 149 transcripts when comparing ductal carcinoma in situ with invasive ductal carcinoma (P < 0.01). A major novelty of our study was the use of a statistical method that correctly accounts for the intra-SAGE and inter-SAGE library sources of variation. The most useful result of applying this modified t statistics beta binomial test is the identification of genes and gene families commonly deregulated across samples within each specific stage in the transition from normal to preinvasive and invasive stages of breast cancer development. Most of the gene expression abnormalities detected at the in situ stage were related to specific genes in charge of regulating the proper homeostasis between cell death and cell proliferation. The comparison of in situ lesions

  9. Using DNA from hairs left at depredated greater sage-grouse nests to detect mammalian nest predators

    Science.gov (United States)

    Christopher P. Kirol; Kristine L. Pilgrim; Andrew L. Sutphin; Thomas L. Maechtle

    2018-01-01

    Despite a multitude of studies on sage-grouse (Centrocercus spp.), there is still sparse information on the predator communities that influence sage-grouse productivity and how these predator communities may change when sagebrush habitats are altered by human activities. As a proof-of-concept, we used mammalian hairs collected at depredated greater sage-grouse (C....

  10. 77 FR 71396 - Humboldt-Toiyabe National Forest; Nevada and California Greater Sage Grouse Bi-State Distinct...

    Science.gov (United States)

    2012-11-30

    ... Greater Sage Grouse Bi-State Distinct Population Segment Forest Plan Amendment Environmental Impact... Sage Grouse Bi- State Distinct Population Segment. DATES: Comments concerning the scope of the analysis..., but precluded'' Endangered Species Act (ESA) listing petition decision for the Greater Sage grouse Bi...

  11. 78 FR 65703 - Notice of Availability of the Idaho and Southwestern Montana Greater Sage-Grouse Draft Land Use...

    Science.gov (United States)

    2013-11-01

    ...] Notice of Availability of the Idaho and Southwestern Montana Greater Sage-Grouse Draft Land Use Plan... Environmental Impact Statement (EIS) for managing Greater Sage- Grouse (GRSG) in the Idaho and Southwestern... Southwestern Montana Greater Sage-Grouse Draft LUP Amendments/Draft EIS by any of the following methods: Email...

  12. 78 FR 50088 - Notice of Availability of the Northwest Colorado Greater Sage-Grouse Draft Resource Management...

    Science.gov (United States)

    2013-08-16

    ... Availability of the Northwest Colorado Greater Sage- Grouse Draft Resource Management Plan Amendment and Draft... Land Management (BLM) has prepared a Northwest Colorado Greater Sage-Grouse Draft Resource Management.../or mailings. ADDRESSES: You may submit comments related to the Northwest Colorado Greater Sage-Grouse...

  13. 77 FR 12792 - Notice of Forest Service Land Management Plans To Be Amended To Incorporate Greater Sage-Grouse...

    Science.gov (United States)

    2012-03-02

    ... Forest Service Land Management Plans To Be Amended To Incorporate Greater Sage-Grouse Conservation... sage-grouse conservation measures into land use plans and land management plans. The BLM is the lead... submitted in writing until March 23, 2012. ADDRESSES: You may submit comments related to the greater sage...

  14. SAGE FOR MACINTOSH (MSAGE) VERSION 1.0 SOLVENT ALTERNATIVES GUIDE - USER'S GUIDE

    Science.gov (United States)

    The guide provides instructions for using the Solvent Alternatives Guide (SAGE) for Macintosh, version 1.0. The guide assumes that the user is familiar with the fundamentals of operating aMacintosh personal computer under the System 7.0 (or higher) operating system. SAGE for ...

  15. Sage-Grouse on the edge: understanding and managing western landscapes for their survival

    Science.gov (United States)

    Noreen Parks; Michael J. Wisdom

    2012-01-01

    Populations of greater sage-grouse have declined dramatically across their North American range for many decades in response to harmful effects of a plethora of human activities and land uses, prompting legal actions to protect the species under the Endangered Species Act (ESA). To evaluate the impacts of land-uses and habitat changes on sage-grouse, Michael Wisdom, a...

  16. Microhabitat selection of brood-rearing sites by greater sage-grouse in Carbon County, Wyoming

    Science.gov (United States)

    Leslie A. Schreiber; Christopher P. Hansen; Mark A. Rumble; Joshua J. Millspaugh; R. Scott Gamo; Jon W. Kehmeier; Nate Wojcik

    2015-01-01

    Declines in Greater Sage-Grouse (Centrocercus urophasianus, hereafter sage-grouse) populations could be attributed to low chick survival, which may be influenced by the availability of food and cover at sites used by females rearing broods. Habitat attributes important to broods may vary regionally; thus, it is necessary to understand factors affecting...

  17. Greater sage-grouse winter habitat use on the eastern edge of their range

    Science.gov (United States)

    Christopher C. Swanson; Mark A. Rumble; Nicholas W. Kaczor; Robert W. Klaver; Katie M. Herman-Brunson; Jonathan A. Jenks; Kent C. Jensen

    2013-01-01

    Greater sage-grouse (Centrocercus urophasianus) at the western edge of the Dakotas occur in the transition zone between sagebrush and grassland communities. These mixed sagebrush (Artemisia sp.) and grasslands differ from those habitats that comprise the central portions of the sage-grouse range; yet, no information is available on winter habitat selection within this...

  18. Stratospheric Aerosol and Gas Experiment III on the International Space Station (SAGE III/ISS)

    Science.gov (United States)

    Gasbarre, Joseph; Walker, Richard; Cisewski, Michael; Zawodny, Joseph; Cheek, Dianne; Thornton, Brooke

    2015-01-01

    The Stratospheric Aerosol and Gas Experiment III on the International Space Station (SAGE III/ISS) mission will extend the SAGE data record from the ideal vantage point of the International Space Station (ISS). The ISS orbital inclination is ideal for SAGE measurements providing coverage between 70 deg north and 70 deg south latitude. The SAGE data record includes an extensively validated data set including aerosol optical depth data dating to the Stratospheric Aerosol Measurement (SAM) experiments in 1975 and 1978 and stratospheric ozone profile data dating to the Stratospheric Aerosol and Gas Experiment (SAGE) in 1979. These and subsequent data records, notably from the SAGE II experiment launched on the Earth Radiation Budget Satellite in 1984 and the SAGE III experiment launched on the Russian Meteor-3M satellite in 2001, have supported a robust, long-term assessment of key atmospheric constituents. These scientific measurements provide the basis for the analysis of five of the nine critical constituents (aerosols, ozone (O3), nitrogen dioxide (NO2), water vapor (H2O), and air density using O2) identified in the U.S. National Plan for Stratospheric Monitoring. SAGE III on ISS was originally scheduled to fly on the ISS in the same timeframe as the Meteor-3M mission, but was postponed due to delays in ISS construction. The project was re-established in 2009.

  19. Greater sage-grouse apparent nest productivity and chick survival in Carbon County, Wyoming

    Science.gov (United States)

    Leslie A. Schreiber; Christopher P. Hansen; Mark A. Rumble; Joshua J. Millspaugh; Frank R. Thompson; R. Scott Gamo; Jon W. Kehmeier; Nate Wojik

    2016-01-01

    Greater sage-grouse Centrocercus urophasianus populations across North America have been declining due to degradation and fragmentation of sagebrush habitat. As part of a study quantifying greater sage-grouse demographics prior to construction of a wind energy facility, we estimated apparent net nest productivity and survival rate of chicks associated with...

  20. Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

    NARCIS (Netherlands)

    van Ruissen, Fred; Ruijter, Jan M.; Schaaf, Gerben J.; Asgharnegad, Lida; Zwijnenburg, Danny A.; Kool, Marcel; Baas, Frank

    2005-01-01

    Background: Serial Analysis of Gene Expression ( SAGE) and microarrays have found awidespread application, but much ambiguity exists regarding the evaluation of these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray technology could reduce the need for

  1. Statistical comparison of two or more SAGE libraries: one tag at a time

    NARCIS (Netherlands)

    Schaaf, Gerben J.; van Ruissen, Fred; van Kampen, Antoine; Kool, Marcel; Ruijter, Jan M.

    2008-01-01

    Several statistical tests have been introduced for the comparison of serial analysis of gene expression (SAGE) libraries to quantitatively analyze the differential expression of genes. As each SAGE library is only one measurement, the necessary information on biological variation or experimental

  2. Observations of territorial breeding common ravens caching eggs of greater sage-grouse

    Science.gov (United States)

    Howe, Kristy B.; Coates, Peter S.

    2015-01-01

    Previous investigations using continuous video monitoring of greater sage-grouse Centrocercus urophasianus nests have unambiguously identified common ravens Corvus corax as an important egg predator within the western United States. The quantity of greater sage-grouse eggs an individual common raven consumes during the nesting period and the extent to which common ravens actively hunt greater sage-grouse nests are largely unknown. However, some evidence suggests that territorial breeding common ravens, rather than nonbreeding transients, are most likely responsible for nest depredations. We describe greater sage-grouse egg depredation observations obtained opportunistically from three common raven nests located in Idaho and Nevada where depredated greater sage-grouse eggs were found at or in the immediate vicinity of the nest site, including the caching of eggs in nearby rock crevices. We opportunistically monitored these nests by counting and removing depredated eggs and shell fragments from the nest sites during each visit to determine the extent to which the common raven pairs preyed on greater sage-grouse eggs. To our knowledge, our observations represent the first evidence that breeding, territorial pairs of common ravens cache greater sage-grouse eggs and are capable of depredating multiple greater sage-grouse nests.

  3. The background of external γ radiation in the proportional counters in SAGE experiment

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.

    2003-01-01

    The influence of external γ radiation on the process of 71 Ge-decay counting in proportional counters in SAGE experiment of solar neutrino flux measurement is examined. One determines the systematic error of SAGE result, connected with radon decays inside the air volume surrounding the counters, and the background counting rate of proportional counters from γ radiation of passive and active shield [ru

  4. Greater sage-grouse nest predators in the Virginia Mountains of northwestern Nevada

    Science.gov (United States)

    Lockyer, Zachary B.; Coates, Peter S.; Casazza, Michael L.; Espinosa, Shawn; Delehanty, David J.

    2013-01-01

    Greater sage-grouse Centrocercus urophasianus, hereafter sage-grouse, populations have declined across their range due to the loss, degradation, and fragmentation of habitat. Habitat alterations can lead not only to vegetative changes but also to shifts in animal behavior and predator composition that may influence population vital rates, such as nest success. For example, common ravens Corvus corax are sage-grouse nest predators, and common raven abundance is positively associated with human-caused habitat alterations. Because nest success is a central component to sage-grouse population persistence, research that identifies factors influencing nest success will better inform conservation efforts. We used videography to unequivocally identify sage-grouse nest predators within the Virginia Mountains of northwestern Nevada, USA, from 2009 to 2011 and used maximum likelihood to calculate daily probability of nest survival. In the Virginia Mountains, fires, energy exploration, and other anthropogenic activities have altered historic sage-grouse habitat. We monitored 71 sage-grouse nests during the study, placing video cameras at 39 nests. Cumulative nest survival for all nests was 22.4% (95% CI, 13.0–33.4%), a survival rate that was significantly lower than other published results for sage-grouse in the Great Basin. Depredation was the primary cause for nest failure in our study (82.5%), and common ravens were the most frequent sage-grouse nest predator, accounting for 46.7% of nest depredations. We also successfully documented a suite of mammalian and reptilian species depredating sage-grouse nests, including some predators never previously confirmed in the literature to be sage-grouse nest predators (i.e., bobcats Lynx rufus and long-tailed weasels Mephitis frenata). Within the high elevation, disturbed habitat of the Virginia Mountains, low sage-grouse nest success may be limiting sage-grouse population growth. These results suggest that management actions that

  5. Headspace screening: A novel approach for fast quality assessment of the essential oil from culinary sage.

    Science.gov (United States)

    Cvetkovikj, Ivana; Stefkov, Gjoshe; Acevska, Jelena; Karapandzova, Marija; Dimitrovska, Aneta; Kulevanova, Svetlana

    2016-07-01

    Quality assessment of essential oil (EO) from culinary sage (Salvia officinalis L., Lamiaceae) is limited by the long pharmacopoeial procedure. The aim of this study was to employ headspace (HS) sampling in the quality assessment of sage EO. Different populations (30) of culinary sage were assessed using GC/FID/MS analysis of the hydrodistilled EO (pharmacopoeial method) and HS sampling directly from leaves. Compound profiles from both procedures were evaluated according to ISO 9909 and GDC standards for sage EO quality, revealing compliance for only 10 populations. Factors to convert HS values, for the target ISO and GDC components, into theoretical EO values were calculated. Statistical analysis revealed a significant relationship between HS and EO values for seven target components. Consequently, HS sampling could be used as a complementary extraction technique for rapid screening in quality assessment of sage EOs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Conservation buffer distance estimates for Greater Sage-Grouse: a review

    Science.gov (United States)

    Manier, Daniel J.; Bowen, Zachary H.; Brooks, Matthew L.; Casazza, Michael L.; Coates, Peter S.; Deibert, Patricia A.; Hanser, Steven E.; Johnson, Douglas H.

    2014-01-01

    This report was prepared at the request of the U.S. Department of the Interior and is a compilation and summary of published scientific studies that evaluate the influence of anthropogenic activities and infrastructure on Greater Sage-Grouse(Centrocercus urophasianus; hereafter, sage-grouse) populations. The purpose of this report is to provide a convenient reference for land managers and others who are working to develop biologically relevant and socioeconomically practical buffer distances around sage-grouse habitats. The framework for this summary includes (1) addressing the potential effects of anthropogenic land use and disturbances on sage-grouse populations, (2) providing ecologically based interpretations of evidence from the scientific literature, and (3) informing implementation of conservation buffers around sage-grouse communal breeding locations—known as leks.

  7. Sparse Variational Bayesian SAGE Algorithm With Application to the Estimation of Multipath Wireless Channels

    DEFF Research Database (Denmark)

    Shutin, Dmitriy; Fleury, Bernard Henri

    2011-01-01

    In this paper, we develop a sparse variational Bayesian (VB) extension of the space-alternating generalized expectation-maximization (SAGE) algorithm for the high resolution estimation of the parameters of relevant multipath components in the response of frequency and spatially selective wireless...... channels. The application context of the algorithm considered in this contribution is parameter estimation from channel sounding measurements for radio channel modeling purpose. The new sparse VB-SAGE algorithm extends the classical SAGE algorithm in two respects: i) by monotonically minimizing...... parametric sparsity priors for the weights of the multipath components. We revisit the Gaussian sparsity priors within the sparse VB-SAGE framework and extend the results by considering Laplace priors. The structure of the VB-SAGE algorithm allows for an analytical stability analysis of the update expression...

  8. Effect of radiation processing on the antioxidant activity of Sage and Cinnamon

    International Nuclear Information System (INIS)

    El-Niley, H. F. G.; Farag, M. D. H.

    2012-12-01

    In the present study, the effect of radiation processing on dried sage leaves and cinnamon barks samples were carried out at dose level of 25 kGy. Total phenolic content was determined in the extracts of these herbs alongside the antioxidant properties of their methanoic extracts were assessed using reducing power assay and by DPPH radical test within an extract concentration range 2.5 to 40 mg/ml of methanol. The result showed the total phenolic compounds were increased by 11.18% and 10.19% for irradiated sage and cinnamon, respectively. The values of EC 50 estimated from the results of reducing power assay and DPPH radical test showed the sage extracts had higher antioxidant activity tham cinnamon extracts. In summary, gamma- irradiation of dried sage leaves and cinnamon barks was found to be significantly increase the antioxidant properties of dried sage leaves and cinnamon barks but also enhanced the antioxidant properties, to some extent. (Author)

  9. Thermal Modeling Method Improvements for SAGE III on ISS

    Science.gov (United States)

    Liles, Kaitlin; Amundsen, Ruth; Davis, Warren; McLeod, Shawn

    2015-01-01

    The Stratospheric Aerosol and Gas Experiment III (SAGE III) instrument is the fifth in a series of instruments developed for monitoring aerosols and gaseous constituents in the stratosphere and troposphere. SAGE III will be delivered to the International Space Station (ISS) via the SpaceX Dragon vehicle. A detailed thermal model of the SAGE III payload, which consists of multiple subsystems, has been developed in Thermal Desktop (TD). Many innovative analysis methods have been used in developing this model; these will be described in the paper. This paper builds on a paper presented at TFAWS 2013, which described some of the initial developments of efficient methods for SAGE III. The current paper describes additional improvements that have been made since that time. To expedite the correlation of the model to thermal vacuum (TVAC) testing, the chambers and GSE for both TVAC chambers at Langley used to test the payload were incorporated within the thermal model. This allowed the runs of TVAC predictions and correlations to be run within the flight model, thus eliminating the need for separate models for TVAC. In one TVAC test, radiant lamps were used which necessitated shooting rays from the lamps, and running in both solar and IR wavebands. A new Dragon model was incorporated which entailed a change in orientation; that change was made using an assembly, so that any potential additional new Dragon orbits could be added in the future without modification of the model. The Earth orbit parameters such as albedo and Earth infrared flux were incorporated as time-varying values that change over the course of the orbit; despite being required in one of the ISS documents, this had not been done before by any previous payload. All parameters such as initial temperature, heater voltage, and location of the payload are defined based on the case definition. For one component, testing was performed in both air and vacuum; incorporating the air convection in a submodel that was

  10. Clustering-based approaches to SAGE data mining

    Directory of Open Access Journals (Sweden)

    Wang Haiying

    2008-07-01

    Full Text Available Abstract Serial analysis of gene expression (SAGE is one of the most powerful tools for global gene expression profiling. It has led to several biological discoveries and biomedical applications, such as the prediction of new gene functions and the identification of biomarkers in human cancer research. Clustering techniques have become fundamental approaches in these applications. This paper reviews relevant clustering techniques specifically designed for this type of data. It places an emphasis on current limitations and opportunities in this area for supporting biologically-meaningful data mining and visualisation.

  11. Greater sage-grouse population trends across Wyoming

    Science.gov (United States)

    Edmunds, David; Aldridge, Cameron L.; O'Donnell, Michael; Monroe, Adrian

    2018-01-01

    The scale at which analyses are performed can have an effect on model results and often one scale does not accurately describe the ecological phenomena of interest (e.g., population trends) for wide-ranging species: yet, most ecological studies are performed at a single, arbitrary scale. To best determine local and regional trends for greater sage-grouse (Centrocercus urophasianus) in Wyoming, USA, we modeled density-independent and -dependent population growth across multiple spatial scales relevant to management and conservation (Core Areas [habitat encompassing approximately 83% of the sage-grouse population on ∼24% of surface area in Wyoming], local Working Groups [7 regional areas for which groups of local experts are tasked with implementing Wyoming's statewide sage-grouse conservation plan at the local level], Core Area status (Core Area vs. Non-Core Area) by Working Groups, and Core Areas by Working Groups). Our goal was to determine the influence of fine-scale population trends (Core Areas) on larger-scale populations (Working Group Areas). We modeled the natural log of change in population size ( peak M lek counts) by time to calculate the finite rate of population growth (λ) for each population of interest from 1993 to 2015. We found that in general when Core Area status (Core Area vs. Non-Core Area) was investigated by Working Group Area, the 2 populations trended similarly and agreed with the overall trend of the Working Group Area. However, at the finer scale where Core Areas were analyzed separately, Core Areas within the same Working Group Area often trended differently and a few large Core Areas could influence the overall Working Group Area trend and mask trends occurring in smaller Core Areas. Relatively close fine-scale populations of sage-grouse can trend differently, indicating that large-scale trends may not accurately depict what is occurring across the landscape (e.g., local effects of gas and oil fields may be masked by increasing

  12. The Chemotaxonomy of Common Sage (Salvia officinalis) Based on the Volatile Constituents.

    Science.gov (United States)

    Craft, Jonathan D; Satyal, Prabodh; Setzer, William N

    2017-06-29

    Background: Common sage ( Salvia officinalis ) is a popular culinary and medicinal herb. A literature survey has revealed that sage oils can vary widely in their chemical compositions. The purpose of this study was to examine sage essential oil from different sources/origins and to define the possible chemotypes of sage oil. Methods: Three different samples of sage leaf essential oil have been obtained and analyzed by GC-MS and GC-FID. A hierarchical cluster analysis was carried out on 185 sage oil compositions reported in the literature as well as the three samples in this study. Results: The major components of the three sage oils were the oxygenated monoterpenoids α-thujone (17.2-27.4%), 1,8-cineole (11.9-26.9%), and camphor (12.8-21.4%). The cluster analysis revealed five major chemotypes of sage oil, with the most common being a α-thujone > camphor > 1,8-cineole chemotype, of which the three samples in this study belong. The other chemotypes are an α-humulene-rich chemotype, a β-thujone-rich chemotype, a 1,8-cineole/camphor chemotype, and a sclareol/α-thujone chemotype. Conclusions: Most sage oils belonged to the "typical", α-thujone > camphor > 1,8-cineole, chemotype, but the essential oil compositions do vary widely and may have a profound effect on flavor and fragrance profiles as well as biological activities. There are currently no studies correlating sage oil composition with fragrance descriptions or with biological activities.

  13. The Stratospheric Aerosol and Gas Experiment (SAGE III) on the International Space Station (ISS) Mission

    Science.gov (United States)

    Cisewski, Michael; Zawodny, Joseph; Gasbarre, Joseph; Eckman, Richard; Topiwala, Nandkishore; Rodriquez-Alvarez, Otilia; Cheek, Dianne; Hall, Steve

    2014-01-01

    The Stratospheric Aerosol and Gas Experiment III on the International Space Station (SAGE III/ISS) mission will provide the science community with high-vertical resolution and nearly global observations of ozone, aerosols, water vapor, nitrogen dioxide, and other trace gas species in the stratosphere and upper-troposphere. SAGE III/ISS measurements will extend the long-term Stratospheric Aerosol Measurement (SAM) and SAGE data record begun in the 1970s. The multi-decadal SAGE ozone and aerosol data sets have undergone intense scrutiny and are considered the international standard for accuracy and stability. SAGE data have been used to monitor the effectiveness of the Montreal Protocol. Key objectives of the mission are to assess the state of the recovery in the distribution of ozone, to re-establish the aerosol measurements needed by both climate and ozone models, and to gain further insight into key processes contributing to ozone and aerosol variability. The space station mid-inclination orbit allows for a large range in latitude sampling and nearly continuous communications with payloads. The SAGE III instrument is the fifth in a series of instruments developed for monitoring atmospheric constituents with high vertical resolution. The SAGE III instrument is a moderate resolution spectrometer covering wavelengths from 290 nm to 1550 nm. Science data is collected in solar occultation mode, lunar occultation mode, and limb scatter measurement mode. A SpaceX Falcon 9 launch vehicle will provide access to space. Mounted in the unpressurized section of the Dragon trunk, SAGE III will be robotically removed from the Dragon and installed on the space station. SAGE III/ISS will be mounted to the ExPRESS Logistics Carrier-4 (ELC-4) location on the starboard side of the station. To facilitate a nadir view from this location, a Nadir Viewing Platform (NVP) payload was developed which mounts between the carrier and the SAGE III Instrument Payload (IP).

  14. SAGE III on ISS Lessons Learned on Thermal Interface Design

    Science.gov (United States)

    Davis, Warren

    2015-01-01

    The Stratospheric Aerosol and Gas Experiment III (SAGE III) instrument - the fifth in a series of instruments developed for monitoring vertical distribution of aerosols, ozone, and other trace gases in the Earth's stratosphere and troposphere - is currently scheduled for delivery to the International Space Station (ISS) via the SpaceX Dragon vehicle in 2016. The Instrument Adapter Module (IAM), one of many SAGE III subsystems, continuously dissipates a considerable amount of thermal energy during mission operations. Although a portion of this energy is transferred via its large radiator surface area, the majority must be conductively transferred to the ExPRESS Payload Adapter (ExPA) to satisfy thermal mitigation requirements. The baseline IAM-ExPA mechanical interface did not afford the thermal conductance necessary to prevent the IAM from overheating in hot on-orbit cases, and high interfacial conductance was difficult to achieve given the large span between mechanical fasteners, less than stringent flatness specifications, and material usage constraints due to strict contamination requirements. This paper will examine the evolution of the IAM-ExPA thermal interface over the course of three design iterations and will include discussion on design challenges, material selection, testing successes and failures, and lessons learned.

  15. J.D.Bernal the sage of science

    CERN Document Server

    Brown, Andrew

    2005-01-01

    Desmond Bernal - or ''Sage'', as he was known, was an extraordinary man by any account - a brilliant scientist, a fervent Marxist, and a colourful, bohemian figure. This biography includes previously unpublished material from his diaries, and sheds new light on his international influence during both WWII and the ensuing peace movement. - ;J. D. Bernal, known as ''Sage'', was an extraordinary man and multifaceted character. A scientist of dazzling intellectual ability and a leading figure in the development of X-ray crystallography, he was a polymath, a fervent Marxist, and much admired worldwide. Although he himself never won a Nobel Prize, several of his distinguished students went on to do so, including Dorothy Hodgkin, Max Perutz, and Aaron Klug. Andrew Brown has had unprecedented access to Bernal''s papers and. diaries, and this biography includes previously unpublished material on Bernal''s role during the Second World War. Bernal not only changed the course of science, but was witness to (and often a p...

  16. SAGE CALCULATIONS OF THE TSUNAMI THREAT FROM LA PALMA

    Directory of Open Access Journals (Sweden)

    Galen Gisler

    2006-01-01

    Full Text Available With the LANL multiphysics hydrocode SAGE, we have performed several two-dimensional calculations and one three-dimensional calculation using the full Navier-Stokes equations, of a hypothetical landslide resembling the event posited by Ward and Day (2001, a lateral flank collapse of the Cumbre Vieja Volcano on La Palma that would produce a tsunami. The SAGE code has previously been used to model the Lituya Bay landslide-generated tsunami (Mader & Gittings, 2002, and has also been used to examine tsunami generation by asteroid impacts (Gisler, Weaver, Mader, & Gittings, 2003. This code uses continuous adaptive mesh refinement to focus computing resources where they are needed most, and accurate equations of state for water, air, and rock. We find that while high-amplitude waves are produced that would be highly dangerous to nearby communities (in the Canary Islands, and the shores of Morocco, Spain, and Portugal, the wavelengths and periods of these waves are relatively short, and they will not propagate efficiently over long distances.

  17. DBGC: A Database of Human Gastric Cancer

    Science.gov (United States)

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

  18. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

    Directory of Open Access Journals (Sweden)

    Stahl Ulf

    2010-05-01

    Full Text Available Abstract Background The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3-β-linked glucose with a (1 → 6-β-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches. Results Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields. Conclusions The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and

  19. Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.

    Science.gov (United States)

    Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Allingham, R Rand; Hauser, Michael A

    2011-04-08

    To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

  20. Preliminary assessment of possible aerosol contamination effects on SAGE ozone trends in the lower stratosphere

    Science.gov (United States)

    Cunnold, Derek M.; Veiga, Robert E.

    1991-01-01

    An investigation of the validity of long-term ozone trends in the lower stratosphere derived from SAGE I and II measurements is described. At altitudes below approximately 20 km, it is important to separate the ozone and aerosol contributions to SAGE extinction at 600 nm. The correlation between SAGE II measurements of ozone and aerosols indicates that most of the variability in these parameters is associated with physically induced variations resulting from quasi-horizontal motions of air parcels. The SAGE ozone measurements are however found to be as much as 20 percent larger than coincident ozonesonde measurements between 15 and 20 km altitude. A sudden change in the difference at approximately 14.5 km altitude for which there is a change in the SAGE aerosol retrieval procedure suggests that SAGE ozone trends below 20 km altitude may be more sensitive to aerosol variations. Between 20 and 25 km altitude, however, both SAGE and the ozonesondes indicate a reduction in ozone of approximately 0.5 percent/year over the period 1979 to 1989 at midlatitudes of the Northern Hemisphere.

  1. Preliminary analysis of Greater Sage-grouse reproduction in the Virginia Mountains of northwestern Nevada

    Science.gov (United States)

    Coates, Peter S.; Lockyer, Zachary B.; Farinha, Melissa A.; Sweeney, Joelle M.; Johnson, Valerie M.; Meshriy, Matthew G.; Espinosa, Shawn P.; Delehanty, David J.; Casazza, Michael L.

    2011-01-01

    Relationships between habitat selection and population vital rates of greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse), recently designated as a candidate species under the Endangered Species Act, within the Great Basin are not well-understood. The growing development of renewable energy infrastructure within areas inhabited by sage-grouse is thought to influence predator and vegetation communities. For example, common ravens (Corvus corax), a synanthropic sage-grouse nest predator, are increasing range-wide and select transmission lines and other tall structures for nesting and perching. In the Virginia Mountains of northwestern Nevada, we collected preliminary information of space-use, habitat selection, and population vital rates during the nesting and brood-rearing period over two years on 56 sage-grouse. Additionally, videography at nest sites (n = 22) was used to identify sage-grouse nest predators. The study area is a potential site for renewable energy developments (i.e., wind and solar), and we plan to continue monitoring this population using a before-after-control-impact study design. The results reported here are preliminary and further data are required before conclusions can be drawn from this population of sage-grouse.

  2. Conservation of greater sage-grouse- a synthesis of current trends and future management

    Science.gov (United States)

    Connelly, John W.; Knick, Steven T.; Braun, Clait E.; Baker, William L.; Beever, Erik A.; Christiansen, Thomas J.; Doherty, Kevin E.; Garton, Edward O.; Hagen, Christian A.; Hanser, Steven E.; Johnson, Douglas H.; Leu, Matthias; Miller, Richard F.; Naugle, David E.; Oyler-McCance, Sara J.; Pyke, David A.; Reese, Kerry P.; Schroeder, Michael A.; Stiver, San J.; Walker, Brett L.; Wisdorn, Michael J.

    2011-01-01

    Recent analyses of Greater Sage-Grouse (Centrocercus urophasianus) populations indicate substantial declines in many areas but relatively stable populations in other portions of the species? range. Sagebrush (Artemisia spp.) habitats neces-sary to support sage-grouse are being burned by large wildfires, invaded by nonnative plants, and developed for energy resources (gas, oil, and wind). Management on public lands, which con-tain 70% of sagebrush habitats, has changed over the last 30 years from large sagebrush control projects directed at enhancing livestock grazing to a greater emphasis on projects that often attempt to improve or restore ecological integrity. Never-theless, the mandate to manage public lands to provide traditional consumptive uses as well as recreation and wilderness values is not likely to change in the near future. Consequently, demand and use of resources contained in sagebrush land-scapes plus the associated infrastructure to sup-port increasing human populations in the western United States will continue to challenge efforts to conserve Greater Sage-Grouse. The continued widespread distribution of sage-grouse, albeit at very low densities in some areas, coupled with large areas of important sagebrush habitat that are relatively unaffected by the human footprint, sug-gest that Greater Sage-Grouse populations may be able to persist into the future. We summarize the status of sage-grouse populations and habitats, provide a synthesis of major threats and chal-lenges to conservation of sage-grouse, and suggest a roadmap to attaining conservation goals.

  3. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    Alejandra Perina

    2017-03-01

    Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

  4. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  5. Ecology of sage grouse on the Idaho National Engineering Laboratory Site

    International Nuclear Information System (INIS)

    Connelly, J.W.; Ball, I.J.

    1978-01-01

    A comprehensive study of the sage grouse ecology was initiated on the INEL Site in 1977. Objectives include documentation of radionuclide concentrations, population size, habitat use, and movement patterns of sage grouse on the Site. Sixteen grouse have been collected and radionuclide concentrations determined. Only part of the Site and surrounding area have been adequately searched for strutting grounds (leks), but 32 have been located to date. Trapping success has been strongly influenced by weather conditions and by the season; 121 sage grouse have been captured, banded, and color- and radio-marked

  6. Effects of lek count protocols on greater sage-grouse population trend estimates

    Science.gov (United States)

    Monroe, Adrian; Edmunds, David; Aldridge, Cameron L.

    2016-01-01

    frequency also improved precision. These results suggest that the current distribution of count timings available in lek count databases such as that of Wyoming (conducted up to 90 minutes after sunrise) can be used to estimate sage-grouse population trends without reducing precision or accuracy relative to trends from counts conducted within 30 minutes of sunrise. However, only 10% of all Wyoming counts in our sample (1995−2014) were conducted 61−90 minutes after sunrise, and further increasing this percentage may still bias trend estimates because of declining lek attendance. 

  7. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  8. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  9. Ageing and adult health status in eight lower-income countries: the INDEPTH WHO-SAGE collaboration

    Directory of Open Access Journals (Sweden)

    Paul Kowal

    2010-09-01

    aged 50 and over from these eight HDSS sites was produced. The SAGE modules resulted in self-reported health, health status, functioning (from the WHO Disability Assessment Scale (WHODAS-II and well-being (from the WHO Quality of Life instrument (WHOQoL variables. The HDSS databases contributed age, sex, marital status, education, socio-economic status and household size variables. Conclusion: The INDEPTH WHO–SAGE collaboration demonstrates the value and future possibilities for this type of research in informing policy and planning for a number of countries. This INDEPTH WHO–SAGE dataset will be placed in the public domain together with this open-access supplement and will be available through the GHA website (www.globalhealthaction.net and other repositories. An improved dataset is being developed containing supplementary HDSS variables and vignette-adjusted health variables. This living collaboration is now preparing for a next wave of data collection.

  10. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  11. Solar neutrino and 51Cr results from SAGE

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Abdurashitov, J.N.; Girin, S.V.

    1997-01-01

    The Russian-American solar neutrino Experiment (SAGE) has carried out measurements of the capture rate of solar neutrinos on metallic gallium in a radiochemical experiment at the Baksan Neutrino Observatory during the period January 1990 to December 1994. The measured capture rate on 71 Ga is 72+12/-10 (stat) +5/-7 (syst) SNU. This represents only 53-59 % of the predicted Standard Solar Model (SSM) rates. Taken together with the measurements of the other solar neutrino experiments, this deficit would appear to be best interpreted as due to Mikheyev-Smirnov-Wolfenstein neutrino oscillations. A measurement of the production rate of 71 Ge by an intense 51 Cr source to test the overall operation of the experiment showed the extraction efficiency was 0.95 ± 0.11 (stat) +0.05/-0.08 (syst), indicating that the experiment is operating as expected. (orig.)

  12. Identifying novel genes in C. elegans using SAGE tags

    Directory of Open Access Journals (Sweden)

    Chen Nansheng

    2010-12-01

    Full Text Available Abstract Background Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required. Results In this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE. Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes. Conclusions The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.

  13. IMPACT OF COSOLVENT FLUSHING ON SUBSURFACE MICROBIAL ECOLOGY AT THE FORMER SAGE'S DRY CLEANER SITE

    Science.gov (United States)

    The Solvent Extraction Residual Biotreatment (SERB) technology was evaluated at the former Sage's Dry Cleaner site in Jacksonville, FL where an area of tetrachloroethylene (PCE) contamination was identified. The SERB technology is a treatment train approach to complete site rest...

  14. Maximum likelihood reconstruction in fully 3D PET via the SAGE algorithm

    International Nuclear Information System (INIS)

    Ollinger, J.M.; Goggin, A.S.

    1996-01-01

    The SAGE and ordered subsets algorithms have been proposed as fast methods to compute penalized maximum likelihood estimates in PET. We have implemented both for use in fully 3D PET and completed a preliminary evaluation. The technique used to compute the transition matrix is fully described. The evaluation suggests that the ordered subsets algorithm converges much faster than SAGE, but that it stops short of the optimal solution

  15. Importance of regional variation in conservation planning: A rangewide example of the Greater Sage-Grouse

    Science.gov (United States)

    Doherty, Kevin E.; Evans, Jeffrey S.; Coates, Peter S.; Juliusson, Lara; Fedy, Bradley C.

    2016-01-01

    We developed rangewide population and habitat models for Greater Sage-Grouse (Centrocercus urophasianus) that account for regional variation in habitat selection and relative densities of birds for use in conservation planning and risk assessments. We developed a probabilistic model of occupied breeding habitat by statistically linking habitat characteristics within 4 miles of an occupied lek using a nonlinear machine learning technique (Random Forests). Habitat characteristics used were quantified in GIS and represent standard abiotic and biotic variables related to sage-grouse biology. Statistical model fit was high (mean correctly classified = 82.0%, range = 75.4–88.0%) as were cross-validation statistics (mean = 80.9%, range = 75.1–85.8%). We also developed a spatially explicit model to quantify the relative density of breeding birds across each Greater Sage-Grouse management zone. The models demonstrate distinct clustering of relative abundance of sage-grouse populations across all management zones. On average, approximately half of the breeding population is predicted to be within 10% of the occupied range. We also found that 80% of sage-grouse populations were contained in 25–34% of the occupied range within each management zone. Our rangewide population and habitat models account for regional variation in habitat selection and the relative densities of birds, and thus, they can serve as a consistent and common currency to assess how sage-grouse habitat and populations overlap with conservation actions or threats over the entire sage-grouse range. We also quantified differences in functional habitat responses and disturbance thresholds across the Western Association of Fish and Wildlife Agencies (WAFWA) management zones using statistical relationships identified during habitat modeling. Even for a species as specialized as Greater Sage-Grouse, our results show that ecological context matters in both the strength of habitat selection (i

  16. U.S. Geological Survey sage-grouse and sagebrush ecosystem research annual report for 2017

    Science.gov (United States)

    Hanser, Steven E.

    2017-09-08

    The sagebrush (Artemisia spp.) ecosystem extends across a large portion of the Western United States, and the greater sage-grouse (Centrocercus urophasianus) is one of the iconic species of this ecosystem. Greater sage-grouse populations occur in 11 States and are dependent on relatively large expanses of sagebrush-dominated habitat. Sage-grouse populations have been experiencing long-term declines owing to multiple stressors, including interactions among fire, exotic plant invasions, and human land uses, which have resulted in significant loss, fragmentation, and degradation of landscapes once dominated by sagebrush. In addition to the sage-grouse, over 350 species of plants and animals are dependent on the sagebrush ecosystem.Increasing knowledge about how these species and the sagebrush ecosystem respond to these stressors and to management actions can inform and improve strategies to maintain existing areas of intact sagebrush and restore degraded landscapes. The U.S. Geological Survey (USGS) has a broad research program focused on providing the science needed to inform these strate-gies and to help land and resource managers at the Federal, State, Tribal, and local levels as they work towards sustainable sage-grouse populations and restored landscapes for the broad range of uses critical to stakeholders in the Western United States.USGS science has provided a foundation for major land and resource management decisions including those that precluded the need to list the greater sage-grouse under the Endangered Species Act. The USGS is continuing to build on that foundation to inform science-based decisions to help support local economies and the continued conservation, management, and restoration of the sagebrush ecosystem.This report contains descriptions of USGS sage-grouse and sagebrush ecosystem research projects that are ongoing or were active during 2017 and is organized into five thematic areas: Fire, Invasive Species, Restoration, Sagebrush and Sage

  17. Does Wyoming's Core Area Policy Protect Winter Habitats for Greater Sage-Grouse?

    Science.gov (United States)

    Smith, Kurt T.; Beck, Jeffrey L.; Pratt, Aaron C.

    2016-10-01

    Conservation reserves established to protect important habitat for wildlife species are used world-wide as a wildlife conservation measure. Effective reserves must adequately protect year-round habitats to maintain wildlife populations. Wyoming's Sage-Grouse Core Area policy was established to protect breeding habitats for greater sage-grouse ( Centrocercus urophasianus). Protecting only one important seasonal habitat could result in loss or degradation of other important habitats and potential declines in local populations. The purpose of our study was to identify the timing of winter habitat use, the extent which individuals breeding in Core Areas used winter habitats, and develop resource selection functions to assess effectiveness of Core Areas in conserving sage-grouse winter habitats in portions of 5 Core Areas in central and north-central Wyoming during winters 2011-2015. We found that use of winter habitats occured over a longer period than current Core Area winter timing stipulations and a substantial amount of winter habitat outside of Core Areas was used by individuals that bred in Core Areas, particularly in smaller Core Areas. Resource selection functions for each study area indicated that sage-grouse were selecting habitats in response to landscapes dominated by big sagebrush and flatter topography similar to other research on sage-grouse winter habitat selection. The substantial portion of sage-grouse locations and predicted probability of selection during winter outside small Core Areas illustrate that winter requirements for sage-grouse are not adequately met by existing Core Areas. Consequently, further considerations for identifying and managing important winter sage-grouse habitats under Wyoming's Core Area Policy are warranted.

  18. Background of external γ radiation in the proportional counters of the SAGE experiment

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.

    2003-01-01

    The effect of external γ radiation on the process of counting 71 Ge decays in the proportional counters of the SAGE experiment measuring the solar-neutrino flux is considered. The systematic uncertainty in the SAGE result due to radon decays inside the air volume surrounding the counters is estimated. The background counting rate in the proportional counters that is caused by γ radiation from the enclosing shield is also determined

  19. Sustainability via Active Garden Education (SAGE): results from two feasibility pilot studies.

    Science.gov (United States)

    Lee, Rebecca E; Parker, Nathan H; Soltero, Erica G; Ledoux, Tracey A; Mama, Scherezade K; McNeill, Lorna

    2017-03-10

    Low physical activity (PA) and fruit and vegetable (F&V) consumption in early childhood are continued public health challenges. This manuscript describes outcomes from two pilot studies for Sustainability via Active Garden Education (SAGE), a program designed to increase PA and F&V consumption among 3 to 5 year old children. SAGE was developed using community-based participatory research (CBPR) and delivered to children (N = 89) in early care and education centers (ECEC, N = 6) in two US cities. Children participated in 12 one-hour sessions that included songs, games, and interactive learning activities involving garden maintenance and taste tests. We evaluated reach, efficacy, adoption, implementation, and potential for maintenance of SAGE following the RE-AIM framework. Reach was evaluated by comparing demographic characteristics among SAGE participants and residents of target geographic areas. Efficacy was evaluated with accelerometer-measured PA, F&V consumption, and eating in the absence of hunger among children, parenting practices regarding PA, and home availability of F&V. Adoption was evaluated by the number of ECEC that participated relative to the number of ECEC that were recruited. Implementation was evaluated by completion rates of planned SAGE lessons and activities, and potential for maintenance was evaluated with a parent satisfaction survey. SAGE reached ECEC in neighborhoods representing a wide range of socioeconomic status, with participants' sociodemographic characteristics representing those of the intervention areas. Children significantly increased PA during SAGE lessons compared to usual lessons, but they also consumed more calories in the absence of hunger in post- vs. pre-intervention tests (both p nutrition guidelines for young children. SAGE successfully translated national PA guidelines to practice for young children but was less successful with nutrition guidelines. High adoption and implementation and favorable parent

  20. Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA.

    Science.gov (United States)

    Chwalenia, Katarzyna; Qin, Fujun; Singh, Sandeep; Tangtrongstittikul, Panjapon; Li, Hui

    2017-11-22

    cis-Splicing between adjacent genes (cis-SAGe) is being recognized as one way to produce chimeric fusion RNAs. However, its detail mechanism is not clear. Recent study revealed induction of transcriptions downstream of genes (DoGs) under osmotic stress. Here, we investigated the influence of osmotic stress on cis-SAGe chimeric RNAs and their connection to DoGs. We found,the absence of induction of at least some cis-SAGe fusions and/or their corresponding DoGs at early time point(s). In fact, these DoGs and their cis-SAGe fusions are inversely correlated. This negative correlation was changed to positive at a later time point. These results suggest a direct competition between the two categories of transcripts when total pool of readthrough transcripts is limited at an early time point. At a later time point, DoGs and corresponding cis-SAGe fusions are both induced, indicating that total readthrough transcripts become more abundant. Finally, we observed overall enhancement of cis-SAGe chimeric RNAs in KCl-treated samples by RNA-Seq analysis.

  1. Data resource profile: the World Health Organization Study on global AGEing and adult health (SAGE).

    Science.gov (United States)

    Kowal, Paul; Chatterji, Somnath; Naidoo, Nirmala; Biritwum, Richard; Fan, Wu; Lopez Ridaura, Ruy; Maximova, Tamara; Arokiasamy, Perianayagam; Phaswana-Mafuya, Nancy; Williams, Sharon; Snodgrass, J Josh; Minicuci, Nadia; D'Este, Catherine; Peltzer, Karl; Boerma, J Ties

    2012-12-01

    Population ageing is rapidly becoming a global issue and will have a major impact on health policies and programmes. The World Health Organization's Study on global AGEing and adult health (SAGE) aims to address the gap in reliable data and scientific knowledge on ageing and health in low- and middle-income countries. SAGE is a longitudinal study with nationally representative samples of persons aged 50+ years in China, Ghana, India, Mexico, Russia and South Africa, with a smaller sample of adults aged 18-49 years in each country for comparisons. Instruments are compatible with other large high-income country longitudinal ageing studies. Wave 1 was conducted during 2007-2010 and included a total of 34 124 respondents aged 50+ and 8340 aged 18-49. In four countries, a subsample consisting of 8160 respondents participated in Wave 1 and the 2002/04 World Health Survey (referred to as SAGE Wave 0). Wave 2 data collection will start in 2012/13, following up all Wave 1 respondents. Wave 3 is planned for 2014/15. SAGE is committed to the public release of study instruments, protocols and meta- and micro-data: access is provided upon completion of a Users Agreement available through WHO's SAGE website (www.who.int/healthinfo/systems/sage) and WHO's archive using the National Data Archive application (http://apps.who.int/healthinfo/systems/surveydata).

  2. Generation of Chimeric RNAs by cis-splicing of adjacent genes (cis-SAGe) in mammals.

    Science.gov (United States)

    Zhuo, Jian-Shu; Jing, Xiao-Yan; Du, Xin; Yang, Xiu-Qin

    2018-02-20

    Chimeric RNA molecules, possessing exons from two or more independent genes, are traditionally believed to be produced by chromosome rearrangement. However, recent studies revealed that cis-splicing of adjacent genes (cis- SAGe) is one of the major mechanisms underlying the formation of chimeric RNAs. cis-SAGe refers to intergenic splicing of directly adjacent genes with the same transcriptional orientation, resulting in read-through transcripts, termed chimeric RNAs, which contain sequences from two or more parental genes. cis-SAGe was first identified in tumor cells, since then its potential in carcinogenesis has attracted extensive attention. More and more scientists are focusing on it. With the development of research, cis-SAGe was found to be ubiquitous in various normal tissues, and might make a crucial contribution to the formation of novel genes in the evolution of genomes. In this review, we summarize the splicing pattern, expression characteristics, possible mechanisms, and significance of cis-SAGe in mammals. This review will be helpful for general understanding of the current status and development tendency of cis-SAGe.

  3. Transcriptome profiling of Curcuma longa L. cv. Suvarna

    Directory of Open Access Journals (Sweden)

    Ambika Sahoo

    2016-12-01

    Full Text Available Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10. Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2.2.1 tool which ended up with 42994 numbers of transcripts. The length of transcripts ranged from 83 to15565, with a N50 value 1216 and median transcript length 773. The transcripts were annotated through number of databases. For the first time transcriptome profiling of cultivar Suvarna has been done, which could help towards identification of single nucleotide polymorphisms (SNPs between Suvarna and other turmeric cultivars for its authentic identification.

  4. Toward a Combined SAGE II-HALOE Aerosol Climatology: An Evaluation of HALOE Version 19 Stratospheric Aerosol Extinction Coefficient Observations

    Science.gov (United States)

    Thomason, L. W.

    2012-01-01

    Herein, the Halogen Occultation Experiment (HALOE) aerosol extinction coefficient data is evaluated in the low aerosol loading period after 1996 as the first necessary step in a process that will eventually allow the production of a combined HALOE/SAGE II (Stratospheric Aerosol and Gas Experiment) aerosol climatology of derived aerosol products including surface area density. Based on these analyses, it is demonstrated that HALOE's 3.46 microns is of good quality above 19 km and suitable for scientific applications above that altitude. However, it is increasingly suspect at lower altitudes and should not be used below 17 km under any circumstances after 1996. The 3.40 microns is biased by about 10% throughout the lower stratosphere due to the failure to clear NO2 but otherwise appears to be a high quality product down to 15 km. The 2.45 and 5.26 micron aerosol extinction coefficient measurements are clearly biased and should not be used for scientific applications after the most intense parts of the Pinatubo period. Many of the issues in the aerosol data appear to be related to either the failure to clear some interfering gas species or doing so poorly. For instance, it is clear that the 3.40micronaerosol extinction coefficient measurements can be improved through the inclusion of an NO2 correction and could, in fact, end up as the highest quality overall HALOE aerosol extinction coefficient measurement. It also appears that the 2.45 and 5.26 micron channels may be improved by updating the Upper Atmosphere Pilot Database which is used as a resource for the removal of gas species otherwise not available from direct HALOE measurements. Finally, a simple model to demonstrate the promise of mixed visible/infrared aerosol extinction coefficient ensembles for the retrieval of bulk aerosol properties demonstrates that a combined HALOE/SAGE II aerosol climatology is feasible and may represent a substantial improvement over independently derived data sets.

  5. Sustainability via Active Garden Education (SAGE: results from two feasibility pilot studies

    Directory of Open Access Journals (Sweden)

    Rebecca E. Lee

    2017-03-01

    Full Text Available Abstract Background Low physical activity (PA and fruit and vegetable (F&V consumption in early childhood are continued public health challenges. This manuscript describes outcomes from two pilot studies for Sustainability via Active Garden Education (SAGE, a program designed to increase PA and F&V consumption among 3 to 5 year old children. Methods SAGE was developed using community-based participatory research (CBPR and delivered to children (N = 89 in early care and education centers (ECEC, N = 6 in two US cities. Children participated in 12 one-hour sessions that included songs, games, and interactive learning activities involving garden maintenance and taste tests. We evaluated reach, efficacy, adoption, implementation, and potential for maintenance of SAGE following the RE-AIM framework. Reach was evaluated by comparing demographic characteristics among SAGE participants and residents of target geographic areas. Efficacy was evaluated with accelerometer-measured PA, F&V consumption, and eating in the absence of hunger among children, parenting practices regarding PA, and home availability of F&V. Adoption was evaluated by the number of ECEC that participated relative to the number of ECEC that were recruited. Implementation was evaluated by completion rates of planned SAGE lessons and activities, and potential for maintenance was evaluated with a parent satisfaction survey. Results SAGE reached ECEC in neighborhoods representing a wide range of socioeconomic status, with participants’ sociodemographic characteristics representing those of the intervention areas. Children significantly increased PA during SAGE lessons compared to usual lessons, but they also consumed more calories in the absence of hunger in post- vs. pre-intervention tests (both p < .05. Parent reports did not suggest changes in F&V consumption, parenting PA practices, or home F&V availability, possibly due to low parent engagement. ECEC had moderate

  6. SAGE (Summer of Applied Geophysical Experience): Learning Geophysics by Doing Geophysics

    Science.gov (United States)

    Jiracek, G. R.; Baldridge, W. S.; Biehler, S.; Braile, L. W.; Ferguson, J. F.; Gilpin, B. E.; Pellerin, L.

    2005-12-01

    SAGE, a field-based educational program in applied geophysical methods has been an REU site for 16 years and completed its 23rd year of operation in July 2005. SAGE teaches the major geophysical exploration methods (including seismics, gravity, magnetics, and electromagnetics) and applies them to the solution of specific local and regional geologic problems. These include delineating buried hazardous material; mapping archaeological sites; and studying the structure, tectonics, and water resources of the Rio Grande rift in New Mexico. Nearly 600 graduates, undergraduates, and professionals have attended SAGE since 1983. Since 1990 REU students have numbered 219 coming from dozens of different campuses. There have been 124 underrepresented REU students including 100 women, 14 Hispanics, 7 Native Americans, and 3 African Americans. Tracking of former REU students has revealed that 81% have gone on to graduate school. Keys to the success of SAGE are hands-on immersion in geophysics for one month and a partnership between academia, industry, and a federal laboratory. Successful approaches at SAGE include: 1) application of the latest equipment by all students; 2) continued updating of equipment, computers, and software by organizing universities and industry affiliates; 3) close ties with industry who provide supplemental instruction, furnish new equipment and software, and alert students to the current industry trends and job opportunities; 4) two-team, student data analysis structure that simultaneously addresses specific geophysical techniques and their integration; and 5) oral and written reports patterned after professional meetings and journals. An eight member, 'blue ribbon' advisory panel from academia, industry, and the federal government has been set up to maintain the vitality of SAGE by addressing such issues as funding, new faculty, organization, and vision. SAGE is open to students from any university (or organization) with backgrounds including

  7. Determination of the biologically active flavour substances thujone and camphor in foods and medicines containing sage (Salvia officinalis L.)

    OpenAIRE

    Walch, Stephan G.; Kuballa, Thomas; Stühlinger, Wolf; Lachenmeier, Dirk W.

    2011-01-01

    Abstract Background The sage plant Salvia officinalis L. is used as ingredient in foods and beverages as well as in herbal medicinal products. A major use is in the form of aqueous infusions as sage tea, which is legal to be sold as either food or medicine. Sage may contain two health relevant substances, thujone and camphor. The aim of this study was to develop and validate an analytical methodology to determine these active principles of sage and give a first overview of their concentration...

  8. Federal databases

    International Nuclear Information System (INIS)

    Welch, M.J.; Welles, B.W.

    1988-01-01

    Accident statistics on all modes of transportation are available as risk assessment analytical tools through several federal agencies. This paper reports on the examination of the accident databases by personal contact with the federal staff responsible for administration of the database programs. This activity, sponsored by the Department of Energy through Sandia National Laboratories, is an overview of the national accident data on highway, rail, air, and marine shipping. For each mode, the definition or reporting requirements of an accident are determined and the method of entering the accident data into the database is established. Availability of the database to others, ease of access, costs, and who to contact were prime questions to each of the database program managers. Additionally, how the agency uses the accident data was of major interest

  9. Transcriptome-wide identification of preferentially expressed genes in the hypothalamus and pituitary gland.

    Science.gov (United States)

    St-Amand, Jonny; Yoshioka, Mayumi; Tanaka, Keitaro; Nishida, Yuichiro

    2011-01-01

    To identify preferentially expressed genes in the central endocrine organs of the hypothalamus and pituitary gland, we generated transcriptome-wide mRNA profiles of the hypothalamus, pituitary gland, and parietal cortex in male mice (12-15 weeks old) using serial analysis of gene expression (SAGE). Total counts of SAGE tags for the hypothalamus, pituitary gland, and parietal cortex were 165824, 126688, and 161045 tags, respectively. This represented 59244, 45151, and 55131 distinct tags, respectively. Comparison of these mRNA profiles revealed that 22 mRNA species, including three potential novel transcripts, were preferentially expressed in the hypothalamus. In addition to well-known hypothalamic transcripts, such as hypocretin, several genes involved in hormone function, intracellular transduction, metabolism, protein transport, steroidogenesis, extracellular matrix, and brain disease were identified as preferentially expressed hypothalamic transcripts. In the pituitary gland, 106 mRNA species, including 60 potential novel transcripts, were preferentially expressed. In addition to well-known pituitary genes, such as growth hormone and thyroid stimulating hormone beta, a number of genes classified to function in transport, amino acid metabolism, intracellular transduction, cell adhesion, disulfide bond formation, stress response, transcription, protein synthesis, and turnover, cell differentiation, the cell cycle, and in the cytoskeleton and extracellular matrix were also preferentially expressed. In conclusion, the current study identified not only well-known hypothalamic and pituitary transcripts but also a number of new candidates likely to be involved in endocrine homeostatic systems regulated by the hypothalamus and pituitary gland.

  10. Transcriptome-wide identification of preferentially expressed genes in the hypothalamus and pituitary gland

    Directory of Open Access Journals (Sweden)

    Jonny eSt-Amand

    2012-01-01

    Full Text Available To identify preferentially expressed genes in the central endocrine organs of the hypothalamus and pituitary gland, we generated transcriptome-wide mRNA profiles of the mouse hypothalamus, pituitary gland and parietal cortex using serial analysis of gene expression (SAGE. Total counts of SAGE tags for the hypothalamus, pituitary gland and parietal cortex were 165824, 126688 and 161045 tags, respectively. This represented 59244, 45151 and 55131 distinct tags, respectively. Comparison of these mRNA profiles revealed that 22 mRNA species, including three potential novel transcripts, were preferentially expressed in the hypothalamus. In addition to well-known hypothalamic transcripts, such as hypocretin, several genes involved in hormone function, intracellular transduction, metabolism, protein transport, steroidogenesis, extracellular matrix and brain disease were identified as preferentially expressed hypothalamic transcripts. In the pituitary gland, 106 mRNA species, including 60 potential novel transcripts, were preferentially expressed. In addition to well-known pituitary genes, such as growth hormone and thyroid stimulating hormone beta, a number of genes classified to function in transport, amino acid metabolism, intracellular transduction, cell adhesion, disulfide bond formation, stress response, transcription, protein synthesis and turnover, cell differentiation, the cell cycle and in the cytoskeleton and extracellular matrix were also preferentially expressed. In conclusion, the current study identified not only well-known hypothalamic and pituitary transcripts but also a number of new candidates likely to be involved in endocrine homeostatic systems regulated by the hypothalamus and pituitary gland.

  11. A feature selection approach for identification of signature genes from SAGE data

    Directory of Open Access Journals (Sweden)

    Silva Paulo JS

    2007-05-01

    Full Text Available Abstract Background One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements. Results A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology. Conclusion The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS or the recent Sequencing-By-Synthesis (SBS technique. Some of such genes identified by the proposed method may be useful to generate classifiers.

  12. Microhabitat Conditions in Wyoming's Sage-Grouse Core Areas: Effects on Nest Site Selection and Success.

    Science.gov (United States)

    Dinkins, Jonathan B; Smith, Kurt T; Beck, Jeffrey L; Kirol, Christopher P; Pratt, Aaron C; Conover, Michael R

    2016-01-01

    The purpose of our study was to identify microhabitat characteristics of greater sage-grouse (Centrocercus urophasianus) nest site selection and survival to determine the quality of sage-grouse habitat in 5 regions of central and southwest Wyoming associated with Wyoming's Core Area Policy. Wyoming's Core Area Policy was enacted in 2008 to reduce human disturbance near the greatest densities of sage-grouse. Our analyses aimed to assess sage-grouse nest selection and success at multiple micro-spatial scales. We obtained microhabitat data from 928 sage-grouse nest locations and 819 random microhabitat locations from 2008-2014. Nest success was estimated from 924 nests with survival data. Sage-grouse selected nests with greater sagebrush cover and height, visual obstruction, and number of small gaps between shrubs (gap size ≥0.5 m and sage-grouse were selecting different nest sites in Core Areas relative to areas outside of Core. The Kaplan-Meier nest success estimate for a 27-day incubation period was 42.0% (95% CI: 38.4-45.9%). Risk of nest failure was negatively associated with greater rock and more medium-sized gaps between shrubs (gap size ≥2.0 m and <3.0 m). Within our study areas, Wyoming's Core Areas did not have differing microhabitat quality compared to outside of Core Areas. The close proximity of our locations within and outside of Core Areas likely explained our lack of finding differences in microhabitat quality among locations within these landscapes. However, the Core Area Policy is most likely to conserve high quality habitat at larger spatial scales, which over decades may have cascading effects on microhabitat quality available between areas within and outside of Core Areas.

  13. Antioxidant properties of biohybrids based on liposomes and sage silver nanoparticles.

    Science.gov (United States)

    Barbinta-Patrascu, Marcela Elisabeta; Bunghez, Ioana-Raluca; Iordache, Stefan Marian; Badea, Nicoleta; Fierascu, Radu-Claudiu; Ion, Rodica Mariana

    2013-03-01

    This paper is aimed to describe a simple and rapid eco-friendly bottom-up approach for the preparation of antioxidant silver bionanostructures using a leaf extract from sage (Salvia officinalis L.). The bioreduction property of sage in the synthesis of silver nanoparticles was investigated by UV-VIS and Attenuated Total Reflectance Fourier Transform Infrared spectroscopy. During their preparation, the particle size analysis was performed by using Dynamic Light Scattering technique. Ultrasonic irradiation was used to obtain sage silver nanoparticles. The morphology (size and shape) of the herbal silver nanoparticles was evaluated by Scanning Electron Microscopy that revealed the formation of spherical phytonanoparticles with size less than 80 nm. In order to increase their stability and their biocompatibility, the sage silver nanoparticles were introduced in two types of liposomes: soybean lecithin- and Chla-DPPC-lipid vesicles which were prepared by thin film hydration method. X-Ray Fluorescence analysis confirmed the silver presence in liposomes/sage-AgNPs biohybrids. The stability of liposomes/herbal AgNPs bioconstructs was checked by zeta potential measurements. The most stable biohybrids: Chla-DPPC/sage-AgNPs with zeta potential value of -34.2 mV, were characterized by Atomic Force Microscopy revealing the spherical and quasi-spherical shaped profiles of these nanobiohybrids with size less than 96 nm. The antioxidant activity of the silver bionanostructures was evaluated using chemiluminescence assay. The developed eco-friendly silver phytonanostructures based on lipid membranes, nanosilver and sage extract, manifest strong antioxidant properties (between 86.5% and 98.6%).

  14. Mitigation effectiveness for improving nesting success of greater sage-grouse influenced by energy development

    Science.gov (United States)

    Kirol, Christopher P.; Sutphin, Andrew L.; Bond, Laura S.; Fuller, Mark R.; Maechtle, Thomas L.

    2015-01-01

    Sagebrush Artemisia spp. habitats being developed for oil and gas reserves are inhabited by sagebrush obligate species — including the greater sage-grouse Centrocercus urophasianus (sage-grouse) that is currently being considered for protection under the U.S. Endangered Species Act. Numerous studies suggest increasing oil and gas development may exacerbate species extinction risks. Therefore, there is a great need for effective on-site mitigation to reduce impacts to co-occurring wildlife such as sage-grouse. Nesting success is a primary factor in avian productivity and declines in nesting success are also thought to be an important contributor to population declines in sage-grouse. From 2008 to 2011 we monitored 296 nests of radio-marked female sage-grouse in a natural gas (NG) field in the Powder River Basin, Wyoming, USA, and compared nest survival in mitigated and non-mitigated development areas and relatively unaltered areas to determine if specific mitigation practices were enhancing nest survival. Nest survival was highest in relatively unaltered habitats followed by mitigated, and then non-mitigated NG areas. Reservoirs used for holding NG discharge water had the greatest support as having a direct relationship to nest survival. Within a 5-km2 area surrounding a nest, the probability of nest failure increased by about 15% for every 1.5 km increase in reservoir water edge. Reducing reservoirs was a mitigation focus and sage-grouse nesting in mitigated areas were exposed to almost half of the amount of water edge compared to those in non-mitigated areas. Further, we found that an increase in sagebrush cover was positively related to nest survival. Consequently, mitigation efforts focused on reducing reservoir construction and reducing surface disturbance, especially when the surface disturbance results in sagebrush removal, are important to enhancing sage-grouse nesting success.

  15. Landscape characteristics and livestock presence influence common ravens: Relevance to greater sage-grouse conservation

    Science.gov (United States)

    Coates, Peter S.; Brussee, Brianne E.; Howe, Kristy; Gustafson, K. Ben; Casazza, Michael L.; Delehanty, David J.

    2016-01-01

    Common raven (Corvus corax; hereafter, raven) population abundance in the sagebrush steppe of the American West has increased threefold during the previous four decades, largely as a result of unintended resource subsidies from human land-use practices. This is concerning because ravens frequently depredate nests of species of conservation concern, such as greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse). Grazing by livestock in sagebrush ecosystems is common practice on most public lands, but associations between livestock and ravens are poorly understood. The primary objective of this study was to identify the effects of livestock on raven occurrence while accounting for landscape characteristics within human-altered sagebrush steppe habitat, particularly in areas occupied by breeding sage-grouse. Using data from southeastern Idaho collected during spring and summer across 3 yr, we modeled raven occurrence as a function of the presence of livestock while accounting for multiple landscape covariates, including land cover features, topographical features, and proximity to sage-grouse lek sites (breeding grounds), as well as site-level anthropogenic features. While accounting for landscape characteristics, we found that the odds of raven occurrence increased 45.8% in areas where livestock were present. In addition, ravens selected areas near sage-grouse leks, with the odds of occurrence decreasing 8.9% for every 1-km distance, increase away from the lek. We did not find an association between livestock use and distance to lek. We also found that ravens selected sites with relatively lower elevation containing increased amounts of cropland, wet meadow, and urbanization. Limiting raven access to key anthropogenic subsidies and spatially segregating livestock from sage-grouse breeding areas would likely reduce exposure of predatory ravens to sage-grouse nests and chicks.

  16. Low footwall accelerations and variable surface rupture behavior on the Fort Sage Mountains fault, northeast California

    Science.gov (United States)

    Briggs, Richard W.; Wesnousky, Steven G.; Brune, James N.; Purvance, Matthew D.; Mahan, Shannon

    2013-01-01

    The Fort Sage Mountains fault zone is a normal fault in the Walker Lane of the western Basin and Range that produced a small surface rupture (L 5.6 earthquake in 1950. We investigate the paleoseismic history of the Fort Sage fault and find evidence for two paleoearthquakes with surface displacements much larger than those observed in 1950. Rupture of the Fort Sage fault ∼5.6  ka resulted in surface displacements of at least 0.8–1.5 m, implying earthquake moment magnitudes (Mw) of 6.7–7.1. An older rupture at ∼20.5  ka displaced the ground at least 1.5 m, implying an earthquake of Mw 6.8–7.1. A field of precariously balanced rocks (PBRs) is located less than 1 km from the surface‐rupture trace of this Holocene‐active normal fault. Ground‐motion prediction equations (GMPEs) predict peak ground accelerations (PGAs) of 0.2–0.3g for the 1950 rupture and 0.3–0.5g for the ∼5.6  ka paleoearthquake one kilometer from the fault‐surface trace, yet field tests indicate that the Fort Sage PBRs will be toppled by PGAs between 0.1–0.3g. We discuss the paleoseismic history of the Fort Sage fault in the context of the nearby PBRs, GMPEs, and probabilistic seismic hazard maps for extensional regimes. If the Fort Sage PBRs are older than the mid‐Holocene rupture on the Fort Sage fault zone, this implies that current GMPEs may overestimate near‐fault footwall ground motions at this site.

  17. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  18. Transcriptome analysis and related databases of Lactococcus lactis

    NARCIS (Netherlands)

    Kuipers, Oscar P.; Jong, Anne de; Baerends, Richard J.S.; Hijum, Sacha A.F.T. van; Zomer, Aldert L.; Karsens, Harma A.; Hengst, Chris D. den; Kramer, Naomi E.; Buist, Girbe; Kok, Jan

    Several complete genome sequences of Lactococcus lactis and their annotations will become available in the near future, next to the already published genome sequence of L. lactis ssp. lactis IL1403. This will allow intraspecies comparative genomics studies as well as functional genomics studies

  19. Analysis of a human brain transcriptome map

    Directory of Open Access Journals (Sweden)

    Greene Jonathan R

    2002-04-01

    Full Text Available Abstract Background Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence. Results Examination of ESTs derived from brain tissues (excluding brain tumor tissues suggests that these genes are distributed on chromosomes in a non-random fashion. Some regions on the genome are dense with brain-enriched genes while some regions lack brain-enriched genes, suggesting a significant correlation between distribution of genes along the chromosome and tissue type. ESTs from brain tumor tissues have also been mapped to the human genome working draft. We reveal that some regions enriched in brain genes show a significant decrease in gene expression in brain tumors, and, conversely that some regions lacking in brain genes show an increased level of gene expression in brain tumors. Conclusions This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

  20. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas; Vue, Zer; Voolstra, Christian R.; Medina, Mó nica; Moroz, Leonid L.

    2010-01-01

    developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms

  1. SPITZER SAGE INFRARED PHOTOMETRY OF MASSIVE STARS IN THE LARGE MAGELLANIC CLOUD

    International Nuclear Information System (INIS)

    Bonanos, A. Z.; Massa, D. L.; Sewilo, M.

    2009-01-01

    We present a catalog of 1750 massive stars in the Large Magellanic Cloud (LMC), with accurate spectral types compiled from the literature, and a photometric catalog for a subset of 1268 of these stars, with the goal of exploring their infrared properties. The photometric catalog consists of stars with infrared counterparts in the Spitzer SAGE survey database, for which we present uniform photometry from 0.3 to 24 μm in the UBVIJHK s +IRAC+MIPS24 bands. The resulting infrared color-magnitude diagrams illustrate that the supergiant B[e], red supergiant, and luminous blue variable (LBV) stars are among the brightest infrared point sources in the LMC, due to their intrinsic brightness, and at longer wavelengths, due to dust. We detect infrared excesses due to free-free emission among ∼900 OB stars, which correlate with luminosity class. We confirm the presence of dust around 10 supergiant B[e] stars, finding the shape of their spectral energy distributions (SEDs) to be very similar, in contrast to the variety of SED shapes among the spectrally variable LBVs. The similar luminosities of B[e] supergiants (log L/L sun ≥ 4) and the rare, dusty progenitors of the new class of optical transients (e.g., SN 2008S and NGC 300 OT), plus the fact that dust is present in both types of objects, suggests a common origin for them. We find the infrared colors for Wolf-Rayet stars to be independent of spectral type and their SEDs to be flatter than what models predict. The results of this study provide the first comprehensive roadmap for interpreting luminous, massive, resolved stellar populations in nearby galaxies at infrared wavelengths.

  2. SPITZER SAGE-SMC INFRARED PHOTOMETRY OF MASSIVE STARS IN THE SMALL MAGELLANIC CLOUD

    International Nuclear Information System (INIS)

    Bonanos, A. Z.; Lennon, D. J.; Massa, D. L.

    2010-01-01

    We present a catalog of 5324 massive stars in the Small Magellanic Cloud (SMC), with accurate spectral types compiled from the literature, and a photometric catalog for a subset of 3654 of these stars, with the goal of exploring their infrared properties. The photometric catalog consists of stars with infrared counterparts in the Spitzer SAGE-SMC survey database, for which we present uniform photometry from 0.3to24 μm in the UBVIJHK s +IRAC+MIPS24 bands. We compare the color-magnitude diagrams and color-color diagrams to those of stars in the Large Magellanic Cloud (LMC), finding that the brightest infrared sources in the SMC are also the red supergiants, supergiant B[e] (sgB[e]) stars, luminous blue variables, and Wolf-Rayet stars, with the latter exhibiting less infrared excess, the red supergiants being less dusty and the sgB[e] stars being on average less luminous. Among the objects detected at 24 μm in the SMC are a few very luminous hypergiants, four B-type stars with peculiar, flat spectral energy distributions, and all three known luminous blue variables. We detect a distinct Be star sequence, displaced to the red, and suggest a novel method of confirming Be star candidates photometrically. We find a higher fraction of Oe and Be stars among O and early-B stars in our SMC catalog, respectively, when compared to the LMC catalog, and that the SMC Be stars occur at higher luminosities. We estimate mass-loss rates for the red supergiants, confirming the correlation with luminosity even at the metallicity of the SMC. Finally, we confirm the new class of stars displaying composite A and F type spectra, the sgB[e] nature of 2dFS1804 and find the F0 supergiant 2dFS3528 to be a candidate luminous blue variable with cold dust.

  3. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  4. Simulations of linear and Hamming codes using SageMath

    Science.gov (United States)

    Timur, Tahta D.; Adzkiya, Dieky; Soleha

    2018-03-01

    Digital data transmission over a noisy channel could distort the message being transmitted. The goal of coding theory is to ensure data integrity, that is, to find out if and where this noise has distorted the message and what the original message was. Data transmission consists of three stages: encoding, transmission, and decoding. Linear and Hamming codes are codes that we discussed in this work, where encoding algorithms are parity check and generator matrix, and decoding algorithms are nearest neighbor and syndrome. We aim to show that we can simulate these processes using SageMath software, which has built-in class of coding theory in general and linear codes in particular. First we consider the message as a binary vector of size k. This message then will be encoded to a vector with size n using given algorithms. And then a noisy channel with particular value of error probability will be created where the transmission will took place. The last task would be decoding, which will correct and revert the received message back to the original message whenever possible, that is, if the number of error occurred is smaller or equal to the correcting radius of the code. In this paper we will use two types of data for simulations, namely vector and text data.

  5. Visualization of Atmospheric Water Vapor Data for SAGE

    Science.gov (United States)

    Kung, Mou-Liang; Chu, W. P. (Technical Monitor)

    2000-01-01

    The goal of this project was to develop visualization tools to study the water vapor dynamics using the Stratospheric Aerosol and Gas Experiment 11 (SAGE 11) water vapor data. During the past years, we completed the development of a visualization tool called EZSAGE, and various Gridded Water Vapor plots, tools deployed on the web to provide users with new insight into the water vapor dynamics. Results and experiences from this project, including papers, tutorials and reviews were published on the main Web page. Additional publishing effort has been initiated to package EZSAGE software for CD production and distribution. There have been some major personnel changes since Fall, 1998. Dr. Mou-Liang Kung, a Professor of Computer Science assumed the PI position vacated by Dr. Waldo Rodriguez who was on leave. However, former PI, Dr. Rodriguez continued to serve as a research adviser to this project to assure smooth transition and project completion. Typically in each semester, five student research assistants were hired and trained. Weekly group meetings were held to discuss problems, progress, new research direction, and activity planning. Other small group meetings were also held regularly for different objectives of this project. All student research assistants were required to submit reports for conference submission.

  6. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  7. Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA.

    Science.gov (United States)

    Fox, Rebecca M; Vaishnavi, Aria; Maruyama, Rika; Andrew, Deborah J

    2013-05-01

    FoxA transcription factors play major roles in organ-specific gene expression, regulating, for example, glucagon expression in the pancreas, GLUT2 expression in the liver, and tyrosine hydroxylase expression in dopaminergic neurons. Organ-specific gene regulation by FoxA proteins is achieved through cooperative regulation with a broad array of transcription factors with more limited expression domains. Fork head (Fkh), the sole Drosophila FoxA family member, is required for the development of multiple distinct organs, yet little is known regarding how Fkh regulates tissue-specific gene expression. Here, we characterize Sage, a bHLH transcription factor expressed exclusively in the Drosophila salivary gland (SG). We show that Sage is required for late SG survival and normal tube morphology. We find that many Sage targets, identified by microarray analysis, encode SG-specific secreted cargo, transmembrane proteins, and the enzymes that modify these proteins. We show that both Sage and Fkh are required for the expression of Sage target genes, and that co-expression of Sage and Fkh is sufficient to drive target gene expression in multiple cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage-Fkh targets, and Sage, Fkh and Sens colocalize on SG chromosomes. Importantly, expression of Sage-Fkh target genes appears to simply add to the tissue-specific gene expression programs already established in other cell types, and Sage and Fkh cannot alter the fate of most embryonic cell types even when expressed early and continuously.

  8. Greater sage-grouse science (2015–17)—Synthesis and potential management implications

    Science.gov (United States)

    Hanser, Steven E.; Deibert, Patricia A.; Tull, John C.; Carr, Natasha B.; Aldridge, Cameron L.; Bargsten, Travis D.; Christiansen, Thomas J.; Coates, Peter S.; Crist, Michele R.; Doherty, Kevin E.; Ellsworth, Ethan A.; Foster, Lee J.; Herren, Vicki A.; Miller, Kevin H.; Moser, Ann; Naeve, Robin M.; Prentice, Karen L.; Remington, Thomas E.; Ricca, Mark A.; Shinneman, Douglas J.; Truex, Richard L.; Wiechman , Lief A.; Wilson, Dereck C.; Bowen, Zachary H.

    2018-02-15

    Executive SummaryThe greater sage-grouse (Centrocercus urophasianus; hereafter called “sage-grouse”), a species that requires sagebrush (Artemisia spp.), has experienced range-wide declines in its distribution and abundance. These declines have prompted substantial research and management investments to improve the understanding of sage-grouse and its habitats and reverse declines in distribution and population numbers.Over the past two decades, the U.S. Fish and Wildlife Service (USFWS) has responded to eight petitions to list the sage-grouse under the Endangered Species Act of 1973, with the completion of the most recent listing determination in September 2015. At that time, the USFWS determined that the sage-grouse did not warrant a listing, primarily because of the large scale science-based conservation and planning efforts completed or started by Federal, State, local agencies, private landowners, and other entities across the range. The planning efforts culminated in the development of the 2015 Bureau of Land Management (BLM) and U.S. Forest Service Land Use Plan Amendments, which provided regulatory certainty and commitment from Federal land-management agencies to limit, mitigate, and track anthropogenic disturbance and implement other sage-grouse conservation measures.After these policy decisions, the scientific community has continued to refine and expand the knowledge available to inform implementation of management actions, increase the efficiency and effectiveness of those actions, and continue developing an overall understanding of sage-grouse populations, habitat requirements, and their response to human activity and other habitat changes. The development of science has been driven by multiple prioritization documents including the “Greater Sage-Grouse National Research Strategy” (Hanser and Manier, 2013) and, most recently, the “Integrated Rangeland Fire Management Strategy Actionable Science Plan” (Integrated Rangeland Fire Management

  9. Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L and its parental lines based on SAGE data

    Directory of Open Access Journals (Sweden)

    Chen Chen

    2007-09-01

    Full Text Available Abstract Background It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE data from an elite Chinese super-hybrid rice (LYP9 and its parental cultivars (93-11 and PA64s in three major tissue types (leaves, roots and panicles at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis. Results By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (93-11 and PA64s, we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages with P-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (P Conclusion We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.

  10. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  11. Snowstorm Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Snowstorm Database is a collection of over 500 snowstorms dating back to 1900 and updated operationally. Only storms having large areas of heavy snowfall (10-20...

  12. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  13. Using resilience and resistance concepts to manage threats to sagebrush ecosystems, Gunnison sage-grouse, and Greater sage-grouse in their eastern range: A strategic multi-scale approach

    Science.gov (United States)

    Jeanne C. Chambers; Jeffrey L. Beck; Steve Campbell; John Carlson; Thomas J. Christiansen; Karen J. Clause; Jonathan B. Dinkins; Kevin E. Doherty; Kathleen A. Griffin; Douglas W. Havlina; Kenneth F. Henke; Jacob D. Hennig; Laurie L. Kurth; Jeremy D. Maestas; Mary Manning; Kenneth E. Mayer; Brian A. Mealor; Clinton McCarthy; Marco A. Perea; David A. Pyke

    2016-01-01

    This report provides a strategic approach developed by a Western Association of Fish and Wildlife Agencies interagency working group for conservation of sagebrush ecosystems, Greater sage-grouse, and Gunnison sage-grouse. It uses information on (1) factors that influence sagebrush ecosystem resilience to disturbance and resistance to nonnative invasive annual grasses...

  14. Using resilience and resistance concepts to manage threats to sagebrush ecosystems, Gunnison sage-grouse, and Greater sage-grouse in their eastern range: A strategic multi-scale approach

    Science.gov (United States)

    Chambers, Jeanne C.; Beck, Jeffrey L.; Campbell, Steve; Carlson, John; Christiansen, Thomas J.; Clause, Karen J.; Dinkins, Jonathan B.; Doherty, Kevin E.; Griffin, Kathleen A.; Havlina, Douglas W.; Mayer, Kenneth F.; Hennig, Jacob D.; Kurth, Laurie L.; Maestas, Jeremy D.; Manning, Mary E.; Mealor, Brian A.; McCarthy, Clinton; Perea, Marco A.; Pyke, David A.

    2016-01-01

    This report provides a strategic approach developed by a Western Association of Fish and Wildlife Agencies interagency working group for conservation of sagebrush ecosystems, Greater sage-grouse, and Gunnison sage-grouse. It uses information on (1) factors that influence sagebrush ecosystem resilience to disturbance and resistance to nonnative invasive annual grasses and (2) distribution and relative abundance of sage-grouse populations to address persistent ecosystem threats, such as invasive annual grasses and wildfire, and land use and development threats, such as oil and gas development and cropland conversion, to develop effective management strategies. A sage-grouse habitat matrix links relative resilience and resistance of sagebrush ecosystems with modeled sage-grouse breeding habitat probabilities to help decisionmakers assess risks and determine appropriate management strategies at both landscape and site scales. Areas for targeted management are assessed by overlaying matrix components with Greater sage-grouse Priority Areas for Conservation and Gunnison sage-grouse critical habitat and linkages, breeding bird concentration areas, and specific habitat threats. Decision tools are discussed for determining the suitability of target areas for management and the most appropriate management actions. A similar approach was developed for the Great Basin that was incorporated into the Federal land use plan amendments and served as the basis of a Bureau of Land Management Fire and Invasives Assessment Tool, which was used to prioritize sage-grouse habitat for targeted management activities.

  15. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  16. Investigating impacts of oil and gas development on greater sage-grouse

    Science.gov (United States)

    Green, Adam; Aldridge, Cameron L.; O'Donnell, Michael

    2017-01-01

    The sagebrush (Artemisia spp.) ecosystem is one of the largest ecosystems in western North America providing habitat for species found nowhere else. Sagebrush habitats have experienced dramatic declines since the 1950s, mostly due to anthropogenic disturbances. The greater sage-grouse (Centrocercus urophasianus) is a sagebrush-obligate species that has experienced population declines over the last several decades, which are attributed to a variety of disturbances including the more recent threat of oil and gas development. We developed a hierarchical, Bayesian state-space model to investigate the impacts of 2 measures of oil and gas development, and environmental and habitat conditions, on sage-grouse populations in Wyoming, USA using male lek counts from 1984 to 2008. Lek attendance of male sage-grouse declined by approximately 2.5%/year and was negatively related to oil and gas well density. We found little support for the influence of sagebrush cover and precipitation on changes in lek counts. Our results support those of other studies reporting negative impacts of oil and gas development on sage-grouse populations and our modeling approach allowed us to make inference to a longer time scale and larger spatial extent than in previous studies. In addition to sage-grouse, development may also negatively affect other sagebrush-obligate species, and active management of sagebrush habitats may be necessary to maintain some species. 

  17. The effect of clary sage oil on staphylococci responsible for wound infections.

    Science.gov (United States)

    Sienkiewicz, Monika; Głowacka, Anna; Poznańska-Kurowska, Katarzyna; Kaszuba, Andrzej; Urbaniak, Anna; Kowalczyk, Edward

    2015-02-01

    The spreading of bacterial antibiotic resistance among clinical strains of pathogenic bacteria has made investigators to search for other active antibacterial agents which could provide a valuable complement to the existing therapies. To determine the antibacterial activity of clary sage oil (Salvia sclarea L.) against Staphylococcus clinical strains which were isolated from patients with wound infections. A comprehensive evaluation of Staphylococcus clinical strain resistance to antibiotics was performed. The constituents of clary sage oil were assayed by GC-FID-MS analysis. The minimal inhibitory concentration (MIC) of the tested essential oil against staphylococci by the micro-dilution broth method was determined. The clary sage oil was active against Staphylococcus aureus, S. epidermidis and S. xylosus with MIC values ranging from 3.75 to 7.00 µl/ml. The results of the in vitro tests encourage to use formulations containing sage oil as the active natural antimicrobial agent. Because of its antimicrobial properties clary sage oil may be applied to treat wounds and skin infections.

  18. Mapping SAGE questionnaire to the International Classification of Functioning, Disability and Health (ICF).

    Science.gov (United States)

    Raggi, Alberto; Quintas, Rui; Russo, Emanuela; Martinuzzi, Andrea; Costardi, Daniela; Frisoni, Giovanni Battista; Franco, Maria Grazia; Andreotti, Alessandra; Ojala, Matti; Peña, Sebastián; Perales, Jaime; Chatterji, Somnath; Miret, Marta; Tobiasz-Adamczyk, Beata; Koskinen, Seppo; Frattura, Lucilla; Leonardi, Matilde

    2014-01-01

    The collaborative research on ageing in Europe protocol was based on that of the World Health Organization Study on global AGEing and adult health (SAGE) project that investigated the relationship between health and well-being and provided a set of instruments that can be used across countries to monitor health and health-related outcomes of older populations as well as the strategies for addressing issues concerning the ageing process. To evaluate the degree to which SAGE protocol covered the spectrum of disability given the scope of the World Health Organization International Classification of Functioning, Disability and Health (ICF), a mapping exercise was performed with SAGE protocol. Results show that the SAGE protocol covers ICF domains in a non-uniform way, with environmental factors categories being underrepresented, whereas mental, cardiovascular, sensory functions and mobility were overrepresented. To overcome this partial coverage of ICF functioning categories, new assessment instruments have been developed. PRACTITIONER MESSAGE: Mapping exercises are valid procedures to understand the extent to which a survey protocol covers the spectrum of functioning. The mapping exercise with SAGE protocol shows that it provides only a partial representation of body functions and activities and participation domains, and the coverage of environmental factors is poor. New instruments are therefore needed for researchers to properly understand the health and disability of ageing populations. Copyright © 2013 John Wiley & Sons, Ltd.

  19. Patterns in Greater Sage-grouse population dynamics correspond with public grazing records at broad scales.

    Science.gov (United States)

    Monroe, Adrian P; Aldridge, Cameron L; Assal, Timothy J; Veblen, Kari E; Pyke, David A; Casazza, Michael L

    2017-06-01

    Human land use, such as livestock grazing, can have profound yet varied effects on wildlife interacting within common ecosystems, yet our understanding of land-use effects is often generalized from short-term, local studies that may not correspond with trends at broader scales. Here we used public land records to characterize livestock grazing across Wyoming, USA, and we used Greater Sage-grouse (Centrocercus urophasianus) as a model organism to evaluate responses to livestock management. With annual counts of male Sage-grouse from 743 leks (breeding display sites) during 2004-2014, we modeled population trends in response to grazing level (represented by a relative grazing index) and timing across a gradient in vegetation productivity as measured by the Normalized Vegetation Difference Index (NDVI). We found grazing can have both positive and negative effects on Sage-grouse populations depending on the timing and level of grazing. Sage-grouse populations responded positively to higher grazing levels after peak vegetation productivity, but populations declined when similar grazing levels occurred earlier, likely reflecting the sensitivity of cool-season grasses to grazing during peak growth periods. We also found support for the hypothesis that effects of grazing management vary with local vegetation productivity. These results illustrate the importance of broad-scale analyses by revealing patterns in Sage-grouse population trends that may not be inferred from studies at finer scales, and could inform sustainable grazing management in these ecosystems. © 2017 by the Ecological Society of America.

  20. Colon Cancer Chemoprevention by Sage Tea Drinking: Decreased DNA Damage and Cell Proliferation.

    Science.gov (United States)

    Pedro, Dalila F N; Ramos, Alice A; Lima, Cristovao F; Baltazar, Fatima; Pereira-Wilson, Cristina

    2016-02-01

    Salvia officinalis and some of its isolated compounds have been found to be preventive of DNA damage and increased proliferation in vitro in colon cells. In the present study, we used the azoxymethane model to test effects of S. officinalis on colon cancer prevention in vivo. The results showed that sage treatment reduced the number of ACF formed only if administered before azoxymethane injection, demonstrating that sage tea drinking has a chemopreventive effect on colorectal cancer. A decrease in the proliferation marker Ki67 and in H2 O2 -induced and azoxymethane-induced DNA damage to colonocytes and lymphocytes were found with sage treatment. This confirms in vivo the chemopreventive effects of S. officinalis. Taken together, our results show that sage treatment prevented initiation phases of colon carcinogenesis, an effect due, at least in part, to DNA protection, and reduced proliferation rates of colon epithelial cell that prevent mutations and their fixation through cell replication. These chemopreventive effects of S. officinalis on colon cancer add to the many health benefits attributed to sage and encourage its consumption. Copyright © 2015 John Wiley & Sons, Ltd.

  1. Better living through conifer removal: A demographic analysis of sage-grouse vital rates.

    Directory of Open Access Journals (Sweden)

    John P Severson

    Full Text Available Sagebrush (Artemisia spp. obligate wildlife species such as the imperiled greater sage-grouse (Centrocercus urophasianus face numerous threats including altered ecosystem processes that have led to conifer expansion into shrub-steppe. Conifer removal is accelerating despite a lack of empirical evidence on grouse population response. Using a before-after-control-impact design at the landscape scale, we evaluated effects of conifer removal on two important demographic parameters, annual survival of females and nest survival, by monitoring 219 female sage-grouse and 225 nests in the northern Great Basin from 2010 to 2014. Estimates from the best treatment models showed positive trends in the treatment area relative to the control area resulting in an increase of 6.6% annual female survival and 18.8% nest survival relative to the control area by 2014. Using stochastic simulations of our estimates and published demographics, we estimated a 25% increase in the population growth rate in the treatment area relative to the control area. This is the first study to link sage-grouse demographics with conifer removal and supports recommendations to actively manage conifer expansion for sage-grouse conservation. Sage-grouse have become a primary catalyst for conservation funding to address conifer expansion in the West, and these findings have important implications for other ecosystem services being generated on the wings of species conservation.

  2. Ecology of Greater Sage-Grouse in the Bi-State Planning Area Final Report, September 2007

    Science.gov (United States)

    Casazza, Michael L.; Overton, Cory T.; Farinha, Melissa A.; Torregrosa, Alicia; Fleskes, Joseph P.; Miller, Michael R.; Sedinger, James S.; Kolada, Eric J.

    2009-01-01

    Conservation efforts for greater sage-grouse (Centrocercus urophasianus), hereafter sage-grouse, are underway across the range of this species. Over 70 local working groups have been established and are implementing on-the-ground sage-grouse oriented conservation projects. Early on in this process, the California Department of Fish and Game (CDFG) recognized the need to join in these efforts and received funding from the U.S. Fish and Wildlife Service (USFWS) under the Candidate Species Conservation Program to help develop a species conservation plan for sage-grouse in the Mono County area. This conservation plan covers portions of Alpine, Mono, and Inyo counties in California and Douglas, Esmeralda, Lyon, and Mineral counties in Nevada. A concurrent effort underway through the Nevada Governor's Sage-grouse Conservation Team established Local Area Working Groups across Nevada and eastern California. The Mono County populations of sage-grouse were encompassed by the Bi-State Local Planning Area, which was comprised of six population management units (PMUs). The state agencies from California (CDFG) and Nevada (Nevada Department of Wildlife; NDOW) responsible for the management of sage-grouse agreed to utilize the process that had begun with the Nevada Governor's Team in order to develop local plans for conservation planning and implementation. Resources from the USFWS were applied to several objectives in support of the development of the Bi-State Local Area Sage-grouse Conservation Plan through a grant to the U.S. Geological Survey (USGS). Objectives included: (1) participate in the development of the Bi-State Conservation Plan, (2) compile and synthesize existing sage-grouse data, (3) document seasonal movements of sage-grouse, (4) identify habitats critical to sage-grouse, (5) determine survival rates and identify causal factors of mortality, (6) determine nest success and brood success of sage-grouse, and (7) identify sage-grouse lek sites. Progress reports

  3. A transcriptome anatomy of human colorectal cancers

    International Nuclear Information System (INIS)

    Lü, Bingjian; Xu, Jing; Lai, Maode; Zhang, Hao; Chen, Jian

    2006-01-01

    Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers

  4. Greater sage-grouse: general use and roost site occurrence with pellet counts as a measure of relative abundance

    Science.gov (United States)

    Steven E. Hanser; Cameron L. Aldridge; Matthias Leu; Mary M. Rowland; Scott E. Nielsen; Steven T. Knick

    2011-01-01

    Greater sage-grouse (Centrocercus urophasianus) have been declining both spatially and numerically throughout their range because of anthropogenic disturbance and loss and fragmentation of sagebrush (Artemisia spp.) habitats. Understanding how sage-grouse respond to these habitat alterations and disturbances, particularly the...

  5. Conservation and restoration of sagebrush ecosystems and sage-grouse: An assessment of USDA Forest Service Science

    Science.gov (United States)

    Deborah M. Finch; Douglas A. Boyce; Jeanne C. Chambers; Chris J. Colt; Kas Dumroese; Stanley G. Kitchen; Clinton McCarthy; Susan E. Meyer; Bryce A. Richardson; Mary M. Rowland; Mark A. Rumble; Michael K. Schwartz; Monica S. Tomosy; Michael J. Wisdom

    2016-01-01

    Sagebrush ecosystems are among the largest and most threatened ecosystems in North America. Greater sage-grouse has served as the bellwether for species conservation in these ecosystems and has been considered for listing under the Endangered Species Act eight times. In September 2015, the decision was made not to list greater sage-grouse, but to reevaluate its status...

  6. The Sagebrush Steppe Treatment Evaluation Project (SageSTEP): a test of state-and-transition theory

    Science.gov (United States)

    James D. McIver; Mark Brunson; Steve C. Bunting; Jeanne Chambers; Nora Devoe; Paul Doescher; James Grace; Dale Johnson; Steve Knick; Richard Miller; Mike Pellant; Fred Pierson; David Pyke; Kim Rollins; Bruce Roundy; Eugene Schupp; Robin Tausch; David Turner

    2010-01-01

    The Sagebrush Steppe Treatment Evaluation Project (SageSTEP) is a comprehensive, integrated, long-term study that evaluates the ecological effects of fire and fire surrogate treatments designed to reduce fuel and to restore sagebrush (Artemisia spp.) communities of the Great Basin and surrounding areas. SageSTEP has several features that make it ideal for testing...

  7. Effect of γ-irradiation on bioactivity, fatty acid compositions and volatile compounds of clary sage seed (Salvia sclarea L.).

    Science.gov (United States)

    Yalcin, Hasan; Ozturk, Ismet; Tulukcu, Eray; Sagdic, Osman

    2011-09-01

    Clary sage seeds (Salvia sclarea L.) were obtained from plants cultivated, and 2.5, 4.0, 5.5, and 7.0 kGy doses of γ-irradiation were applied to the clary sage seeds. They were then analyzed for their protein, ash, oil and dry matter contents, and fatty acid composition. Additionally, the total phenolic contents, antiradical, antioxidant activities, and volatile compounds of the clary sage seed extract were determined. There was no significant difference in protein content. However, the moisture, oil, and ash contents of the samples were affected by irradiation. While the 7 kGy dose had a positive effect on the total phenolic content and antiradical activity of the sage seed extract, all doses have negative effects on the antioxidant activity of the sage seed. The main fatty acid of the sage seed was remarkably found as α-linolenic acid. The four irradiation levels caused significant differences in fatty acid composition by affecting all fatty acids except palmitic, palmitoleic, and eicosenoic acids. The dominant volatile compounds of control sage seed were found as β-pinene (18.81%) and limonene (15.60%). Higher doses of the irradiation decreased volatile components of sage seed. Clary sage seed including high omega-3 can be irradiated with low doses (≤ 2.5 kGy) of γ-irradiation. Clary sage is one of the most popular Salvia species in Turkey and many countries. Clary sage seed has approximately 29% oil content and this oil contains >50% of α-linolenic acid. γ-Irradiation is widely applied in the preservation of spice quality. The present study shows that the antioxidant activity of the clary sage seed is decreased by γ-irradiation. Additionally, higher doses of irradiation also decreased the volatile components of sage seed. Therefore, we suggest that clary sage seed which includes high levels of omega-3 should be irradiated with low doses (≤ 2.5 kGy) of γ-irradiation. © 2011 Institute of Food Technologists®

  8. Comparison of aerosol extinction between lidar and SAGE II over Gadanki, a tropical station in India

    Directory of Open Access Journals (Sweden)

    P. Kulkarni

    2015-03-01

    Full Text Available An extensive comparison of aerosol extinction has been performed using lidar and Stratospheric Aerosol and Gas Experiment (SAGE II data over Gadanki (13.5° N, 79.2° E, a tropical station in India, following coincident criteria during volcanically quiescent conditions from 1998 to 2005. The aerosol extinctions derived from lidar are higher than SAGE II during all seasons in the upper troposphere (UT, while in the lower-stratosphere (LS values are closer. The seasonal mean percent differences between lidar and SAGE II aerosol extinctions are > 100% in the UT and Ba (sr−1, the ratio between aerosol backscattering and extinction, are needed for the tropics for a more accurate derivation of aerosol extinction.

  9. Brine saturation technique for extraction of light filth from rubbed, ground, and whole sage: collaborative study.

    Science.gov (United States)

    Freeman, C C

    1985-01-01

    A new approach to the isolation of light filth from the 3 commercial forms of sage was studied collaboratively. It incorporates a simple isopropanol defatting, followed by saturation of the product with brine by alternately heating and cooling, and subsequent trapping of filth from tap water with olive oil. This method circumvents the use of hazardous, expensive solvents and more time-consuming pretreatment procedures. Overall recoveries were 92.1% for rodent hair and 78.7% for insect fragments on clean, easy-to-read papers. An additional blending step was necessary to obtain satisfactory recovery of rodent hair fragments from whole sage. The method has been adopted official first action for light filth in rubbed and ground sage only.

  10. Experiment Databases

    Science.gov (United States)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  11. Annotated bibliography of scientific research on greater sage-grouse published since January 2015

    Science.gov (United States)

    Carter, Sarah K.; Manier, Daniel J.; Arkle, Robert S.; Johnston, Aaron; Phillips, Susan L.; Hanser, Steven E.; Bowen, Zachary H.

    2018-02-14

    The greater sage-grouse (Centrocercus urophasianus; hereafter GRSG) has been a focus of scientific investigation and management action for the past two decades. The 2015 U.S. Fish and Wildlife Service listing determination of “not warranted” was in part due to a large-scale collaborative effort to develop strategies to conserve GRSG populations and their habitat and to reduce threats to both. New scientific information augments existing knowledge and can help inform updates or modifications to existing plans for managing GRSG and sagebrush ecosystems. However, the sheer number of scientific publications can be a challenge for managers tasked with evaluating and determining the need for potential updates to existing planning documents. To assist in this process, the U.S. Geological Survey (USGS) has reviewed and summarized the scientific literature published since January 1, 2015.To identify articles and reports published about GRSG, we first conducted a structured search of three reference databases (Web of Science, Scopus, and Google Scholar) using the search term “greater sage-grouse.” We refined the initial list of products by (1) removing duplicates, (2) excluding products that were not published as research or scientific review articles in peer-reviewed journals or as formal government technical reports, and (3) retaining only those products for which GRSG or their habitat was a research focus.We summarized the contents of each product by using a consistent structure (background, objectives, methods, location, findings, and implications) and assessed the content of each product relevant to a list of 31 management topics. These topics include GRSG biology and habitat characteristics along with potential management actions, land uses, and environmental factors related to GRSG management and conservation. We also noted which articles/reports created new geospatial data.The final search was conducted on January 6, 2018, and application of our criteria

  12. De novo transcriptome assembly of mangosteen (Garcinia mangostana L. fruit

    Directory of Open Access Journals (Sweden)

    Deden Derajat Matra

    2016-12-01

    Full Text Available Garcinia mangostana L. (Mangosteen, of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  13. Phenology largely explains taller grass at successful nests in greater sage-grouse.

    Science.gov (United States)

    Smith, Joseph T; Tack, Jason D; Doherty, Kevin E; Allred, Brady W; Maestas, Jeremy D; Berkeley, Lorelle I; Dettenmaier, Seth J; Messmer, Terry A; Naugle, David E

    2018-01-01

    Much interest lies in the identification of manageable habitat variables that affect key vital rates for species of concern. For ground-nesting birds, vegetation surrounding the nest may play an important role in mediating nest success by providing concealment from predators. Height of grasses surrounding the nest is thought to be a driver of nest survival in greater sage-grouse ( Centrocercus urophasianus ; sage-grouse), a species that has experienced widespread population declines throughout their range. However, a growing body of the literature has found that widely used field methods can produce misleading inference on the relationship between grass height and nest success. Specifically, it has been demonstrated that measuring concealment following nest fate (failure or hatch) introduces a temporal bias whereby successful nests are measured later in the season, on average, than failed nests. This sampling bias can produce inference suggesting a positive effect of grass height on nest survival, though the relationship arises due to the confounding effect of plant phenology, not an effect on predation risk. To test the generality of this finding for sage-grouse, we reanalyzed existing datasets comprising >800 sage-grouse nests from three independent studies across the range where there was a positive relationship found between grass height and nest survival, including two using methods now known to be biased. Correcting for phenology produced equivocal relationships between grass height and sage-grouse nest survival. Viewed in total, evidence for a ubiquitous biological effect of grass height on sage-grouse nest success across time and space is lacking. In light of these findings, a reevaluation of land management guidelines emphasizing specific grass height targets to promote nest success may be merited.

  14. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.

    Science.gov (United States)

    Azim, M Kamran; Khan, Ishtaiq A; Zhang, Yong

    2014-05-01

    We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80% of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37%) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

  15. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

    Science.gov (United States)

    Wu, Hong-xia; Jia, Hui-min; Ma, Xiao-wei; Wang, Song-biao; Yao, Quan-sheng; Xu, Wen-tian; Zhou, Yi-gang; Gao, Zhong-shan; Zhan, Ru-lin

    2014-06-13

    Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. High Throughput Transcriptomics @ USEPA (Toxicology ...

    Science.gov (United States)

    The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

  17. Antioxidant Capacity and Polyphenolic Composition as Quality Indicators for Aqueous Infusions of Salvia officinalis L. (sage tea).

    Science.gov (United States)

    Walch, Stephan G; Tinzoh, Laura Ngaba; Zimmermann, Benno F; Stühlinger, Wolf; Lachenmeier, Dirk W

    2011-01-01

    Sage (Salvia officinalis L.) is used as an herbal medicinal product, with the most typical form of application as infusion with boiling water (sage tea). The well-established traditional uses include symptomatic treatment of mild dyspeptic complaints, the treatment of inflammations in the mouth and the throat, and relief of excessive sweating and relief of minor skin inflammations. In this study, sage teas prepared from commercially available products were chemically analyzed for polyphenolic content using liquid chromatography, for antioxidant potential using the oxygen radical absorbance capacity method, and for the Folin-Ciocalteu (FC) index. The sage teas showed a high variation for all parameters studied (up to 20-fold differences for rosmarinic acid). Univariate and multivariate analyses showed that the antioxidant potential, which varied between 0.4 and 1.8 mmol trolox equivalents/100 mL, was highly dependent on rosmarinic acid and its derivatives. The FC index also showed a high correlation to these polyphenols, and could therefore be used as a screening parameter for sage tea quality. The considerable differences in polyphenolic composition and antioxidant capacity between the brands lead to a demand for quality standardization, especially if these sage teas are to be used for therapeutic purposes. Further research also appears to be necessary to characterize the dose-benefit relationship, as sage may also contain a constituent (thujone) with potentially adverse effects.

  18. Antioxidant capacity and polyphenolic composition as quality indicators for aqueous infusions of Salvia officinalis L. (sage tea

    Directory of Open Access Journals (Sweden)

    Stephan G Walch

    2011-12-01

    Full Text Available Sage (Salvia officinalis L. is used as an herbal medicinal product, with the most typical form of application as infusion with boiling water (sage tea. The well-established traditional uses include symptomatic treatment of mild dyspeptic complaints, the treatment of inflammations in the mouth and the throat, and relief of excessive sweating and relief of minor skin inflammations. In this study, sage teas prepared from commercially available products were chemically analysed for polyphenolic content using liquid chromatography, for antioxidant potential using the oxygen radical absorbance capacity (ORAC method, and for the Folin-Ciocalteu (FC index. The sage teas showed a high variation for all parameters studied (up to 20-fold differences for rosmarinic acid. Univariate and multivariate analyses showed that the antioxidant potential, which varied between 0.4 and 1.8 mmol trolox equivalents/100 mL, was highly dependent on rosmarinic acid and its derivatives. The FC index also showed a high correlation to these polyphenols, and could therefore be used as a screening parameter for sage tea quality. The considerable differences in polyphenolic composition and antioxidant capacity between the brands lead to a demand for quality standardisation, especially if these sage teas are to be used for therapeutic purposes. Further research also appears to be necessary to characterise the dose-benefit relationship, as sage may also contain a constituent (thujone with potentially adverse effects.

  19. Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

    Directory of Open Access Journals (Sweden)

    Moon Young Lee

    Full Text Available Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC, which serve as slow-wave electrical pacemakers for gastrointestinal (GI smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

  20. Multi-species benefits of the proposed North American sage-grouse management plan

    Science.gov (United States)

    Clait E. Braun

    2005-01-01

    The population size and distribution of the two species of sage-grouse (Greater – Centrocercus urophasianus and Gunnison – C. minimus) populations have become greatly reduced throughout western North America because of habitat changes. Threats are ongoing to the remaining sagebrush (Artemisia ...

  1. SAGE FOR WINDOWS (WSAGE) VERSION 1.0 SOLVENT ALTERNATIVES GUIDE - USER'S GUIDE

    Science.gov (United States)

    The guide provides instructions for using the Solvent Alternatives Guide (SAGE) for Windows, version 1.0. The guide assumes that the user is familiar with the fundamentals of operating Windows 3.1 (or higher) on a personal computer under the DOS 5.0 (or higher) operating system. ...

  2. Landscape restoration for greater sage-grouse: implications for multiscale planning and monitoring

    Science.gov (United States)

    Michael J. Wisdom; Mary M. Rowland; Miles A. Hemstrom; Barbara C. Wales

    2005-01-01

    Habitats and populations of greater sage-grouse (Centrocercus urophasianus) have declined throughout western North America in response to a myriad of detrimental land uses. Successful restoration of this species' habitat, therefore, is of keen interest to Federal land agencies who oversee management of most remaining habitat. To illustrate the...

  3. Salvia officinalis l. (sage) Ameliorates Radiation-Induced Oxidative Brain Damage In Rats

    International Nuclear Information System (INIS)

    Osman, N. N.; Abd El Azime, A.Sh.

    2013-01-01

    The present study was designed to investigate the oxidative stress and the role of antioxidant system in the management of gamma irradiation induced whole brain damage in rats . Also, to elucidate the potential role of Salvia officinalis (sage) in alleviating such negative effects. Rats were subjected to gamma radiation (6 Gy). Sage extract was daily given to rats during 14 days before starting irradiation and continued after radiation exposure for another 14 days. The results revealed that the levels of thiobarbituric acid reactive substances (TBARS), protein carbonyl content (PCC) and nitric oxide (NO) content were significantly increased, while the activities of superoxide dismutase (SOD) and catalase (CAT) as well as the reduced glutathione (GSH) content were significantly decreased in the brain homogenate of irradiated rats. Additionally, brain acetylcholinesterase (AChE) as well as alkaline phosphatase (ALP), acid phosphatase (ACP) and lactate dehydrogenase (LDH) activities were significantly increased. On the other hand, the results showed that, administration of sage extract to rats was able to ameliorate the mentioned parameters and the values returned close to the normal ones. It could be concluded that sage extract, by its antioxidant constituents, could modulate radiation induced oxidative stress and enzyme activities in the brain.

  4. SAGE SOLVENT ALTERNATIVES GUIDE: SYSTEM IMPROVEMENTS FOR SELECTING INDUSTRIAL SURFACE CLEANING ALTERNATIVES

    Science.gov (United States)

    The paper describes computer software, called SAGE, that can provide not only cleaning recommendations but also general information on various surface cleaning options. In short, it is an advisory system which can provide users with vital information on the cleaning process optio...

  5. Restoration handbook for sagebrush steppe ecosystems with emphasis on greater sage-grouse habitat - Part 1

    Science.gov (United States)

    David A. Pyke; Jeanne C. Chambers; Mike Pellant; Steven T. Knick; Richard F. Miller; Jeffrey L. Beck; Paul S. Doescher; Eugene W. Schupp; Bruce A. Roundy; Mark Brunson; James D. McIver

    2015-01-01

    Sagebrush steppe ecosystems in the United States currently occur on only about one-half of their historical land area because of changes in land use, urban growth, and degradation of land, including invasions of non-native plants. The existence of many animal species depends on the existence of sagebrush steppe habitat. The greater sage-grouse (Centrocercus...

  6. Hierarchical population structure in greater sage-grouse provides insight into management boundary delineation

    Science.gov (United States)

    Todd B. Cross; David E. Naugle; John C. Carlson; Michael K. Schwartz

    2016-01-01

    Understanding population structure is important for guiding ongoing conservation and restoration efforts. The greater sage-grouse (Centrocercus urophasianus) is a species of concern distributed across 1.2 million km2 of western North America. We genotyped 1499 greater sagegrouse from 297 leks across Montana, North Dakota and South Dakota using a 15 locus...

  7. Information Retrieval from SAGE II and MFRSR Multi-Spectral Extinction Measurements

    Science.gov (United States)

    Lacis, Andrew A.; Hansen, James E. (Technical Monitor)

    2001-01-01

    Direct beam spectral extinction measurements of solar radiation contain important information on atmospheric composition in a form that is essentially free from multiple scattering contributions that otherwise tend to complicate the data analysis and information retrieval. Such direct beam extinction measurements are available from the solar occultation satellite-based measurements made by the Stratospheric and Aerosol Gas Experiment (SAGE II) instrument and by ground-based Multi-Filter Shadowband Radiometers (MFRSRs). The SAGE II data provide cross-sectional slices of the atmosphere twice per orbit at seven wavelengths between 385 and 1020 nm with approximately 1 km vertical resolution, while the MFRSR data provide atmospheric column measurements at six wavelengths between 415 and 940 nm but at one minute time intervals. We apply the same retrieval technique of simultaneous least-squares fit to the observed spectral extinctions to retrieve aerosol optical depth, effective radius and variance, and ozone, nitrogen dioxide, and water vapor amounts from the SAGE II and MFRSR measurements. The retrieval technique utilizes a physical model approach based on laboratory measurements of ozone and nitrogen dioxide extinction, line-by-line and numerical k-distribution calculations for water vapor absorption, and Mie scattering constraints on aerosol spectral extinction properties. The SAGE II measurements have the advantage of being self-calibrating in that deep space provides an effective zero point for the relative spectral extinctions. The MFRSR measurements require periodic clear-day Langley regression calibration events to maintain accurate knowledge of instrument calibration.

  8. Greater sage-grouse as an umbrella species for sagebrush-associated vertebrates.

    Science.gov (United States)

    Mary M. Rowland; Michael J. Wisdom; Lowell Suring; Cara W. Meinke

    2006-01-01

    Widespread degradation of the sagebrush ecosystem in the western United States, including the invasion of cheatgrass, has prompted resource managers to consider a variety of approaches to restore and conserve habitats for sagebrush-associated species. One such approach involves the use of greater sage-grouse, a species of prominent conservation interest, as an umbrella...

  9. Metabolism of monoterpenes in cell cultures of common sage (Salvia officinalis)

    International Nuclear Information System (INIS)

    Falk, K.L.; Gershenzon, J.; Croteau, R.

    1990-01-01

    Leaves of common sage (Salvia officinalis) accumulate monoterpenes in glandular trichomes at levels exceeding 15 milligrams per gram fresh weight at maturity, whereas sage cells in suspension culture did not accumulate detectable levels of monoterpenes ( 14 C]sucrose was also virtually undetectable in this cell culture system. In vitro assay of each of the enzymes required for the sequential conversion of the ubiquitous isoprenoid precursor geranyl pyrophosphate to (+)-camphor (a major monoterpene product of sage) in soluble extracts of the cells revealed the presence of activity sufficient to produce (+)-camphor at a readily detectable level (>0.3 micrograms per gram fresh weight) at the late log phase of growth. Other monoterpene synthetic enzymes were present as well. In vivo measurement of the ability to catabolize (+)-camphor in these cells indicated that degradative capability exceeded biosynthetic capacity by at least 1,000-fold. Therefore, the lack of monoterpene accumulation in undifferentiated sage cultures could be attributed to a low level of biosynthetic activity (relative to the intact plant) coupled to a pronounced capacity for monoterpene catabolism

  10. Characteristics of coastal sage scrub in relation to fire history and use by California gnatcatchers

    Science.gov (United States)

    Jan L. Beyers; Ginger C. Pena

    1995-01-01

    Abstract: Plant cover and vegetation structure were examined at two inland coastal sage scrub sites differing in fire history and use by California gnatcatchers. Salvia mellifera and Eriogonum fasciculatum dominated one site; shrub cover on gnatcatcher occupied plots averaged 50 percent greater than on unoccupied plots. At the other site, gnatcatcher-occupied plots had...

  11. Revealing the Mind of the Sage: The Narrative Rhetoric of the "Chuang Tzu."

    Science.gov (United States)

    Kirkwood, William G.

    1992-01-01

    Argues that one of the formative texts of Taoism, the "Chuang Tzu," is worthy of study by rhetoric scholars because it reveals a unique approach to rhetoric in its attempt to disclose the mind of the sage not through logic but through intuition, and it shows how storytelling can acquaint people with previously unsuspected possibilities of thought…

  12. Peroxidase gene discovery from the horseradish transcriptome.

    Science.gov (United States)

    Näätsaari, Laura; Krainer, Florian W; Schubert, Michael; Glieder, Anton; Thallinger, Gerhard G

    2014-03-24

    Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes.

  13. Microhabitat Conditions in Wyoming's Sage-Grouse Core Areas: Effects on Nest Site Selection and Success.

    Directory of Open Access Journals (Sweden)

    Jonathan B Dinkins

    Full Text Available The purpose of our study was to identify microhabitat characteristics of greater sage-grouse (Centrocercus urophasianus nest site selection and survival to determine the quality of sage-grouse habitat in 5 regions of central and southwest Wyoming associated with Wyoming's Core Area Policy. Wyoming's Core Area Policy was enacted in 2008 to reduce human disturbance near the greatest densities of sage-grouse. Our analyses aimed to assess sage-grouse nest selection and success at multiple micro-spatial scales. We obtained microhabitat data from 928 sage-grouse nest locations and 819 random microhabitat locations from 2008-2014. Nest success was estimated from 924 nests with survival data. Sage-grouse selected nests with greater sagebrush cover and height, visual obstruction, and number of small gaps between shrubs (gap size ≥0.5 m and <1.0 m, while selecting for less bare ground and rock. With the exception of more small gaps between shrubs, we did not find any differences in availability of these microhabitat characteristics between locations within and outside of Core Areas. In addition, we found little supporting evidence that sage-grouse were selecting different nest sites in Core Areas relative to areas outside of Core. The Kaplan-Meier nest success estimate for a 27-day incubation period was 42.0% (95% CI: 38.4-45.9%. Risk of nest failure was negatively associated with greater rock and more medium-sized gaps between shrubs (gap size ≥2.0 m and <3.0 m. Within our study areas, Wyoming's Core Areas did not have differing microhabitat quality compared to outside of Core Areas. The close proximity of our locations within and outside of Core Areas likely explained our lack of finding differences in microhabitat quality among locations within these landscapes. However, the Core Area Policy is most likely to conserve high quality habitat at larger spatial scales, which over decades may have cascading effects on microhabitat quality available

  14. Sagebrush, greater sage-grouse, and the occurrence and importance of forbs

    Science.gov (United States)

    Pennington, Victoria E.; Schlaepfer, Daniel R.; Beck, Jeffrey L.; Bradford, John B.; Palmquist, Kyle A.; Lauenroth, William K.

    2016-01-01

    Big sagebrush (Artemisia tridentata Nutt.) ecosystems provide habitat for sagebrush-obligate wildlife species such as the Greater Sage-Grouse (Centrocercus urophasianus). The understory of big sagebrush plant communities is composed of grasses and forbs that are important sources of cover and food for wildlife. The grass component is well described in the literature, but the composition, abundance, and habitat role of forbs in these communities is largely unknown. Our objective was to synthesize information about forbs and their importance to Greater Sage-Grouse diets and habitats, how rangeland management practices affect forbs, and how forbs respond to changes in temperature and precipitation. We also sought to identify research gaps and needs concerning forbs in big sagebrush plant communities. We searched for relevant literature including journal articles and state and federal agency reports. Our results indicated that in the spring and summer, Greater Sage-Grouse diets consist of forbs (particularly species in the Asteraceae family), arthropods, and lesser amounts of sagebrush. The diets transition to sagebrush in fall and winter. Forbs provide cover for Greater Sage-Grouse individuals at their lekking, nesting, and brood-rearing sites, and the species has a positive relationship with arthropod presence. The effect of grazing on native forbs may be compounded by invasion of nonnative species and differs depending on grazing intensity. The effect of fire on forbs varies greatly and may depend on time elapsed since burning. In addition, chemical and mechanical treatments affect annual and perennial forbs differently. Temperature and precipitation influence forb phenology, biomass, and abundance differently among species. Our review identified several uncertainties and research needs about forbs in big sagebrush ecosystems. First, in many cases the literature about forbs is reported only at the genus or functional type level. Second, information about forb

  15. Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation

    Science.gov (United States)

    Wang, Ying; Ding, Jia-tong; Yang, Hai-ming; Yan, Zheng-jie; Cao, Wei; Li, Yang-bai

    2015-01-01

    Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp) were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species. PMID:26599806

  16. Analysis of Pigeon (Columba Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  17. The SAGE spectrometer: A tool for combined in-beam γ-ray and conversion electron spectroscopy

    International Nuclear Information System (INIS)

    Papadakis, P; Herzberg, R-D; Pakarinen, J; Butler, P A; Cox, D; Cresswell, J R; Parr, E; Sampson, J; Greenlees, P T; Sorri, J; Hauschild, K; Jones, P; Julin, R; Peura, P; Rahkila, P; Sandzelius, M; Coleman-Smith, P J; Lazarus, I H; Letts, S C; Pucknell, V F E

    2011-01-01

    The SAGE spectrometer allows simultaneous in-beam γ-ray and internal conversion electron measurements, by combining a germanium detector array with a highly segmented silicon detector and an electron transport system. SAGE is coupled with the ritu gas-filled recoil separator and the great focal-plane spectrometer for recoil-decay tagging studies. Digital electronics are used both for the γ ray and the electron parts of the spectrometer. SAGE was commissioned in the Accelerator Laboratory of the University of Jyvaeskylae in the beginning of 2010.

  18. Bioaccessibility and inhibitory effects on digestive enzymes of carnosic acid in sage and rosemary.

    Science.gov (United States)

    Ercan, Pınar; El, Sedef Nehir

    2018-04-28

    In this study, the aim was to determine the bioaccessibilities of carnosic acid in sage and rosemary and in vitro inhibitory effects of these samples on lipid and starch digestive enzymes by evaluating the lipase, α-amylase and α-glucosidase enzyme inhibition activities. The content of carnosic acid in rosemary (18.72 ± 0.33 mg/g) was found to be higher than that content of that in sage (3.76 ± 0.13 mg/g) (p sage and rosemary, respectively. The tested sage and rosemary showed inhibitory activity against α-glucosidase (Concentration of inhibitor required to produce a 50% inhibition of the initial rate of reaction - IC 50 88.49 ± 2.35, 76.80 ± 1.68 μg/mL, respectively), α-amylase (IC 50 107.65 ± 12.64, 95.65 ± 2.73 μg/mL, respectively) and lipase (IC 50 6.20 ± 0.63, 4.31 ± 0.62 μg/mL, respectively). Furthermore, to the best of our knowledge, this is the first work that carnosic acid standard equivalent inhibition capacities (CAEIC 50 ) for these food samples were determined and these values were in agreement with the IC 50 values. These results show that sage and rosemary are potent inhibitors of lipase, α-amylase and α-glucosidase digestive enzymes. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Gravity in the Century of Light: The Gravitation Theory of Georges-Louis Le Sage

    Science.gov (United States)

    Evans, James

    2006-05-01

    Each generation of physicists, or natural philosophers, has sought to place universal gravitation in the context of its own worldview. Often this has entailed an effort to reduce gravitation to something more fundamental. But what is deemed fundamental has, of course, changed with time. Each generation attacked the problem of universal gravitation with the tools of its day and brought to bear the concepts of its own standard model. The most successful eighteenth-century attempt to provide a mechanical explanation of gravity was that of Georges-Louis Le Sage (1724-1803) of Geneva. Le Sage postulated a sea of ultramundane corpuscles, streaming in all directions and characterized by minute mass, great velocity, and complete inelasticity. Mostly these corpuscles just pass through gross bodies such as apples or planets, but a few are absorbed, leading to all the phenomena of attraction. In a voluminous correspondence with nearly all the savants of the day, Le Sage constantly reshaped his arguments for his system in order to appeal to metaphysicians, mechanicians and Newtonians of several varieties. Le Sage's theory is an especially interesting one, for several reasons. First, it serves as the prototype of a dynamical explanation of Newtonian gravity. Second, the theory came quite close to accomplishing its aim. Third, the theory had a long life and attracted comment by the leading physical thinkers of several successive generations, including Laplace, Kelvin, Maxwell and Feynman. Le Sage's theory therefore provides an excellent opportunity for the study of the evolution of attitudes toward physical explanation. The effects of national style in science and generational change take on a new clarity.

  20. Toward a combined SAGE II-HALOE aerosol climatology: an evaluation of HALOE version 19 stratospheric aerosol extinction coefficient observations

    Directory of Open Access Journals (Sweden)

    L. W. Thomason

    2012-09-01

    Full Text Available Herein, the Halogen Occultation Experiment (HALOE aerosol extinction coefficient data is evaluated in the low aerosol loading period after 1996 as the first necessary step in a process that will eventually allow the production of a combined HALOE/SAGE II (Stratospheric Aerosol and Gas Experiment aerosol climatology of derived aerosol products including surface area density. Based on these analyses, it is demonstrated that HALOE's 3.46 μm is of good quality above 19 km and suitable for scientific applications above that altitude. However, it is increasingly suspect at lower altitudes and should not be used below 17 km under any circumstances after 1996. The 3.40 μm is biased by about 10% throughout the lower stratosphere due to the failure to clear NO2 but otherwise appears to be a high quality product down to 15 km. The 2.45 and 5.26 μm aerosol extinction coefficient measurements are clearly biased and should not be used for scientific applications after the most intense parts of the Pinatubo period. Many of the issues in the aerosol data appear to be related to either the failure to clear some interfering gas species or doing so poorly. For instance, it is clear that the 3.40 μm aerosol extinction coefficient measurements can be improved through the inclusion of an NO2 correction and could, in fact, end up as the highest quality overall HALOE aerosol extinction coefficient measurement. It also appears that the 2.45 and 5.26 μm channels may be improved by updating the Upper Atmosphere Pilot Database which is used as a resource for the removal of gas species otherwise not available from direct HALOE measurements. Finally, a simple model to demonstrate the promise of mixed visible/infrared aerosol extinction coefficient ensembles for the retrieval of bulk aerosol properties demonstrates that a combined HALOE/SAGE II aerosol climatology is feasible and may represent a substantial improvement over independently derived

  1. Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox).

    Science.gov (United States)

    Liu, Daofeng; Sui, Shunzhao; Ma, Jing; Li, Zhineng; Guo, Yulong; Luo, Dengpan; Yang, Jianfeng; Li, Mingyang

    2014-01-01

    Wintersweet (Chimonanthus praecox) is familiar as a garden plant and woody ornamental flower. On account of its unique flowering time and strong fragrance, it has a high ornamental and economic value. Despite a long history of human cultivation, our understanding of wintersweet genetics and molecular biology remains scant, reflecting a lack of basic genomic and transcriptomic data. In this study, we assembled three cDNA libraries, from three successive stages in flower development, designated as the flower bud with displayed petal, open flower and senescing flower stages. Using the Illumina RNA-Seq method, we obtained 21,412,928, 26,950,404, 24,912,954 qualified Illumina reads, respectively, for the three successive stages. The pooled reads from all three libraries were then assembled into 106,995 transcripts, 51,793 of which were annotated in the NCBI non-redundant protein database. Of these annotated sequences, 32,649 and 21,893 transcripts were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 15,587 transcripts onto 312 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at the open flower and senescing flower stages. An analysis of differentially expressed genes involved in plant hormone signal transduction pathways indicated that although flower opening and senescence may be independent of the ethylene signaling pathway in wintersweet, salicylic acid may be involved in the regulation of flower senescence. We also succeeded in isolating key genes of floral scent biosynthesis and proposed a biosynthetic pathway for monoterpenes and sesquiterpenes in wintersweet flowers, based on the annotated sequences. This comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in wintersweet. And our data

  2. Transcriptome analysis in cotton boll weevil (Anthonomus grandis and RNA interference in insect pests.

    Directory of Open Access Journals (Sweden)

    Alexandre Augusto Pereira Firmino

    Full Text Available Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families' data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.

  3. Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA interference in insect pests.

    Science.gov (United States)

    Firmino, Alexandre Augusto Pereira; Fonseca, Fernando Campos de Assis; de Macedo, Leonardo Lima Pepino; Coelho, Roberta Ramos; Antonino de Souza, José Dijair; Togawa, Roberto Coiti; Silva-Junior, Orzenil Bonfim; Pappas, Georgios Joannis; da Silva, Maria Cristina Mattar; Engler, Gilbert; Grossi-de-Sa, Maria Fatima

    2013-01-01

    Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi) as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families' data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.

  4. Transcriptome profiling of tobacco under water deficit conditions

    Directory of Open Access Journals (Sweden)

    Roel C. Rabara

    2015-09-01

    Full Text Available Drought is one of the limiting environmental factors that affect crop production. Understanding the molecular basis of how plants respond to this water deficit stress is key to developing drought tolerant crops. In this study we generated time course-based transcriptome profiles of tobacco plants under water deficit conditions using microarray technology. In this paper, we describe in detail the experimental procedures and analyses performed in our study. The data set we generated (available in the NCBI/GEO database under GSE67434 has been analysed to identify genes that are involved in the regulation of tobacco's responses to drought.

  5. De novo transcriptome assembly of two contrasting pumpkin cultivars

    Directory of Open Access Journals (Sweden)

    Aliki Xanthopoulou

    2016-03-01

    Full Text Available Cucurbita pepo (squash, pumpkin, gourd, a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, ‘Big Moose’ with large round fruits and ‘Munchkin’ with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882 and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883 sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively, which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for ‘Big Moose’ and ‘Munchkin’ were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. Keywords: RNA-Seq, Pumpkin, Contrasting cultivars, Cucurbita pepo

  6. Annotation of nerve cord transcriptome in earthworm Eisenia fetida

    Directory of Open Access Journals (Sweden)

    Vasanthakumar Ponesakki

    2017-12-01

    Full Text Available In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.

  7. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Sour cherry (Prunus cerasus in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170. De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

  8. Whole transcriptome organisation in the dehydrated supraoptic nucleus

    Directory of Open Access Journals (Sweden)

    C.C.T. Hindmarch

    2013-12-01

    Full Text Available The supraoptic nucleus (SON is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our previously published euhydrated and dehydrated SON data to observe this trend and how it changes following dehydration. In accordance with other studies, our whole transcriptome data fit well with this model in the euhydrated SON microarrays, but interestingly, fit better in the dehydrated arrays. This trend was observed in a subset of differentially regulated genes and also following network reconstruction using a third-party database that mines public data. We make use of language as a metaphor that helps us philosophise about the role of the whole transcriptome in providing a suitable environment for the delivery of Avp following a survival threat like dehydration.

  9. De novo transcriptome assembly associated with fumonisin production by the rice pathogen Fusarium fujikuroi

    Directory of Open Access Journals (Sweden)

    Keerthi S. Guruge

    2018-06-01

    Full Text Available The present study employed a next-generation sequencing method to assemble a de novo transcriptome database designed to distinguish gene expression changes exhibited by the fumonisin-producing fungus Fusarium fujikuroi when grown under ‘fumonisin-producing’ compared to ‘non-fumonisin-producing’ conditions. The raw data of this study have been deposited at DNA Data Bank of Japan (DDBJ under the accession ID DRA006146. Keywords: Fusarium fujikuroi, Fumonisin, Next-generation sequencing, Transcriptome, Gene-expression

  10. 75 FR 59803 - Endangered and Threatened Wildlife and Plants; Determination for the Gunnison Sage-grouse as a...

    Science.gov (United States)

    2010-09-28

    ... sage-grouse do not possess muscular gizzards and, therefore, lack the ability to grind and digest seeds...-grouse exhibit a polygamous mating system where a male mates with several females. Males perform...

  11. Stackfile Database

    Science.gov (United States)

    deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

    2013-01-01

    This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

  12. Detailed transcriptome description of the neglected cestode Taenia multiceps.

    Science.gov (United States)

    Wu, Xuhang; Fu, Yan; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

    2012-01-01

    The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS) of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. We obtained a total of 31,282 unigenes (mean length 920 bp) using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam). We identified 26,110 (83.47%) unigenes and inferred 20,896 (66.8%) coding sequences (CDS). Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis) and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum) showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of the biology of T. multiceps, and helps in the identification of drug targets and

  13. Detailed transcriptome description of the neglected cestode Taenia multiceps.

    Directory of Open Access Journals (Sweden)

    Xuhang Wu

    Full Text Available BACKGROUND: The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. METHODOLOGY/PRINCIPAL FINDINGS: We obtained a total of 31,282 unigenes (mean length 920 bp using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam. We identified 26,110 (83.47% unigenes and inferred 20,896 (66.8% coding sequences (CDS. Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. CONCLUSIONS/SIGNIFICANCE: This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of

  14. Transcriptome analysis of the Asian honey bee Apis cerana cerana.

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    Zi Long Wang

    Full Text Available BACKGROUND: The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE analysis. RESULTS: Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG with a cut-off E-value of 10(-5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. CONCLUSIONS: Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes.

  15. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds.

    Science.gov (United States)

    Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata

    2014-01-01

    Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  16. Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

    Directory of Open Access Journals (Sweden)

    Seema ePradhan

    2014-12-01

    Full Text Available Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L. seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilised to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analysed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs, about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  17. 76 FR 37826 - Notice of Availability of the Environmental Assessment and Notice of Public Hearing for the Sage...

    Science.gov (United States)

    2011-06-28

    ...In accordance with the Federal coal management regulations, the Sage Creek Holdings, LLC, Federal Coal Lease-By-Application (LBA) Environmental Assessment (EA) is available for public review and comment. The Department of the Interior, Bureau of Land Management (BLM) Colorado State Office, will hold a public hearing to receive comments on the EA, Fair Market Value (FMV), and Maximum Economic Recovery (MER) of the coal resources for Sage Creek Holdings, LLC, COC- 74219.

  18. 75 FR 49512 - Notice of Availability of the Environmental Assessment and Notice of Public Hearing for the Sage...

    Science.gov (United States)

    2010-08-13

    ...In accordance with the Federal coal management regulations, the Sage Creek Holdings, LLC Federal Coal Lease-By-Application (LBA) Environmental Assessment (EA) is available for public review and comment. The Department of the Interior, Bureau of Land Management (BLM) Colorado State Office will hold a public hearing to receive comments on the EA, Finding of No Significant Impact (FONSI), Fair Market Value (FMV), and Maximum Economic Recovery (MER) of the coal resources for Sage Creek Holdings, LLC LBA COC-74219.

  19. Deodorant effects of a sage extract stick: Antibacterial activity and sensory evaluation of axillary deodorancy.

    Science.gov (United States)

    Shahtalebi, Mohammad Ali; Ghanadian, Mustafa; Farzan, Ali; Shiri, Niloufar; Shokri, Dariush; Fatemi, Syed Ali

    2013-10-01

    Deodorant products prevent the growth and activity of the degrading apocrine gland bacteria living in the armpit. Common antibacterial agents in the market like triclosan and aluminum salts, in spite of their suitable antibacterial effects, increase the risk of Alzheimer's disease, breast and prostate cancers or induce contact dermatitis. Therefore, plant extracts possessing antibacterial effects are of interest. The aim of the present study was to verify the in vitro antimicrobial effects of different sage extracts against two major bacteria responsible for axillary odor, and to evaluate the deodorant effect of a silicon-based stick containing sage extracts in different densities in humans. Different fractions of methanolic extract of Salvia officinalis (sage) were evaluated on a culture of armpit skin surface of volunteers through agar microdilution antimicrobial assay. Then, randomized, double-blind placebo-controlled clinical trial with the best antibacterial fraction was conducted on 45 female healthy volunteers. Participants were treated with a single dose in four groups, each containing 15 individuals: Group 1 (200 μg/mL), 2 (400 μg/mL), 3 (600 μg/mL) of dichloromethane sage extract, and placebo (without extract). A standard sensory evaluation method for the evaluation of deodorant efficacy was used before, and two hours, four hours, and eight hours after single application of a deodorant or placebo (ASTM method E 1207-87 Standard Practice for the Sensory Evaluation of Axillary Deodorancy). The data were analyzed with two factors relating to densities and time. In 45 participants with a mean [± standard deviation (SD)] age of 61.5±11.8 years, statistically significant within-group differences were observed before and two, four, and eight hours after deodorant treatment for groups 1, 2, and 3. Groups 1, 2, and 3 had a significantly smaller odor score than placebo after two, four, and eight hours (P sage extract sticks (P sage extract of 200, 400, or 600

  20. Deodorant effects of a sage extract stick: Antibacterial activity and sensory evaluation of axillary deodorancy

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Shahtalebi

    2013-01-01

    Full Text Available Background: Deodorant products prevent the growth and activity of the degrading apocrine gland bacteria living in the armpit. Common antibacterial agents in the market like triclosan and aluminum salts, in spite of their suitable antibacterial effects, increase the risk of Alzheimer′s disease, breast and prostate cancers or induce contact dermatitis. Therefore, plant extracts possessing antibacterial effects are of interest. The aim of the present study was to verify the in vitro antimicrobial effects of different sage extracts against two major bacteria responsible for axillary odor, and to evaluate the deodorant effect of a silicon-based stick containing sage extracts in different densities in humans. Materials and Methods: Different fractions of methanolic extract of Salvia officinalis (sage were evaluated on a culture of armpit skin surface of volunteers through agar microdilution antimicrobial assay. Then, randomized, double-blind placebo-controlled clinical trial with the best antibacterial fraction was conducted on 45 female healthy volunteers. Participants were treated with a single dose in four groups, each containing 15 individuals: Group 1 (200 μg/mL, 2 (400 μg/mL, 3 (600 μg/mL of dichloromethane sage extract, and placebo (without extract. A standard sensory evaluation method for the evaluation of deodorant efficacy was used before, and two hours, four hours, and eight hours after single application of a deodorant or placebo (ASTM method E 1207-87 Standard Practice for the Sensory Evaluation of Axillary Deodorancy. Results: The data were analyzed with two factors relating to densities and time. In 45 participants with a mean [± standard deviation (SD] age of 61.5±11.8 years, statistically significant within-group differences were observed before and two, four, and eight hours after deodorant treatment for groups 1, 2, and 3. Groups 1, 2, and 3 had a significantly smaller odor score than placebo after two, four, and eight hours

  1. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

    Directory of Open Access Journals (Sweden)

    Sanz Libia

    2011-05-01

    Full Text Available Abstract Background A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. Results The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27% were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements and class II (DNA transposons mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large

  2. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  3. Identification of irradiated sage tea (Salvia officinalis L.) by ESR spectroscopy

    International Nuclear Information System (INIS)

    Tepe Cam, Semra; Engin, Birol

    2010-01-01

    The use of electron spin resonance (ESR) spectroscopy to accurately distinguish irradiated from unirradiated sage tea was examined. Before irradiation, sage tea samples exhibit one asymmetric singlet ESR signal centered at g=2.0037. Besides this central signal, two weak satellite signals situated about 3 mT left and right to it in radiation-induced spectra. Irradiation with increasing doses caused a significant increase in radiation-induced ESR signal intensity at g=2.0265 (the left satellite signal) and this increase was found to be explained by a polynomial varying function. The stability of that radiation-induced ESR signal at room temperature was studied over a storage period of 9 months. Also, the kinetic of signal at g=2.0265 was studied in detail over a temperature range 313-353 K by annealing samples at different temperatures for various times.

  4. Opportunities of Gallium Sage experiment with artificial neutrino sources for investigation of neutrino to sterile states

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachiev, V.V.; Veretenkin, E.P.

    2011-01-01

    The unexpectedly low capture rate of neutrino in Ga source experiments in SAGE and GALLEX can be explained assuming electron neutrino transitions to sterile states with a mass-squared difference ∼ 1eV 2 . To test this oscillation hypothesis, we propose to place a very intense 51 Cr source at the center of a 50 tonne target of gallium metal that is divided into two zones and to measure the neutrino capture rate in each zone. The Experiment has the potential to test neutrino oscillation transitions with mass-squared difference Δm 2 > 0.5 eV 2 . An optimized SAGE setup and 3 MCi source of 51 Cr would provide a sensitivity to electron neutrino disappearance of a few percent.

  5. Identification of irradiated sage tea (Salvia officinalis L.) by ESR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tepe Cam, Semra, E-mail: stepe06@gmail.co [Gazi University, Faculty of Medicine, Biophysics Department, 06500 Besevler, Ankara (Turkey); Engin, Birol [Turkish Atomic Energy Authority, Saraykoey Nuclear Research and Training Center, 06983 Ankara (Turkey)

    2010-04-15

    The use of electron spin resonance (ESR) spectroscopy to accurately distinguish irradiated from unirradiated sage tea was examined. Before irradiation, sage tea samples exhibit one asymmetric singlet ESR signal centered at g=2.0037. Besides this central signal, two weak satellite signals situated about 3 mT left and right to it in radiation-induced spectra. Irradiation with increasing doses caused a significant increase in radiation-induced ESR signal intensity at g=2.0265 (the left satellite signal) and this increase was found to be explained by a polynomial varying function. The stability of that radiation-induced ESR signal at room temperature was studied over a storage period of 9 months. Also, the kinetic of signal at g=2.0265 was studied in detail over a temperature range 313-353 K by annealing samples at different temperatures for various times.

  6. Rate of germanium-isotope production by background processes in the SAGE experiment

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.; Ibragimova, T.V.; Cleveland, B.T.

    2002-01-01

    Data on a direct determination of systematic uncertainties caused by the background production of germanium isotopes in the radiochemical SAGE experiment measuring the solar-neutrino flux are analyzed. The result obtained for the rate of 68 Ge production is 6.5(1±1.0) times greater than the expected one; the rate of 69 Ge production does not exceed preliminary estimates. The above result for 68 Ge corresponds to the systematic uncertainty that is caused by the interaction of cosmic-ray muons and which is equal to 5.8% (4.5 SNU) at a solar-neutrino-capture rate of 77.0 SNU. An experiment is proposed that would test the effect of cosmic-ray muon influence on the SAGE systematic uncertainty and which would be performed at the location of the underground scintillation telescope facilities of the Baksan Neutrino Observatory (Institute for Nuclear Research, Russian Academy of Sciences)

  7. The germanium isotopes production rate in background process in SAGE experiment

    International Nuclear Information System (INIS)

    Gavrin, V.N.; Gorbachev, V.V.; Ibragimova, T.V.; Cleveland, B.T.

    2002-01-01

    The analysis of the direct determination of systematics connected with the germanium isotopes generation of in background processes in radiochemical SAGE experiments on measuring solar neutrinos is described. The found 68 Ge generation rate is 6.5 (1 ± 1.0) times higher than expected; the generation rate of 69 Ge does not exceed preliminary evaluations. The result on 68 Ge corresponds to the systematic of cosmic ray muons of 5.8% (4.5 SNU) for the measured capture rate of solar neutrino of 77.0 SNU. To check the cosmic-ray muon influence of the SAGE systematic one suggests the experiment in place of underground scintillation telescope of the Baksan neutrino observatory on the Institute for Nuclear Research of the RAS [ru

  8. Connaissance des pharmaciens d'officine à propos du droit de prescription des sages-femmes

    OpenAIRE

    Gache, Brune

    2012-01-01

    Introduction : La profession de sage-femme est une profession médicale à compétences définies. L'une d'entre elles nous intéresse particulièrement : le droit de prescription. Nous avons voulu évaluer les connaissances des pharmaciens d'officine, principaux intéressés de la mise en application de cette compétence. Matériel et méthode : L'objectif de ce travail de recherche était d'évaluer les connaissances des pharmaciens d'officine à propos du droit de prescription des sages-femmes ainsi que ...

  9. Extending Database Integration Technology

    National Research Council Canada - National Science Library

    Buneman, Peter

    1999-01-01

    Formal approaches to the semantics of databases and database languages can have immediate and practical consequences in extending database integration technologies to include a vastly greater range...

  10. Mining biological databases for candidate disease genes

    Science.gov (United States)

    Braun, Terry A.; Scheetz, Todd; Webster, Gregg L.; Casavant, Thomas L.

    2001-07-01

    The publicly-funded effort to sequence the complete nucleotide sequence of the human genome, the Human Genome Project (HGP), has currently produced more than 93% of the 3 billion nucleotides of the human genome into a preliminary `draft' format. In addition, several valuable sources of information have been developed as direct and indirect results of the HGP. These include the sequencing of model organisms (rat, mouse, fly, and others), gene discovery projects (ESTs and full-length), and new technologies such as expression analysis and resources (micro-arrays or gene chips). These resources are invaluable for the researchers identifying the functional genes of the genome that transcribe and translate into the transcriptome and proteome, both of which potentially contain orders of magnitude more complexity than the genome itself. Preliminary analyses of this data identified approximately 30,000 - 40,000 human `genes.' However, the bulk of the effort still remains -- to identify the functional and structural elements contained within the transcriptome and proteome, and to associate function in the transcriptome and proteome to genes. A fortuitous consequence of the HGP is the existence of hundreds of databases containing biological information that may contain relevant data pertaining to the identification of disease-causing genes. The task of mining these databases for information on candidate genes is a commercial application of enormous potential. We are developing a system to acquire and mine data from specific databases to aid our efforts to identify disease genes. A high speed cluster of Linux of workstations is used to analyze sequence and perform distributed sequence alignments as part of our data mining and processing. This system has been used to mine GeneMap99 sequences within specific genomic intervals to identify potential candidate disease genes associated with Bardet-Biedle Syndrome (BBS).

  11. De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

    Directory of Open Access Journals (Sweden)

    Jacqueline D Farrell

    Full Text Available Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.De novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.

  12. Uptake and kinetics of 226Ra, 210Pb and 210Po in big sage brush

    International Nuclear Information System (INIS)

    Simon, S.L.

    1985-01-01

    Root uptake of 226 Pb and 210 Po by mature sage brush was studied using a soil injection method for spiking the soil with minimal root disturbance. The main objective was to measure vegetation concentrations and determine concentration ratios (CR's) due to root uptake as a function of time in mature big sage brush. Concentration ratios obtained in mature vegetation and in steady-state situations may be valuable in assessing the impact of uranium mining and milling. The vegetation was sampled approximately every 3 mo for A 2 y period. Significant levels of activity were detected in the vegetation beginning at the first sampling (81 d after soil injection for 226 Ra, 28 d for 210 Pb and 210 Po). There was an exponential decrease in concentration to an apparent steady state value. Mean values (geometric) of the data pooled over the second year period indicated that steady-state Cr's for 226 Ra, 210 Pb and 210 Po, as determined in mature sage brush, were 0.04, 0.009, and 0.08, respectively. Investigations were also carried out to verify the suitability of soil injection for uptake studies and to evaluate the time dependence of 226 Ra leaching from sage brush leaves. The soil injection method was determined to produce, on the average, uptake equivalent to that produce by a uniform soil distribution, however, the variety of uptake for plants growing in injected soil was higher than for plants growing in uniformly contaminated soil. A three compartment mathematical model was formulated to help understand mechanisms of plant uptake and to predict, if possible, the concentration of 226 Ra, 210 Po in vegetation as a function of time after soil spiking

  13. Linking occurrence and fitness to persistence: Habitat-based approach for endangered Greater Sage-Grouse

    Science.gov (United States)

    Aldridge, Cameron L.; Boyce, Mark S.

    2007-01-01

    Detailed empirical models predicting both species occurrence and fitness across a landscape are necessary to understand processes related to population persistence. Failure to consider both occurrence and fitness may result in incorrect assessments of habitat importance leading to inappropriate management strategies. We took a two-stage approach to identifying critical nesting and brood-rearing habitat for the endangered Greater Sage-Grouse (Centrocercus urophasianus) in Alberta at a landscape scale. First, we used logistic regression to develop spatial models predicting the relative probability of use (occurrence) for Sage-Grouse nests and broods. Secondly, we used Cox proportional hazards survival models to identify the most risky habitats across the landscape. We combined these two approaches to identify Sage-Grouse habitats that pose minimal risk of failure (source habitats) and attractive sink habitats that pose increased risk (ecological traps). Our models showed that Sage-Grouse select for heterogeneous patches of moderate sagebrush cover (quadratic relationship) and avoid anthropogenic edge habitat for nesting. Nests were more successful in heterogeneous habitats, but nest success was independent of anthropogenic features. Similarly, broods selected heterogeneous high-productivity habitats with sagebrush while avoiding human developments, cultivated cropland, and high densities of oil wells. Chick mortalities tended to occur in proximity to oil and gas developments and along riparian habitats. For nests and broods, respectively, approximately 10% and 5% of the study area was considered source habitat, whereas 19% and 15% of habitat was attractive sink habitat. Limited source habitats appear to be the main reason for poor nest success (39%) and low chick survival (12%). Our habitat models identify areas of protection priority and areas that require immediate management attention to enhance recruitment to secure the viability of this population. This novel

  14. Stratospheric aerosol effects from Soufriere Volcano as measured by the SAGE satellite system

    Science.gov (United States)

    Mccormick, M. P.; Kent, G. S.; Yue, G. K.; Cunnold, D. M.

    1982-01-01

    During its April 1979 eruption series, Soufriere Volcano produced two major stratospheric plumes that the SAGE (Stratospheric Aerosol and Gas Experiment) satellite system tracked to West Africa and the North Atlantic Ocean. The total mass of these plumes, whose movement and dispersion are in agreement with those deduced from meteorological data and dispersion theory, was less than 0.5 percent of the global stratospheric aerosol burden; no significant temperature or climate perturbation is therefore expected.

  15. SAGES Foregut Surgery Masters Program: a surgeon's social media resource for collaboration, education, and professional development.

    Science.gov (United States)

    Jackson, Hope T; Young, Monica T; Rodriguez, H Alejandro; Wright, Andrew S

    2018-06-01

    Facebook is a popular online social networking platform increasingly used for professional collaboration. Literature regarding use of Facebook for surgeon professional development and education is limited. The Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) has established a Facebook group dedicated to discussion of surgery of the esophagus, stomach, and small intestine-the "SAGES Foregut Surgery Masters Program." The aim of this study is to examine how this forum is used for professional development, education, and quality improvement. Member and post statistics were obtained from https://grytics.com , a Facebook group analytics service. All posts added to the Foregut forum since its creation in April 2015 through December 2016 were reviewed and categorized for content and topic. Posts were reviewed for potential identifiable protected health information. As of December 2016, there were 649 total members in the group. There have been a total of 411 posts and 4116 comments with a median of 10.1 comments/post (range 0-72). Posts were categorized as operative technique (64%), patient management (52%), continuing education (10%), networking (10%), or other (6%). Video and/or photos were included in 53% of posts with 4% of posts depicting radiologic studies and 13% with intraoperative photos or videos. An additional 40 posts included links to other pages, such as YouTube, journal articles, or the SAGES website. One post (0.2%) contained identifiable protected health information and was deleted once recognized by the moderators of the group. Social media is a unique, real-time platform where surgeons can learn, discuss, and collaborate towards the goal of optimal treatment of surgical disease. Active online surgical communities such as the SAGES Foregut Surgery Masters Program have the potential to enhance communication between surgeons and are a potential innovative adjunct to traditional methods of continuing surgical education. Surgical societies

  16. Successes and Challenges in the SAGE (Summer of Applied Geophysical Experience) REU Program

    Science.gov (United States)

    Braile, L. W.; Baldridge, W. S.; Pellerin, L.; Ferguson, J. F.; Bedrosian, P.; Biehler, S.; Jiracek, G. R.; Snelson, C. M.; Kelley, S.; McPhee, D.

    2014-12-01

    The SAGE program was initiated in 1983 to provide an applied geophysics research and education experience for students. Since 1983, 820 students have completed the SAGE summer program. Beginning in 1992, with funding from the NSF, SAGE has included an REU (Research Experience for Undergraduates) experience for selected undergraduate students from U.S. colleges and universities. Since 1992, 380 undergraduate REU students have completed the SAGE program. The four week, intensive, summer program is based in Santa Fe, New Mexico, and involves students in learning geophysical theory and applications; collection of geophysical field data in the northern Rio Grande Rift area; data processing, modeling and interpretation; and presentation (oral and written) of results of each student's research results. Students (undergraduates, graduates and professionals) and faculty are together on a school campus for the summer program. Successful strategies (developed over the years) of the program include teamwork experience, mentoring of REUs (by faculty and more senior students), cultural interchange due to students from many campuses across the U.S. and international graduate students, including industry visitors who work with the students and provide networking, a capstone experience of the summer program that includes all students making a "professional-meeting" style presentation of their research and submitting a written report, a follow-up workshop for the REU students to enhance and broaden their experience, and providing professional development for the REUs through oral or poster presentations and attendance at a professional meeting. Program challenges include obtaining funding from multiple sources; significant time investment in program management, reporting, and maintaining contact with our many funding sources and industry affiliates; and, despite significant efforts, limited success in recruiting racial and ethnic minority students to the program.

  17. Utilisation du partographe modifie de l'oms par les sages-femmes ...

    African Journals Online (AJOL)

    ) de l'OMS par les sages-femmes de Lomé et leur position face à cet outil de surveillance du travail. Matériel et méthode : Il s'agit d'une étude prospective, transversale descriptive, menée du 01er juillet au 30 septembre 2011 (soit une période ...

  18. Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid

    Directory of Open Access Journals (Sweden)

    Xiaoshen Zhang

    2014-03-01

    Full Text Available Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx. About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.

  19. De novo transcriptome assembly of Sorghum bicolor variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Sorghum (Sorghum bicolor, also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  20. De novo transcriptome assembly of Setatria italica variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Foxtail millet (Setaria italica belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

  1. De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

    Directory of Open Access Journals (Sweden)

    Alexey V. Beletsky

    2017-03-01

    Full Text Available Monotropa hypopitys (pinesap is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform. The raw data obtained in this study can be available in NCBI SRA database with accession number of SRP069226. A total of 10.3 GB raw sequence data were obtained, corresponding to 103,357,809 raw reads. A total of 103,025,683 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 98,349 unigens with an N50 of 1342 bp. Using the TransDecoder program, we predicted 43,505 putative proteins. 38,416 unigenes were annotated in the Swiss-Prot protein sequence database using BLASTX. The obtained transcriptomic data will be useful for further studies of the evolution of plant genomes upon transition to a non-photosynthetic lifestyle and the loss of photosynthesis-related functions.

  2. Effect of zinc gluconate, sage oil on inflammatory patterns and hyperglycemia in zinc deficient diabetic rats.

    Science.gov (United States)

    Elseweidy, Mohamed M; Ali, Abdel-Moniem A; Elabidine, Nabila Zein; Mursey, Nada M

    2017-11-01

    The relationship between zinc homeostasis and pancreatic function had been established. In this study we aimed firstly to configure the inflammatory pattern and hyperglycemia in zinc deficient diabetic rats. Secondly to illustrate the effect of two selected agents namely Zinc gluconate and sage oil (Salvia Officinalis, family Lamiaceae). Rats were fed on Zinc deficient diet, deionized water for 28days along with Zinc level check up at intervals to achieve zinc deficient state then rats were rendered diabetic through receiving one dose of alloxan monohydrate (120mg/kg) body weight, classified later into 5 subgroups. Treatment with sage oil (0.042mg/kg IP) and Zinc gluconate orally (150mg/kg) body weight daily for 8 weeks significantly reduced serum glucose, C-reactive protein (CRP), Tumor necrosis factor alpha (TNF- α), interleukins-6 1 β, inflammatory8 (IFN ȣ), pancreatic 1L1-β along with an increase in serum Zinc and pancreatic Zinc transporter 8 (ZNT8). Histopathological results of pancreatic tissues showed a good correlation with the biochemical findings. Both sage oil and zinc gluconate induced an improvement in the glycemic and inflammatory states. This may be of value like the therapeutic agent for diabetes. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Characterisation of a SAGe well detector using GEANT4 and LabSOCS

    Energy Technology Data Exchange (ETDEWEB)

    Britton, R., E-mail: rich.britton@awe.co.uk [AWE, Aldermaston, Reading, Berkshire RG7 4PR (United Kingdom); University of Surrey, Guildford GU2 7XH (United Kingdom); Davies, A.V. [AWE, Aldermaston, Reading, Berkshire RG7 4PR (United Kingdom)

    2015-06-21

    This paper reports on the performance of a recently developed Small Anode Germanium (SAGe) well detector from Canberra Industries. This has been specifically designed to improve the energy resolution of the detector, such that it is comparable to the performance of broad-energy designs while achieving far higher efficiencies. Accurate efficiency characterisations and cascade summing correction factors are crucial for quantifying the radionuclides present in environmental samples, and these were calculated for the complex geometry posed by the well detector using two different methodologies. The first relied on Monte-Carlo simulations based upon the GEANT4 toolkit, and the second utilised Canberra Industries GENIE™ 2000 Gamma Analysis software in conjunction with a LabSOCS™ characterisation. Both were found to be in excellent agreement for all nuclides except for {sup 152}Eu, which presents a known issue in the Canberra software (all nuclides affected by this issue were well documented, and fixes are being developed). The correction factors were used to analyse two fully characterised reference samples, yielding results in good agreement with the accepted activity concentrations. Given the sensitivity of well type geometries to cascade summing, this represents a considerable achievement, and paves the way for the use of the SAGe well detector in analysis of ‘real-world’ environmental samples. With the efficiency increase when using the SAGe well in place of a BEGe, substantial reductions in the Minimum Detectable Activity (MDA) should be achievable for a range of nuclides.

  4. Reevaluation of Stratospheric Ozone Trends From SAGE II Data Using a Simultaneous Temporal and Spatial Analysis

    Science.gov (United States)

    Damadeo, R. P.; Zawodny, J. M.; Thomason, L. W.

    2014-01-01

    This paper details a new method of regression for sparsely sampled data sets for use with time-series analysis, in particular the Stratospheric Aerosol and Gas Experiment (SAGE) II ozone data set. Non-uniform spatial, temporal, and diurnal sampling present in the data set result in biased values for the long-term trend if not accounted for. This new method is performed close to the native resolution of measurements and is a simultaneous temporal and spatial analysis that accounts for potential diurnal ozone variation. Results show biases, introduced by the way data is prepared for use with traditional methods, can be as high as 10%. Derived long-term changes show declines in ozone similar to other studies but very different trends in the presumed recovery period, with differences up to 2% per decade. The regression model allows for a variable turnaround time and reveals a hemispheric asymmetry in derived trends in the middle to upper stratosphere. Similar methodology is also applied to SAGE II aerosol optical depth data to create a new volcanic proxy that covers the SAGE II mission period. Ultimately this technique may be extensible towards the inclusion of multiple data sets without the need for homogenization.

  5. SEMI-ANALYTIC GALAXY EVOLUTION (SAGE): MODEL CALIBRATION AND BASIC RESULTS

    Energy Technology Data Exchange (ETDEWEB)

    Croton, Darren J.; Stevens, Adam R. H.; Tonini, Chiara; Garel, Thibault; Bernyk, Maksym; Bibiano, Antonio; Hodkinson, Luke; Mutch, Simon J.; Poole, Gregory B.; Shattow, Genevieve M. [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122 (Australia)

    2016-02-15

    This paper describes a new publicly available codebase for modeling galaxy formation in a cosmological context, the “Semi-Analytic Galaxy Evolution” model, or sage for short.{sup 5} sage is a significant update to the 2006 model of Croton et al. and has been rebuilt to be modular and customizable. The model will run on any N-body simulation whose trees are organized in a supported format and contain a minimum set of basic halo properties. In this work, we present the baryonic prescriptions implemented in sage to describe the formation and evolution of galaxies, and their calibration for three N-body simulations: Millennium, Bolshoi, and GiggleZ. Updated physics include the following: gas accretion, ejection due to feedback, and reincorporation via the galactic fountain; a new gas cooling–radio mode active galactic nucleus (AGN) heating cycle; AGN feedback in the quasar mode; a new treatment of gas in satellite galaxies; and galaxy mergers, disruption, and the build-up of intra-cluster stars. Throughout, we show the results of a common default parameterization on each simulation, with a focus on the local galaxy population.

  6. Relationship between collapse history and ore distribution in Sage Breccia pipe, northwestern Arizona

    International Nuclear Information System (INIS)

    Brown, N.A.; Mead, R.H.; McMurray, J.M.

    1989-01-01

    The Sage pipe is similar to other collapse breccia pipes in northern Arizona which have their beginnings in cave systems in the Redwall Limestone. Stoping of successively younger units caused the upward propagation of the pipe and provided the pipe-filling breccia. The Sage pipe extends at least 2,500 ft (762 m) vertically; the horizontal dimensions range from 100 to 300 ft (30.5-91 m), depending on variations in the adjoining host stratigraphy. The composition and distribution of breccia facies suggest a complex collapse history and variability in the mechanics of collapse. Rock failure took place both by block stoping and by decementation of sandstone and siltstone followed by flow of unconsolidated grains. The resulting breccias range from matrix to fragment-dominated, to sand flow breccia resulting from flow of individual grains. Episodic secondary collapse or readjustment within the breccia pile complicated facies distribution. Paragenetic studies indicate multiple periods of mineralization at Sage resulting in enrichment in an extensive suite of elements. Ore-grade uranium mineralization extends vertically for nearly 700 ft (213 m). Lateral distribution of the ore is variable and is directly related to breccia facies distribution. In generally, the more permeable breccias tend to be the most highly mineralized. Fracture, intergranular, and interfragment permeability were important to mineral distribution. Breccia continuity or plumbing was also important to lateral and vertical mineral distribution

  7. Evaluating lek occupancy of greater sage-grouse in relation to landscape cultivation in the Dakotas

    Science.gov (United States)

    Smith, Joe T.; Flake, Lester D.; Higgins, Kenneth F.; Kobriger, Gerald D.; Homer, Collin G.

    2005-01-01

    Greater Sage-Grouse (Centrocercus urophasianus) have been declining in many states and provinces of North America, and North and South Dakota hold no exception to these declines. We studied effects of cultivated land on Greater Sage-Grouse lek abandonment in North and South Dakota. Landscape-level data were assessed using satellite imagery within a geographic information system. Comparisons were made of 1972-1976 and 1999-2000 percent cultivated and noncultivated land. These comparisons were made between land uses surrounding active leks versus inactive leks, active leks versus random locations, and abandoned regions versus active regions. The 1999-2000 imagery illustrated that percent cultivated land was greater near abandoned leks (4-km buffers) than near active leks in North Dakota or random sites, but this did not hold true in South Dakota. Comparison of an extensive region of abandoned leks with a region of active leks in North Dakota illustrated a similar increase as well as dispersion of cultivation within the abandoned region. However, 1972-1976 imagery revealed that this relationship between percentage of cultivated land and lek activity in North Dakota has been static over the last 30 years. Thus, if the decline of Greater Sage-Grouse is the result of cultivated land infringements, it occurred prior to 1972 in North Dakota.

  8. SAGES TAVAC safety and effectiveness analysis: da Vinci ® Surgical System (Intuitive Surgical, Sunnyvale, CA).

    Science.gov (United States)

    Tsuda, Shawn; Oleynikov, Dmitry; Gould, Jon; Azagury, Dan; Sandler, Bryan; Hutter, Matthew; Ross, Sharona; Haas, Eric; Brody, Fred; Satava, Richard

    2015-10-01

    The da Vinci(®) Surgical System (Intuitive Surgical, Sunnyvale, CA, USA) is a computer-assisted (robotic) surgical system designed to enable and enhance minimally invasive surgery. The Food and Drug Administration (FDA) has cleared computer-assisted surgical systems for use by trained physicians in an operating room environment for laparoscopic surgical procedures in general, cardiac, colorectal, gynecologic, head and neck, thoracic and urologic surgical procedures. There are substantial numbers of peer-reviewed papers regarding the da Vinci(®) Surgical System, and a thoughtful assessment of evidence framed by clinical opinion is warranted. The SAGES da Vinci(®) TAVAC sub-committee performed a literature review of the da Vinci(®) Surgical System regarding gastrointestinal surgery. Conclusions by the sub-committee were vetted by the SAGES TAVAC Committee and SAGES Executive Board. Following revisions, the document was evaluated by the TAVAC Committee and Executive Board again for final approval. Several conclusions were drawn based on expert opinion organized by safety, efficacy, and cost for robotic foregut, bariatric, hepatobiliary/pancreatic, colorectal surgery, and single-incision cholecystectomy. Gastrointestinal surgery with the da Vinci(®) Surgical System is safe and comparable, but not superior to standard laparoscopic approaches. Although clinically acceptable, its use may be costly for select gastrointestinal procedures. Current data are limited to the da Vinci(®) Surgical System; further analyses are needed.

  9. SEMI-ANALYTIC GALAXY EVOLUTION (SAGE): MODEL CALIBRATION AND BASIC RESULTS

    International Nuclear Information System (INIS)

    Croton, Darren J.; Stevens, Adam R. H.; Tonini, Chiara; Garel, Thibault; Bernyk, Maksym; Bibiano, Antonio; Hodkinson, Luke; Mutch, Simon J.; Poole, Gregory B.; Shattow, Genevieve M.

    2016-01-01

    This paper describes a new publicly available codebase for modeling galaxy formation in a cosmological context, the “Semi-Analytic Galaxy Evolution” model, or sage for short. 5 sage is a significant update to the 2006 model of Croton et al. and has been rebuilt to be modular and customizable. The model will run on any N-body simulation whose trees are organized in a supported format and contain a minimum set of basic halo properties. In this work, we present the baryonic prescriptions implemented in sage to describe the formation and evolution of galaxies, and their calibration for three N-body simulations: Millennium, Bolshoi, and GiggleZ. Updated physics include the following: gas accretion, ejection due to feedback, and reincorporation via the galactic fountain; a new gas cooling–radio mode active galactic nucleus (AGN) heating cycle; AGN feedback in the quasar mode; a new treatment of gas in satellite galaxies; and galaxy mergers, disruption, and the build-up of intra-cluster stars. Throughout, we show the results of a common default parameterization on each simulation, with a focus on the local galaxy population

  10. Characterisation of a SAGe well detector using GEANT4 and LabSOCS

    International Nuclear Information System (INIS)

    Britton, R.; Davies, A.V.

    2015-01-01

    This paper reports on the performance of a recently developed Small Anode Germanium (SAGe) well detector from Canberra Industries. This has been specifically designed to improve the energy resolution of the detector, such that it is comparable to the performance of broad-energy designs while achieving far higher efficiencies. Accurate efficiency characterisations and cascade summing correction factors are crucial for quantifying the radionuclides present in environmental samples, and these were calculated for the complex geometry posed by the well detector using two different methodologies. The first relied on Monte-Carlo simulations based upon the GEANT4 toolkit, and the second utilised Canberra Industries GENIE™ 2000 Gamma Analysis software in conjunction with a LabSOCS™ characterisation. Both were found to be in excellent agreement for all nuclides except for 152 Eu, which presents a known issue in the Canberra software (all nuclides affected by this issue were well documented, and fixes are being developed). The correction factors were used to analyse two fully characterised reference samples, yielding results in good agreement with the accepted activity concentrations. Given the sensitivity of well type geometries to cascade summing, this represents a considerable achievement, and paves the way for the use of the SAGe well detector in analysis of ‘real-world’ environmental samples. With the efficiency increase when using the SAGe well in place of a BEGe, substantial reductions in the Minimum Detectable Activity (MDA) should be achievable for a range of nuclides

  11. Supercritical carbon dioxide extraction of antioxidants from rosemary (Rosmarinus officinalis L. and sage (Salvia officinalis L.

    Directory of Open Access Journals (Sweden)

    JASNA IVANOVIĆ

    2009-07-01

    Full Text Available The aim of the present study was to isolate and characterize antioxidant extracts obtained from dried leaves of rosemary (Rosmarinus officinalis L. and sage (Salvia officinalis L., originating from the southern Balkan Region. The antioxidant fraction was isolated from the plant material by supercritical carbon dioxide (SC-CO2 fractional extraction under a pressure of 30 MPa and at temperatures of 40 and 100 °C. In the present study, kinetic data and yields of antioxidant extracts obtained from dried leaves of rosemary and sage under different conditions were determined. Electron spin resonance (ESR spectroscopy assay on the ability of the extracts to scavenge stable 2,2-diphenyl-1-picrylhydrazyl (DPPH free radicals and reactive hydroxyl radicals during the Fenton reaction trapped by 5,5-dimethyl-1-pyrroline-N-oxide (DMPO showed that the investigated extracts had antioxidant activity comparable to that of butylated hydroxyanisole (BHA and commercial rosemary extract. The antioxidant fractions isolated at the higher temperature had higher antioxidant activities. A tentative analysis of the chemical composition of the antioxidant fractions obtained at the higher temperature was accomplished by LC-DAD and LC-MS analytical methods. Abietane-type diterpenoids, flavonoids and fatty acids were identified in the SC-CO2 extract of rosemary and sage.

  12. De novo transcriptome assembly of two different peach cultivars grown in Korea

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Peach (Prunus persica is one of the most popular stone fruits worldwide. Next generation sequencing (NGS has facilitated genome and transcriptome analyses of several stone fruit trees. In this study, we conducted de novo transcriptome analyses of two peach cultivars grown in Korea. Leaves of two cultivars, referred to as Jangtaek and Mibaek, were harvested and used for library preparation. The two prepared libraries were paired-end sequenced by the HiSeq2000 system. We obtained 8.14 GB and 9.62 GB sequence data from Jangtaek and Mibaek (NCBI accession numbers: SRS1056585 and SRS1056587, respectively. The Trinity program was used to assemble two transcriptomes de novo, resulting in 110,477 (Jangtaek and 136,196 (Mibaek transcripts. TransDecoder identified possible coding regions in assembled transcripts. The identified proteins were subjected to BLASTP search against NCBI's non-redundant database for functional annotation. This study provides transcriptome data for two peach cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.

  13. Data Resource Profile: Cross-national and cross-study sociodemographic and health-related harmonized domains from SAGE plus ELSA, HRS and SHARE (SAGE+, Wave 1).

    Science.gov (United States)

    Minicuci, Nadia; Naidoo, Nirmala; Chatterji, Somnath; Kowal, Paul

    2016-10-01

    Four longitudinal studies were included in this rigorous harmonization process: the Study on global AGEing and adult health (SAGE); English Longitudinal Study on Ageing (ELSA); US Health and Retirement Study (HRS); and Survey of Health, Ageing and Retirement in Europe (SHARE). An ex-post harmonized process was applied to nine health-related thematic domains (socio-demographic and economic, health states, overall self-report of health and mental state, health examinations, physical and mental performance tests, risk factors, chronic conditions, social network and subjective well-being) for data from the 2004 wave of each study. Large samples of adults aged 50 years and older were available from each study: SAGE, n = 18 886; ELSA, n = 9181; HRS, n = 19 303; and SHARE, n = 29 917. The microdata, along with further details about the harmonization process and all metadata, are available through the World Health Organization (WHO) data archive at [http://apps.who.int/healthinfo/systems/surveydata/index.php/catalog]. Further information and enquiries can be made to [sagesurvey@who.int] or the corresponding author. The data resource will continue to be updated with data across additional waves of these surveys and new waves. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

  14. Aerosol extinction profiles at 525 nm and 1020 nm derived from ACE imager data: comparisons with GOMOS, SAGE II, SAGE III, POAM III, and OSIRIS

    Directory of Open Access Journals (Sweden)

    F. Vanhellemont

    2008-04-01

    Full Text Available The Canadian ACE (Atmospheric Chemistry Experiment mission is dedicated to the retrieval of a large number of atmospheric trace gas species using the solar occultation technique in the infrared and UV/visible spectral domain. However, two additional solar disk imagers (at 525 nm and 1020 nm were added for a number of reasons, including the retrieval of aerosol and cloud products. In this paper, we present first comparison results for these imager aerosol/cloud optical extinction coefficient profiles, with the ones derived from measurements performed by 3 solar occultation instruments (SAGE II, SAGE III, POAM III, one stellar occultation instrument (GOMOS and one limb sounder (OSIRIS. The results indicate that the ACE imager profiles are of good quality in the upper troposphere/lower stratosphere, although the aerosol extinction for the visible channel at 525 nm contains a significant negative bias at higher altitudes, while the relative differences indicate that ACE profiles are almost always too high at 1020 nm. Both problems are probably related to ACE imager instrumental issues.

  15. De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing.

    Science.gov (United States)

    Ong, Wen Dee; Voo, Lok-Yung Christopher; Kumar, Vijay Subbiah

    2012-01-01

    Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed. To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown. The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.

  16. Strategic and Operational Plan for Integrating Transcriptomics ...

    Science.gov (United States)

    Plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT; the details are in the attached slide presentation presentation on plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT, given at the OECD meeting on June 23, 2016

  17. Determination of the biologically active flavour substances thujone and camphor in foods and medicines containing sage (Salvia officinalis L.).

    Science.gov (United States)

    Walch, Stephan G; Kuballa, Thomas; Stühlinger, Wolf; Lachenmeier, Dirk W

    2011-07-21

    The sage plant Salvia officinalis L. is used as ingredient in foods and beverages as well as in herbal medicinal products. A major use is in the form of aqueous infusions as sage tea, which is legal to be sold as either food or medicine. Sage may contain two health relevant substances, thujone and camphor. The aim of this study was to develop and validate an analytical methodology to determine these active principles of sage and give a first overview of their concentrations in a wide variety of sage foods and medicines. A GC/MS procedure was applied for the analysis of α- and β-thujone and camphor with cyclodecanone as internal standard. The precision was between 0.8 and 12.6%, linearity was obtained from 0.1 - 80 mg/L. The recoveries of spiked samples were between 93.7 and 104.0% (average 99.1%). The time of infusion had a considerable influence on the content of analytes found in the teas. During the brewing time, thujone and camphor show an increase up to about 5 min, after which saturation is reached. No effect was found for preparation with or without a lid on the pot used for brewing the infusion. Compared to extracts with ethanol (60% vol), which provide a maximum yield, an average of 30% thujone are recovered in the aqueous tea preparations. The average thujone and camphor contents were 4.4 mg/L and 16.7 mg/L in food tea infusions and 11.3 mg/L and 25.4 mg/L in medicinal tea infusions. The developed methodology allows the efficient determination of thujone and camphor in a wide variety of sage food and medicine matrices and can be applied to conduct surveys for exposure assessment. The current results suggest that on average between 3 and 6 cups of sage tea could be daily consumed without reaching toxicological thresholds.

  18. Improving communication with palliative care cancer patients at home - A pilot study of SAGE & THYME communication skills model.

    Science.gov (United States)

    Griffiths, Jane; Wilson, Charlotte; Ewing, Gail; Connolly, Michael; Grande, Gunn

    2015-10-01

    To pilot an evidence-based communication skills model (SAGE & THYME) with UK District Nurses (DNs) who visit patients with advanced cancer early in the dying trajectory. Evidence suggests that DNs lack confidence in communication skills and in assessing cancer patients' psycho-social needs; also that they lack time. SAGE & THYME is a highly structured model for teaching patient centred interactions. It addresses concerns about confidence and time. Mixed methods. 33 DNs were trained in SAGE & THYME in a three hour workshop and interviewed in focus groups on three occasions: pre-training, immediately post-training and two months post-training. Questionnaires measuring perceived outcomes of communication, confidence in communication and motivation to use SAGE & THYME were administered at the focus groups. SAGE & THYME provided a structure for conversations and facilitated opening and closing of interactions. The main principle of patient centeredness was reportedly used by all. Knowledge about communication behaviours helpful to patients improved and was sustained two months after training. Increased confidence in communication skills was also sustained. Motivation to use SAGE & THYME was high and remained so at two months, and some said the model saved them time. Challenges with using the model included controlling the home environment and a change in style of communication which was so marked some DNs preferred to use it with new patients. Training DNs in SAGE & THYME in a three hour workshop appears to be a promising model for improving communication skills when working with cancer patients. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  19. Daily nest survival rates of Gunnison Sage-Grouse (Centrocercus minimus): assessing local- and landscape-scale drivers

    Science.gov (United States)

    Stanley, Thomas R.; Aldridge, Cameron L.; Joanne Saher,; Theresa Childers,

    2015-01-01

    The Gunnison Sage-Grouse (Centrocercus minimus) is a species of conservation concern and is a candidate for listing under the U.S. Endangered Species Act because of substantial declines in populations from historic levels. It is thought that loss, fragmentation, and deterioration of sagebrush (Artemisia spp.) habitat have contributed to the decline and isolation of this species into seven geographically distinct subpopulations. Nest survival is known to be a primary driver of demography of Greater Sage-Grouse (C. urophasianus), but no unbiased estimates of daily nest survival rates (hereafter nest survival) exist for Gunnison Sage-Grouse or published studies identifying factors that influence nest survival. We estimated nest survival of Gunnison Sage-Grouse for the western portion of Colorado's Gunnison Basin subpopulation, and assessed the effects and relative importance of local- and landscape-scale habitat characteristics on nest survival. Our top performing model was one that allowed variation in nest survival among areas, suggesting a larger landscape-area effect. Overall nest success during a 38-day nesting period (egg-laying plus incubation) was 50% (daily survival rate; SE  =  0.982 [0.003]), which is higher than previous estimates for Gunnison Sage-Grouse and generally higher than published for the closely related Greater Sage-Grouse. We did not find strong evidence that local-scale habitat variables were better predictors of nest survival than landscape-scale predictors, nor did we find strong evidence that any of the habitat variables we measured were good predictors of nest survival. Nest success of Gunnison Sage-Grouse in the western portion of the Gunnison Basin was higher than previously believed.

  20. Decadal-Scale Responses in Middle and Upper Stratospheric Ozone From SAGE II Version 7 Data

    Science.gov (United States)

    Remsberg, E. E.

    2014-01-01

    Stratospheric Aerosol and Gas Experiment (SAGE II) version 7 (v7) ozone profiles are analyzed for their decadal-scale responses in the middle and upper stratosphere for 1991 and 1992-2005 and compared with those from its previous version 6.2 (v6.2). Multiple linear regression (MLR) analysis is applied to time series of its ozone number density vs. altitude data for a range of latitudes and altitudes. The MLR models that are fit to the time series data include a periodic 11 yr term, and it is in-phase with that of the 11 yr, solar UV (Ultraviolet)-flux throughout most of the latitude/ altitude domain of the middle and upper stratosphere. Several regions that have a response that is not quite in-phase are interpreted as being affected by decadal-scale, dynamical forcings. The maximum minus minimum, solar cycle (SClike) responses for the ozone at the low latitudes are similar from the two SAGE II data versions and vary from about 5 to 2.5% from 35 to 50 km, although they are resolved better with v7. SAGE II v7 ozone is also analyzed for 1984-1998, in order to mitigate effects of end-point anomalies that bias its ozone in 1991 and the analyzed results for 1991-2005 or following the Pinatubo eruption. Its SC-like ozone response in the upper stratosphere is of the order of 4%for 1984-1998 vs. 2.5 to 3%for 1991-2005. The SAGE II v7 results are also recompared with the responses in ozone from the Halogen Occultation Experiment (HALOE) that are in terms of mixing ratio vs. pressure for 1991-2005 and then for late 1992- 2005 to avoid any effects following Pinatubo. Shapes of their respective response profiles agree very well for 1992-2005. The associated linear trends of the ozone are not as negative in 1992-2005 as in 1984-1998, in accord with a leveling off of the effects of reactive chlorine on ozone. It is concluded that the SAGE II v7 ozone yields SC-like ozone responses and trends that are of better quality than those from v6.2.

  1. Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

    International Nuclear Information System (INIS)

    Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K.

    2015-01-01

    Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm 3 . The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

  2. Characteristic Performance Evaluation of a new SAGe Well Detector for Small and Large Sample Geometries

    Energy Technology Data Exchange (ETDEWEB)

    Adekola, A.S.; Colaresi, J.; Douwen, J.; Jaederstroem, H.; Mueller, W.F.; Yocum, K.M.; Carmichael, K. [Canberra Industries Inc., 800 Research Parkway, Meriden, CT 06450 (United States)

    2015-07-01

    Environmental scientific research requires a detector that has sensitivity low enough to reveal the presence of any contaminant in the sample at a reasonable counting time. Canberra developed the germanium detector geometry called Small Anode Germanium (SAGe) Well detector, which is now available commercially. The SAGe Well detector is a new type of low capacitance germanium well detector manufactured using small anode technology capable of advancing many environmental scientific research applications. The performance of this detector has been evaluated for a range of sample sizes and geometries counted inside the well, and on the end cap of the detector. The detector has energy resolution performance similar to semi-planar detectors, and offers significant improvement over the existing coaxial and Well detectors. Energy resolution performance of 750 eV Full Width at Half Maximum (FWHM) at 122 keV γ-ray energy and resolution of 2.0 - 2.3 keV FWHM at 1332 keV γ-ray energy are guaranteed for detector volumes up to 425 cm{sup 3}. The SAGe Well detector offers an optional 28 mm well diameter with the same energy resolution as the standard 16 mm well. Such outstanding resolution performance will benefit environmental applications in revealing the detailed radionuclide content of samples, particularly at low energy, and will enhance the detection sensitivity resulting in reduced counting time. The detector is compatible with electric coolers without any sacrifice in performance and supports the Canberra Mathematical efficiency calibration method (In situ Object Calibration Software or ISOCS, and Laboratory Source-less Calibration Software or LABSOCS). In addition, the SAGe Well detector supports true coincidence summing available in the ISOCS/LABSOCS framework. The improved resolution performance greatly enhances detection sensitivity of this new detector for a range of sample sizes and geometries counted inside the well. This results in lower minimum detectable

  3. De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology.

    Science.gov (United States)

    Canales, Javier; Bautista, Rocio; Label, Philippe; Gómez-Maldonado, Josefa; Lesur, Isabelle; Fernández-Pozo, Noe; Rueda-López, Marina; Guerrero-Fernández, Dario; Castro-Rodríguez, Vanessa; Benzekri, Hicham; Cañas, Rafael A; Guevara, María-Angeles; Rodrigues, Andreia; Seoane, Pedro; Teyssier, Caroline; Morel, Alexandre; Ehrenmann, François; Le Provost, Grégoire; Lalanne, Céline; Noirot, Céline; Klopp, Christophe; Reymond, Isabelle; García-Gutiérrez, Angel; Trontin, Jean-François; Lelu-Walter, Marie-Anne; Miguel, Celia; Cervera, María Teresa; Cantón, Francisco R; Plomion, Christophe; Harvengt, Luc; Avila, Concepción; Gonzalo Claros, M; Cánovas, Francisco M

    2014-04-01

    Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  4. Ingredients for an Integrated Dinner: Parsley, Sage, Rosemary and Thyme

    Science.gov (United States)

    Baumann, Peter

    2013-04-01

    In 1966, Simon and Garfunkel combined the English traditional "Scarborough Fair" with a counter melody. This is one of the manifold techniques of the Kontrapunktik described by Bach around 1745 in "The Art of the Fugue": combining completely different and seemingly independent melodies (or motifs) into a coherent piece of music, pleasant for the audience. This achievement, transposed into Computer Science, could be of great benefit for geo services as we look at the currently disparate situation: On the one hand, we have metadata - traditionally, they are understood as being small in volume, but rich in content and semantics, and flexibly queryable through the rich body of technologies established over several decades of database research, centering around query languages like SQL. On the other hand, we have data themselves, such as remote sensing and other measured and observed data sets - they are considered difficult to interpret, semantic-poor, and only for clumsy download, as they are the main constituent of what we today call Big Data. The traditional advantages of databases, such as information integration, query flexibility, and scalability seem to be unavailable. These are the melodies that require a kontrapunctic harmonization, leading to a Holy Grail where different information categories enjoy individually tailored support, while an overall integrating framework allows seamless and convenient access and processing by the user. Most of the data categories to be integrated are well known in fact: ontologies, geospatial meshes, spatiotemporal arrays, and free text constitute major ingredients in this orchestration. For many of them, isolated solutions have been presented, and for some of them (like ontologies and text) integration has been achieved already; a complete harmonic integration, though, is still lacking as of today. In our talk, we detail our vision on such integration through query models and languages which merge established concepts and novel

  5. Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

    NARCIS (Netherlands)

    Ballerstedt, H.; Volkers, R.J.M.; Mars, A.E.; Hallsworth, J.E.; Santos, V.A.M.D.; Puchalka, J.; Duuren, J. van; Eggink, G.; Timmis, K.N.; Bont, J.A.M. de; Wery, J.

    2007-01-01

    Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for

  6. Database development and management

    CERN Document Server

    Chao, Lee

    2006-01-01

    Introduction to Database Systems Functions of a DatabaseDatabase Management SystemDatabase ComponentsDatabase Development ProcessConceptual Design and Data Modeling Introduction to Database Design Process Understanding Business ProcessEntity-Relationship Data Model Representing Business Process with Entity-RelationshipModelTable Structure and NormalizationIntroduction to TablesTable NormalizationTransforming Data Models to Relational Databases .DBMS Selection Transforming Data Models to Relational DatabasesEnforcing ConstraintsCreating Database for Business ProcessPhysical Design and Database

  7. Earth Science With the Stratospheric Aerosol and Gas Experiment III (SAGE III) on the International Space Station

    Science.gov (United States)

    Zawodny, Joe; Vernier, Jean-Paul; Thomason, Larry; Roell, Marilee; Pitts, Mike; Moore, Randy; Hill, Charles; Flittner, David; Damadeo, Rob; Cisewski, Mike

    2015-01-01

    The Stratospheric Aerosol and Gas Experiment (SAGE) III is the fourth generation of solar occultation instruments operated by NASA, the first coming under a different acronym, to investigate the Earth's upper atmosphere. Three flight-ready SAGE III instruments were built by Ball Aerospace in the late 1990s, with one launched aboard the former Russian Aviation and Space Agency (now known as Roskosmos) Meteor-3M platform on 10 December 2001 (continuing until the platform lost power in 2006). Another of the original instruments was manifested for the ISS in the 2004 time frame, but was delayed because of budgetary considerations. Fortunately, that SAGE III/ISS mission was restarted in 2009 with a major focus upon filling an anticipated gap in ozone and aerosol observation in the second half of this decade. Here we discuss the mission architecture, its implementation, and data that will be produced by SAGE III/ISS, including their expected accuracy and coverage. The 52-degree inclined orbit of the ISS is well-suited for solar occultation and provides near-global observations on a monthly basis with excellent coverage of low and mid-latitudes. This is similar to that of the SAGE II mission (1985-2005), whose data set has served the international atmospheric science community as a standard for stratospheric ozone and aerosol measurements. The nominal science products include vertical profiles of trace gases, such as ozone, nitrogen dioxide and water vapor, along with multi-wavelength aerosol extinction. Though in the visible portion of the spectrum the brightness of the Sun is one million times that of the full Moon, the SAGE III instrument is designed to cover this large dynamic range and also perform lunar occultations on a routine basis to augment the solar products. The standard lunar products were demonstrated during the SAGE III/M3M mission and include ozone, nitrogen dioxide & nitrogen trioxide. The operational flexibility of the SAGE III spectrometer accomplishes

  8. Integrating spatially explicit indices of abundance and habitat quality: an applied example for greater sage-grouse management.

    Science.gov (United States)

    Coates, Peter S; Casazza, Michael L; Ricca, Mark A; Brussee, Brianne E; Blomberg, Erik J; Gustafson, K Benjamin; Overton, Cory T; Davis, Dawn M; Niell, Lara E; Espinosa, Shawn P; Gardner, Scott C; Delehanty, David J

    2016-02-01

    Predictive species distributional models are a cornerstone of wildlife conservation planning. Constructing such models requires robust underpinning science that integrates formerly disparate data types to achieve effective species management.Greater sage-grouse Centrocercus urophasianus , hereafter 'sage-grouse' populations are declining throughout sagebrush-steppe ecosystems in North America, particularly within the Great Basin, which heightens the need for novel management tools that maximize the use of available information.Herein, we improve upon existing species distribution models by combining information about sage-grouse habitat quality, distribution and abundance from multiple data sources. To measure habitat, we created spatially explicit maps depicting habitat selection indices (HSI) informed by >35 500 independent telemetry locations from >1600 sage-grouse collected over 15 years across much of the Great Basin. These indices were derived from models that accounted for selection at different spatial scales and seasons. A region-wide HSI was calculated using the HSI surfaces modelled for 12 independent subregions and then demarcated into distinct habitat quality classes.We also employed a novel index to describe landscape patterns of sage-grouse abundance and space use (AUI). The AUI is a probabilistic composite of the following: (i) breeding density patterns based on the spatial configuration of breeding leks and associated trends in male attendance; and (ii) year-round patterns of space use indexed by the decreasing probability of use with increasing distance to leks. The continuous AUI surface was then reclassified into two classes representing high and low/no use and abundance. Synthesis and application s. Using the example of sage-grouse, we demonstrate how the joint application of indices of habitat selection, abundance and space use derived from multiple data sources yields a composite map that can guide effective allocation of management

  9. Integrating spatially explicit indices of abundance and habitat quality: an applied example for greater sage-grouse management

    Science.gov (United States)

    Coates, Peter S.; Casazza, Michael L.; Ricca, Mark A.; Brussee, Brianne E.; Blomberg, Erik J.; Gustafson, K. Benjamin; Overton, Cory T.; Davis, Dawn M.; Niell, Lara E.; Espinosa, Shawn P.; Gardner, Scott C.; Delehanty, David J.

    2016-01-01

    Predictive species distributional models are a cornerstone of wildlife conservation planning. Constructing such models requires robust underpinning science that integrates formerly disparate data types to achieve effective species management. Greater sage-grouse Centrocercus urophasianus, hereafter “sage-grouse” populations are declining throughout sagebrush-steppe ecosystems in North America, particularly within the Great Basin, which heightens the need for novel management tools that maximize use of available information. Herein, we improve upon existing species distribution models by combining information about sage-grouse habitat quality, distribution, and abundance from multiple data sources. To measure habitat, we created spatially explicit maps depicting habitat selection indices (HSI) informed by > 35 500 independent telemetry locations from > 1600 sage-grouse collected over 15 years across much of the Great Basin. These indices were derived from models that accounted for selection at different spatial scales and seasons. A region-wide HSI was calculated using the HSI surfaces modelled for 12 independent subregions and then demarcated into distinct habitat quality classes. We also employed a novel index to describe landscape patterns of sage-grouse abundance and space use (AUI). The AUI is a probabilistic composite of: (i) breeding density patterns based on the spatial configuration of breeding leks and associated trends in male attendance; and (ii) year-round patterns of space use indexed by the decreasing probability of use with increasing distance to leks. The continuous AUI surface was then reclassified into two classes representing high and low/no use and abundance. Synthesis and applications. Using the example of sage-grouse, we demonstrate how the joint application of indices of habitat selection, abundance, and space use derived from multiple data sources yields a composite map that can guide effective allocation of management intensity across

  10. Development and Implementation of Efficiency-Improving Analysis Methods for the SAGE III on ISS Thermal Model Originating

    Science.gov (United States)

    Liles, Kaitlin; Amundsen, Ruth; Davis, Warren; Scola, Salvatore; Tobin, Steven; McLeod, Shawn; Mannu, Sergio; Guglielmo, Corrado; Moeller, Timothy

    2013-01-01

    The Stratospheric Aerosol and Gas Experiment III (SAGE III) instrument is the fifth in a series of instruments developed for monitoring aerosols and gaseous constituents in the stratosphere and troposphere. SAGE III will be delivered to the International Space Station (ISS) via the SpaceX Dragon vehicle in 2015. A detailed thermal model of the SAGE III payload has been developed in Thermal Desktop (TD). Several novel methods have been implemented to facilitate efficient payload-level thermal analysis, including the use of a design of experiments (DOE) methodology to determine the worst-case orbits for SAGE III while on ISS, use of TD assemblies to move payloads from the Dragon trunk to the Enhanced Operational Transfer Platform (EOTP) to its final home on the Expedite the Processing of Experiments to Space Station (ExPRESS) Logistics Carrier (ELC)-4, incorporation of older models in varying unit sets, ability to change units easily (including hardcoded logic blocks), case-based logic to facilitate activating heaters and active elements for varying scenarios within a single model, incorporation of several coordinate frames to easily map to structural models with differing geometries and locations, and streamlined results processing using an Excel-based text file plotter developed in-house at LaRC. This document presents an overview of the SAGE III thermal model and describes the development and implementation of these efficiency-improving analysis methods.

  11. Volatile Profile of Croatian Lime Tree (Tilia sp., Fir Honeydew (Abies alba and Sage (Salvia officinalis Honey

    Directory of Open Access Journals (Sweden)

    Olivera Koprivnjak

    2007-01-01

    Full Text Available Volatile profiles of lime tree (Tilia sp., fir honeydew (Abies alba and sage (Salvia officinalis honey produced in Croatia have been studied by using headspace solid phase microextraction (HS-SPME followed by gas chromatography-mass spectrometry (GC-MS analysis. Melissopalynological and sensory characterization have been performed in order to check the reliability of botanical origin of the samples. In case of sage honey, sensory characteristics are reported for the first time and are rather uniform including: colour characterized as beige to jade, depending on the consistency; odour characterized as between light and medium intensity, slightly pungent and wooden; taste characterized as low sweetness, expressive acidity and apple caramel, with persistent fruity aftertaste. Characteristic volatile profiles of the analyzed honeys are described. Taking into consideration similarities with lime and fir honey volatile profiles reported in literature, characteristic volatile compounds resulting from qualitative data evaluation are proposed. Sage honey volatile profile has been reported for the first time and it was found quite different compared to the other studied honeys showing the lowest number of peaks among the studied honeys, 34. Several compounds belonging to the sage honey volatile profile have been identified for the first time in honeys. They include tetrahydro-2,2,5,5-tetramethylfuran, 3-hexenyl ester of butanoic acid, 2-methylbenzene, maltol, methyl ester of 3-furanocarboxylic acid and benzeneacetic acid. Based on the obtained results and with the lack of comparative literature data, they are proposed as characteristic volatiles for the volatile pattern of sage honey.

  12. Self-administered Gerocognitive Examination (SAGE): a brief cognitive assessment Instrument for mild cognitive impairment (MCI) and early dementia.

    Science.gov (United States)

    Scharre, Douglas W; Chang, Shu-Ing; Murden, Robert A; Lamb, James; Beversdorf, David Q; Kataki, Maria; Nagaraja, Haikady N; Bornstein, Robert A

    2010-01-01

    To develop a self-administered cognitive assessment instrument to facilitate the screening of mild cognitive impairment (MCI) and early dementia and determine its association with gold standard clinical assessments including neuropsychologic evaluation. Adults aged above 59 years with sufficient vision and English literacy were recruited from geriatric and memory disorder clinics, educational talks, independent living facilities, senior centers, and memory screens. After Self-administered Gerocognitive Examination (SAGE) screening, subjects were randomly selected to complete a clinical evaluation, neurologic examination, neuropsychologic battery, functional assessment, and mini-mental state examination (MMSE). Subjects were identified as dementia, MCI, or normal based on standard clinical criteria and neuropsychologic testing. Two hundred fifty-four participants took the SAGE screen and 63 subjects completed the extensive evaluation (21 normal, 21 MCI, and 21 dementia subjects). Spearman rank correlation between SAGE and neuropsychologic battery was 0.84 (0.76 for MMSE). SAGE receiver operating characteristics on the basis of clinical diagnosis showed 95% specificity (90% for MMSE) and 79% sensitivity (71% for MMSE) in detecting those with cognitive impairment from normal subjects. This study suggests that SAGE is a reliable instrument for detecting cognitive impairment and compares favorably with the MMSE. The self-administered feature may promote cognitive testing by busy clinicians prompting earlier diagnosis and treatment.

  13. Transcriptomic signatures in cartilage ageing

    Science.gov (United States)

    2013-01-01

    Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome. PMID:23971731

  14. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas

    2010-12-06

    Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages-many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization-a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. © 2010 Wiley-Liss, Inc., A Wiley Company.

  15. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

    Directory of Open Access Journals (Sweden)

    Shin-ichi Hashimoto

    Full Text Available Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza. More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

  16. Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga

    Science.gov (United States)

    2011-10-17

    and none of the TAG enzymatic components. Conversely , utilization of the C. vulgaris transcriptome as a search database allowed us to identify all...for conversion to biodiesel or renewable diesel and jet fuel [1,2,3]. Many of these species can also grow rapidly under a large range of environmental...overnight. Approximately 5 mg of dry biomass was suspended in chloroform-methanol (2:1, v/v), and glyceroli- pids were transesterified in HCl-methanol (5

  17. Exploring Triacylglycerol Biosynthetic Pathway in Developing Seeds of Chia (Salvia hispanica L.): A Transcriptomic Approach

    OpenAIRE

    R. V., Sreedhar; Kumari, Priya; Rupwate, Sunny D.; Rajasekharan, Ram; Srinivasan, Malathi

    2015-01-01

    Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop with great importance in health and nutrition and is also the highest known terrestrial plant source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is no public genomic information or database available for this crop, hindering research on its genetic improvement through genomics-assisted breeding programs. The first comprehensive analysis of the global transcriptome...

  18. Utilizing hunter harvest effort to survey for wildlife disease: a case study of West Nile virus in greater sage-grouse

    Science.gov (United States)

    Dusek, Robert J.; Hagen, Christian A.; Franson, J. Christian; Budeau, David A.; Hofmeister, Erik K.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus; sage-grouse) are highly susceptible to infection with West Nile virus (WNV), with substantial mortality reported in wild populations and in experimentally infected birds. Although sage-grouse are hunted throughout much of their range, they have also recently been considered for protection under the Endangered Species Act. We used blood samples collected on filter-paper strips during the 2006–2010 Oregon, USA, annual sage-grouse hunt to survey for specific WNV-neutralizing antibodies that indicate a previous infection with WNV. During this period, hunters submitted 1,880 blood samples from sage-grouse they harvested. Samples obtained were proportional for all 12 Oregon sage-grouse hunting units. Laboratory testing of 1,839 samples by the WNV epitope-blocking enzyme-linked immunosorbent assay (bELISA) followed by plaque reduction neutralization test on bELISA-positive samples yielded 19 (1%) and 1 (0.05%) positive samples, respectively. These data provided early baseline information for future comparisons regarding the prevalence of WNV-specific neutralizing antibodies in sage-grouse in Oregon. This methodology may provide other states where sage-grouse (or other species) populations are hunted and where WNV constitutes a species conservation concern with a viable option to track the relative prevalence of the virus in populations.

  19. Mathematics for Databases

    NARCIS (Netherlands)

    ir. Sander van Laar

    2007-01-01

    A formal description of a database consists of the description of the relations (tables) of the database together with the constraints that must hold on the database. Furthermore the contents of a database can be retrieved using queries. These constraints and queries for databases can very well be

  20. Databases and their application

    NARCIS (Netherlands)

    Grimm, E.C.; Bradshaw, R.H.W; Brewer, S.; Flantua, S.; Giesecke, T.; Lézine, A.M.; Takahara, H.; Williams, J.W.,Jr; Elias, S.A.; Mock, C.J.

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The

  1. DOT Online Database

    Science.gov (United States)

    Page Home Table of Contents Contents Search Database Search Login Login Databases Advisory Circulars accessed by clicking below: Full-Text WebSearch Databases Database Records Date Advisory Circulars 2092 5 data collection and distribution policies. Document Database Website provided by MicroSearch

  2. A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome.

    Directory of Open Access Journals (Sweden)

    Cristian O Rohr

    Full Text Available Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.

  3. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  4. Greater sage-grouse winter habitat use on the eastern edge of their range

    Science.gov (United States)

    Swanson, Christopher C.; Rumble, Mark A.; Grovenburg, Troy W.; Kaczor, Nicholas W.; Klaver, Robert W.; Herman-Brunson, Katie M.; Jenks, Jonathan A.; Jensen, Kent C.

    2013-01-01

    Greater sage-grouse (Centrocercus urophasianus) at the western edge of the Dakotas occur in the transition zone between sagebrush and grassland communities. These mixed sagebrush (Artemisia sp.) and grasslands differ from those habitats that comprise the central portions of the sage-grouse range; yet, no information is available on winter habitat selection within this region of their distribution. We evaluated factors influencing greater sage-grouse winter habitat use in North Dakota during 2005–2006 and 2006–2007 and in South Dakota during 2006–2007 and 2007–2008. We captured and radio-marked 97 breeding-age females and 54 breeding-age males from 2005 to 2007 and quantified habitat selection for 98 of these birds that were alive during winter. We collected habitat measurements at 340 (177 ND, 163 SD) sage-grouse use sites and 680 random (340 each at 250 m and 500 m from locations) dependent sites. Use sites differed from random sites with greater percent sagebrush cover (14.75% use vs. 7.29% random; P 2 use vs. 0.94 plants/m2 random; P ≤ 0.001), but lesser percent grass cover (11.76% use vs. 16.01% random; P ≤ 0.001) and litter cover (4.34% use vs. 5.55% random; P = 0.001) and lower sagebrush height (20.02 cm use vs. 21.35 cm random; P = 0.13) and grass height (21.47 cm use vs. 23.21 cm random; P = 0.15). We used conditional logistic regression to estimate winter habitat selection by sage-grouse on continuous scales. The model sagebrush cover + sagebrush height + sagebrush cover × sagebrush height (wi = 0.60) was the most supported of the 13 models we considered, indicating that percent sagebrush cover strongly influenced selection. Logistic odds ratios indicated that the probability of selection by sage-grouse increased by 1.867 for every 1% increase in sagebrush cover (95% CI = 1.627–2.141) and by 1.041 for every 1 cm increase in sagebrush height (95% CI = 1.002–1.082). The

  5. Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

    Science.gov (United States)

    Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

    2015-08-07

    The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic

  6. Lack of ADAM2, CALR3 and SAGE1 Cancer/Testis Antigen Expression in Lung and Breast Cancer

    DEFF Research Database (Denmark)

    Maheswaran, Emeaga; Pedersen, Christina B; Ditzel, Henrik J

    2015-01-01

    and antigenic properties, but the expression patterns of most of the more than 200 identified cancer/testis antigens in various cancers remain largely uncharacterized. In this study, we investigated the expression of the cancer/testis antigens ADAM2, CALR3 and SAGE1 in lung and breast cancer, the two most...... frequent human cancers, with the purpose of providing novel therapeutic targets for these diseases. We used a set of previously uncharacterized antibodies against the cancer/testis antigens ADAM2, CALR3 and SAGE1 to investigate their expression in a large panel of normal tissues as well as breast and lung...... cancers. Staining for the well-characterized MAGE-A proteins was included for comparison. Immunohistochemical staining confirmed previous mRNA analysis demonstrating that ADAM2, CALR3 and SAGE1 proteins are confined to testis in normal individuals. Negative tissues included plancenta, which express many...

  7. SAGES: a suite of freely-available software tools for electronic disease surveillance in resource-limited settings.

    Directory of Open Access Journals (Sweden)

    Sheri L Lewis

    Full Text Available Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations.

  8. Transcriptomic signatures of ash (Fraxinus spp. phloem.

    Directory of Open Access Journals (Sweden)

    Xiaodong Bai

    2011-01-01

    Full Text Available Ash (Fraxinus spp. is a dominant tree species throughout urban and forested landscapes of North America (NA. The rapid invasion of NA by emerald ash borer (Agrilus planipennis, a wood-boring beetle endemic to Eastern Asia, has resulted in the death of millions of ash trees and threatens billions more. Larvae feed primarily on phloem tissue, which girdles and kills the tree. While NA ash species including black (F. nigra, green (F. pennsylvannica and white (F. americana are highly susceptible, the Asian species Manchurian ash (F. mandshurica is resistant to A. planipennis perhaps due to their co-evolutionary history. Little is known about the molecular genetics of ash. Hence, we undertook a functional genomics approach to identify the repertoire of genes expressed in ash phloem.Using 454 pyrosequencing we obtained 58,673 high quality ash sequences from pooled phloem samples of green, white, black, blue and Manchurian ash. Intriguingly, 45% of the deduced proteins were not significantly similar to any sequences in the GenBank non-redundant database. KEGG analysis of the ash sequences revealed a high occurrence of defense related genes. Expression analysis of early regulators potentially involved in plant defense (i.e. transcription factors, calcium dependent protein kinases and a lipoxygenase 3 revealed higher mRNA levels in resistant ash compared to susceptible ash species. Lastly, we predicted a total of 1,272 single nucleotide polymorphisms and 980 microsatellite loci, among which seven microsatellite loci showed polymorphism between different ash species.The current transcriptomic data provide an invaluable resource for understanding the genetic make-up of ash phloem, the target tissue of A. planipennis. These data along with future functional studies could lead to the identification/characterization of defense genes involved in resistance of ash to A. planipennis, and in future ash breeding programs for marker development.

  9. Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.

    Directory of Open Access Journals (Sweden)

    Yulan Peng

    Full Text Available Youngia japonica, a weed species distributed worldwide, has been widely used in traditional Chinese medicine. It is an ideal plant for studying the evolution of Asteraceae plants because of its short life history and abundant source. However, little is known about its evolution and genetic diversity. In this study, de novo transcriptome sequencing was conducted for the first time for the comprehensive analysis of the genetic diversity of Y. japonica. The Y. japonica transcriptome was sequenced using Illumina paired-end sequencing technology. We produced 21,847,909 high-quality reads for Y. japonica and assembled them into contigs. A total of 51,850 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 41,752 were annotated in the Swiss-Prot database. We mapped 9,125 unigenes onto 163 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 3,648 simple sequence repeats (SSRs were detected. Our data provide the most comprehensive transcriptome resource currently available for Y. japonica. C4 photosynthesis unigenes were found in the biological process of Y. japonica. There were 5596 unigenes related to defense response and 1344 ungienes related to signal transduction mechanisms (10.95%. These data provide insights into the genetic diversity of Y. japonica. Numerous SSRs contributed to the development of novel markers. These data may serve as a new valuable resource for genomic studies on Youngia and, more generally, Cichoraceae.

  10. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2009-06-01

    Full Text Available Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring. For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able

  11. Large-scale control site selection for population monitoring: an example assessing Sage-grouse trends

    Science.gov (United States)

    Fedy, Bradley C.; O'Donnell, Michael; Bowen, Zachary H.

    2015-01-01

    Human impacts on wildlife populations are widespread and prolific and understanding wildlife responses to human impacts is a fundamental component of wildlife management. The first step to understanding wildlife responses is the documentation of changes in wildlife population parameters, such as population size. Meaningful assessment of population changes in potentially impacted sites requires the establishment of monitoring at similar, nonimpacted, control sites. However, it is often difficult to identify appropriate control sites in wildlife populations. We demonstrated use of Geographic Information System (GIS) data across large spatial scales to select biologically relevant control sites for population monitoring. Greater sage-grouse (Centrocercus urophasianus; hearafter, sage-grouse) are negatively affected by energy development, and monitoring of sage-grouse population within energy development areas is necessary to detect population-level responses. Weused population data (1995–2012) from an energy development area in Wyoming, USA, the Atlantic Rim Project Area (ARPA), and GIS data to identify control sites that were not impacted by energy development for population monitoring. Control sites were surrounded by similar habitat and were within similar climate areas to the ARPA. We developed nonlinear trend models for both the ARPA and control sites and compared long-term trends from the 2 areas. We found little difference between the ARPA and control sites trends over time. This research demonstrated an approach for control site selection across large landscapes and can be used as a template for similar impact-monitoring studies. It is important to note that identification of changes in population parameters between control and treatment sites is only the first step in understanding the mechanisms that underlie those changes. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  12. Crucial nesting habitat for gunnison sage-grouse: A spatially explicit hierarchical approach

    Science.gov (United States)

    Aldridge, Cameron L.; Saher, D.J.; Childers, T.M.; Stahlnecker, K.E.; Bowen, Z.H.

    2012-01-01

    Gunnison sage-grouse (Centrocercus minimus) is a species of special concern and is currently considered a candidate species under Endangered Species Act. Careful management is therefore required to ensure that suitable habitat is maintained, particularly because much of the species' current distribution is faced with exurban development pressures. We assessed hierarchical nest site selection patterns of Gunnison sage-grouse inhabiting the western portion of the Gunnison Basin, Colorado, USA, at multiple spatial scales, using logistic regression-based resource selection functions. Models were selected using Akaike Information Criterion corrected for small sample sizes (AIC c) and predictive surfaces were generated using model averaged relative probabilities. Landscape-scale factors that had the most influence on nest site selection included the proportion of sagebrush cover >5%, mean productivity, and density of 2 wheel-drive roads. The landscape-scale predictive surface captured 97% of known Gunnison sage-grouse nests within the top 5 of 10 prediction bins, implicating 57% of the basin as crucial nesting habitat. Crucial habitat identified by the landscape model was used to define the extent for patch-scale modeling efforts. Patch-scale variables that had the greatest influence on nest site selection were the proportion of big sagebrush cover >10%, distance to residential development, distance to high volume paved roads, and mean productivity. This model accurately predicted independent nest locations. The unique hierarchical structure of our models more accurately captures the nested nature of habitat selection, and allowed for increased discrimination within larger landscapes of suitable habitat. We extrapolated the landscape-scale model to the entire Gunnison Basin because of conservation concerns for this species. We believe this predictive surface is a valuable tool which can be incorporated into land use and conservation planning as well the assessment of

  13. Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus.

    Directory of Open Access Journals (Sweden)

    Victor Zeng

    Full Text Available Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects, representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus (cricket, a well-developed laboratory model organism whose potential for functional genetic experiments is currently limited by the absence of genomic resources. cDNA was prepared using mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryo samples on each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw reads, and assembled them into 21,512 isotigs (predicted transcripts and 120,805 singletons with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over 400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways. BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr identified significant similarity to nr sequences for 55.5% of transcriptome sequences, and suggested that the transcriptome may contain 19,874 unique transcripts. For predicted transcripts without significant similarity to known sequences, we assessed their similarity to other orthopteran sequences, and determined that these transcripts contain recognizable protein domains, largely of unknown function. We created a searchable, web-based database to allow public access to all raw, assembled and annotated data. This database is to our knowledge the largest de novo assembled and annotated transcriptome resource available for any hemimetabolous insect. We therefore anticipate that these data will contribute significantly to more effective and higher-throughput deployment of molecular analysis tools in

  14. De Novo Assembly and Characterization of the Transcriptome of Grasshopper Shirakiacris shirakii

    Directory of Open Access Journals (Sweden)

    Zhongying Qiu

    2016-07-01

    Full Text Available Background: The grasshopper Shirakiacris shirakii is an important agricultural pest and feeds mainly on gramineous plants, thereby causing economic damage to a wide range of crops. However, genomic information on this species is extremely limited thus far, and transcriptome data relevant to insecticide resistance and pest control are also not available. Methods: The transcriptome of S. shirakii was sequenced using the Illumina HiSeq platform, and we de novo assembled the transcriptome. Results: Its sequencing produced a total of 105,408,878 clean reads, and the de novo assembly revealed 74,657 unigenes with an average length of 680 bp and N50 of 1057 bp. A total of 28,173 unigenes were annotated for the NCBI non-redundant protein sequences (Nr, NCBI non-redundant nucleotide sequences (Nt, a manually-annotated and reviewed protein sequence database (Swiss-Prot, Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG databases. Based on the Nr annotation results, we manually identified 79 unigenes encoding cytochrome P450 monooxygenases (P450s, 36 unigenes encoding carboxylesterases (CarEs and 36 unigenes encoding glutathione S-transferases (GSTs in S. shirakii. Core RNAi components relevant to miroRNA, siRNA and piRNA pathways, including Pasha, Loquacious, Argonaute-1, Argonaute-2, Argonaute-3, Zucchini, Aubergine, enhanced RNAi-1 and Piwi, were expressed in S. shirakii. We also identified five unigenes that were homologous to the Sid-1 gene. In addition, the analysis of differential gene expressions revealed that a total of 19,764 unigenes were up-regulated and 4185 unigenes were down-regulated in larvae. In total, we predicted 7504 simple sequence repeats (SSRs from 74,657 unigenes. Conclusions: The comprehensive de novo transcriptomic data of S. shirakii will offer a series of valuable molecular resources for better studying insecticide resistance, RNAi and molecular marker discovery in the transcriptome.

  15. Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica.

    Science.gov (United States)

    Qiu, Zhongying; Liu, Fei; Lu, Huimeng; Huang, Yuan

    2017-05-01

    The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better understanding of its gene expression and develop genomic resources for future work. We sequenced and explored the characteristics of the de novo transcriptome of T. japonica using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end clean reads were assembled into 61 141 unigenes using the trinity software; the mean unigene size was 771 bp, and the N50 length was 1238 bp. A total of 29 225 unigenes were functionally annotated to the NCBI nonredundant protein sequences (Nr), NCBI nonredundant nucleotide sequences (Nt), a manually annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of putative genes that are potentially involved in pigment pathways, juvenile hormone (JH) metabolism and signalling pathways were identified in the T. japonica transcriptome. Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms occurred in the adult and larvae transcriptomes, respectively, and a total of 3162 simple sequence repeats were detected in this assembly. This comprehensive transcriptomic data for T. japonica will provide a usable resource for gene predictions, signalling pathway investigations and molecular marker development for this species and other pygmy grasshoppers. © 2016 John Wiley & Sons Ltd.

  16. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  17. Corticosterone metabolite concentrations in greater sage-grouse are positively associated with the presence of cattle grazing

    Science.gov (United States)

    Jankowski, M.D.; Russell, Robin E.; Franson, J. Christian; Dusek, Robert J.; Hines, M.K.; Gregg, M.; Hofmeister, Erik K.

    2014-01-01

    The sagebrush biome in the western United States is home to the imperiled greater sage-grouse (Centrocercus urophasianus) and encompasses rangelands used for cattle production. Cattle grazing activities have been implicated in the range-wide decline of the sage-grouse, but no studies have investigated the relationship between the physiological condition of sage-grouse and the presence of grazing cattle. We sampled 329 sage-grouse across four sites (two grazed and two ungrazed) encompassing 13 600 km2 during the spring and late summer–early autumn of 2005 to evaluate whether demographic factors, breeding status, plasma protein levels, and residence in a cattle-grazed habitat were associated with the stress hormone corticosterone. Corticosterone was measured in feces as immunoreactive corticosterone metabolites (ICM). Males captured during the lekking season exhibited higher ICM levels than all others. Prenesting female sage-grouse captured in a grazed site had higher ICM levels than those in ungrazed sites and prenesting female plasma protein levels were negatively correlated with ICM concentrations. With the use of a small-scale spatial model, we identified a positive correlation between cattle pat count and sage-grouse ICM levels. Our model indicated that ICM levels increased by 2.60 ng · g-1 dry feces for every increase in the number of cow pats found in the vicinity. Management practices will benefit from future research regarding the consistency and mechanism(s) responsible for this association and, importantly, how ICM levels and demographic rates are related in this species of conservation concern.

  18. A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina.

    Science.gov (United States)

    Philipp, Oliver; Hamann, Andrea; Servos, Jörg; Werner, Alexandra; Koch, Ina; Osiewacz, Heinz D

    2013-01-01

    Aging of biological systems is controlled by various processes which have a potential impact on gene expression. Here we report a genome-wide transcriptome analysis of the fungal aging model Podospora anserina. Total RNA of three individuals of defined age were pooled and analyzed by SuperSAGE (serial analysis of gene expression). A bioinformatics analysis identified different molecular pathways to be affected during aging. While the abundance of transcripts linked to ribosomes and to the proteasome quality control system were found to decrease during aging, those associated with autophagy increase, suggesting that autophagy may act as a compensatory quality control pathway. Transcript profiles associated with the energy metabolism including mitochondrial functions were identified to fluctuate during aging. Comparison of wild-type transcripts, which are continuously down-regulated during aging, with those down-regulated in the long-lived, copper-uptake mutant grisea, validated the relevance of age-related changes in cellular copper metabolism. Overall, we (i) present a unique age-related data set of a longitudinal study of the experimental aging model P. anserina which represents a reference resource for future investigations in a variety of organisms, (ii) suggest autophagy to be a key quality control pathway that becomes active once other pathways fail, and (iii) present testable predictions for subsequent experimental investigations.

  19. A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina.

    Directory of Open Access Journals (Sweden)

    Oliver Philipp

    Full Text Available Aging of biological systems is controlled by various processes which have a potential impact on gene expression. Here we report a genome-wide transcriptome analysis of the fungal aging model Podospora anserina. Total RNA of three individuals of defined age were pooled and analyzed by SuperSAGE (serial analysis of gene expression. A bioinformatics analysis identified different molecular pathways to be affected during aging. While the abundance of transcripts linked to ribosomes and to the proteasome quality control system were found to decrease during aging, those associated with autophagy increase, suggesting that autophagy may act as a compensatory quality control pathway. Transcript profiles associated with the energy metabolism including mitochondrial functions were identified to fluctuate during aging. Comparison of wild-type transcripts, which are continuously down-regulated during aging, with those down-regulated in the long-lived, copper-uptake mutant grisea, validated the relevance of age-related changes in cellular copper metabolism. Overall, we (i present a unique age-related data set of a longitudinal study of the experimental aging model P. anserina which represents a reference resource for future investigations in a variety of organisms, (ii suggest autophagy to be a key quality control pathway that becomes active once other pathways fail, and (iii present testable predictions for subsequent experimental investigations.

  20. Discovery of a new Wolf-Rayet star using SAGE-LMC

    OpenAIRE

    Gvaramadze, V. V.; Chené, A. -N.; Kniazev, A. Y.; Schnurr, O.

    2011-01-01

    We report the first-ever discovery of an extragalactic Wolf-Rayet (WR)star with Spitzer. A new WR star in the Large Magellanic Cloud (LMC) was revealed via detection of its circumstellar shell using 24 {\\mu}m images obtained in the framework of the Spitzer Survey of the Large Magellanic Cloud (SAGE-LMC). Subsequent spectroscopic bservations with the Gemini South resolved the central star in two components, one of which is a WN3b+abs star, while the second one is a B0V star. We consider the lo...

  1. Alternaria Leaf Spot on Mealycup Sage (Salvia farinacea Benth.) Caused by Alternaria alternata (Fr.) Keissler

    OpenAIRE

    Hiromitsu, NEGISHI; Kazuo, SUYAMA; Faculty of Agriculture,Tokyo University of Agriculture; Faculty of Agriculture,Tokyo University of Agriculture

    2002-01-01

    In June 1995, a disease causing round to irregular-shaped, water-soaked, brown to blackish brown spots on mealycup sage (Salvia farinacea Benth.) was found in Atsugi-shi, Kanagawa Prefecture, Japan. The symptoms were seen only on leaves, not on neither flower petals or stems. The disease was also found in Setagaya-ku, Tokyo, Memambetsu-cho, Hokkaido and Shimoda-shi and Matsuzaki-cho, Shizuoka. An Alternaria sp. was frequently isolated from these diseased plants. The isolates were severely pat...

  2. PWR fuel physico chemistry. Improvements of the Sage code to compute thermochemical balance in PWR fuel

    International Nuclear Information System (INIS)

    Garcia, P.; Baron, D.; Piron, J.P.

    1993-02-01

    A physicochemical survey of high burnup fuel has been undertaken in the context of a 3-party action (CEA Cadarache - EDF/DER - FRAMATOME). One of the tasks involved consists in adapting the SAGE code for assessment of the thermochemical equilibria of fission products in solution in the fuel matrix. This paper describes the first stage of this task. Even if other improvements are planned, the oxid oxygen potentials are yet properly reproduced for the simulated burnup. (authors). 63 figs., 4 tabs., 41 refs

  3. Intraseasonal variation in survival and probable causes of mortality in greater sage-grouse Centrocercus urophasianus

    Science.gov (United States)

    Blomberg, Erik J.; Gibson, Daniel; Sedinger, James S.; Casazza, Michael L.; Coates, Peter S.

    2013-01-01

    The mortality process is a key component of avian population dynamics, and understanding factors that affect mortality is central to grouse conservation. Populations of greater sage-grouse Centrocercus urophasianus have declined across their range in western North America. We studied cause-specific mortality of radio-marked sage-grouse in Eureka County, Nevada, USA, during two seasons, nesting (2008-2012) and fall (2008-2010), when survival was known to be lower compared to other times of the year. We used known-fate and cumulative incidence function models to estimate weekly survival rates and cumulative risk of cause-specific mortalities, respectively. These methods allowed us to account for temporal variation in sample size and staggered entry of marked individuals into the sample to obtain robust estimates of survival and cause-specific mortality. We monitored 376 individual sage-grouse during the course of our study, and investigated 87 deaths. Predation was the major source of mortality, and accounted for 90% of all mortalities during our study. During the nesting season (1 April - 31 May), the cumulative risk of predation by raptors (0.10; 95% CI: 0.05-0.16) and mammals (0.08; 95% CI: 0.03-013) was relatively equal. In the fall (15 August - 31 October), the cumulative risk of mammal predation was greater (M(mam) = 0.12; 95% CI: 0.04-0.19) than either predation by raptors (M(rap) = 0.05; 95% CI: 0.00-0.10) or hunting harvest (M(hunt) = 0.02; 95% CI: 0.0-0.06). During both seasons, we observed relatively few additional sources of mortality (e.g. collision) and observed no evidence of disease-related mortality (e.g. West Nile Virus). In general, we found little evidence for intraseasonal temporal variation in survival, suggesting that the nesting and fall seasons represent biologically meaningful time intervals with respect to sage-grouse survival.

  4. SAGE measurements of the stratospheric aerosol dispersion and loading from the Soufriere Volcano

    Science.gov (United States)

    Mccormick, M. P.; Kent, G. S.; Yue, G. K.; Cunnold, D. M.

    1981-01-01

    Explosions of the Soufriere volcano on the Caribbean Island of St. Vincent reduced two major stratospheric plumes which the stratospheric aerosol and gas experiment (SAGE) satellite tracked to West Africa and the North Atlantic Ocean. The total mass of the stratospheric ejecta measured is less than 0.5% of the global stratospheric aerosol burden. No significant temperature or climate perturbation is expected. It is found that the movement and dispersion of the plumes agree with those deduced from high altitude meteorological data and dispersion theory. The stratospheric aerosol dispersion and loading from the Soufrier volcano was measured.

  5. Dietary Supplement Ingredient Database

    Science.gov (United States)

    ... and US Department of Agriculture Dietary Supplement Ingredient Database Toggle navigation Menu Home About DSID Mission Current ... values can be saved to build a small database or add to an existing database for national, ...

  6. Energy Consumption Database

    Science.gov (United States)

    Consumption Database The California Energy Commission has created this on-line database for informal reporting ) classifications. The database also provides easy downloading of energy consumption data into Microsoft Excel (XLSX

  7. Evaluating greater sage-grouse seasonal space use relative to leks: Implications for surface use designations in sagebrush ecosystems

    Science.gov (United States)

    Casazza, Michael L.; Coates, Peter S.

    2013-01-01

    The development of anthropogenic structures, especially those related to energy resources, in sagebrush ecosystems is an important concern among developers, conservationists, and land managers in relation to greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse) populations. Sage-grouse are dependent on sagebrush ecosystems to meet their seasonal life-phase requirements, and research indicates that anthropogenic structures can adversely affect sage-grouse populations. Land management agencies have attempted to reduce the negative effects of anthropogenic development by assigning surface use (SU) designations, such as no surface occupancy, to areas around leks (breeding grounds). However, rationale for the size of these areas is often challenged. To help inform this issue, we used a spatial analysis of sage-grouse utilization distributions (UDs) to quantify seasonal (spring, summer and fall, winter) sage-grouse space use in relation to leks. We sampled UDs from 193 sage-grouse (11,878 telemetry locations) across 4 subpopulations within the Bi-State Distinct Population Segment (DPS, bordering California and Nevada) during 2003–2009. We quantified the volume of each UD (vUD) within a range of areas that varied in size and were centered on leks, up to a distance of 30 km from leks. We also quantified the percentage of nests within those areas. We then estimated the diminishing gains of vUD as area increased and produced continuous response curves that allow for flexibility in land management decisions. We found nearly 90% of the total vUD (all seasons combined) was contained within 5 km of leks, and we identified variation in vUD for a given distance related to season and migratory status. Five kilometers also represented the 95th percentile of the distribution of nesting distances. Because diminishing gains of vUD was not substantial until distances exceeded 8 km, managers should consider the theoretical optimal distances for SU designation

  8. Leading edge analysis of transcriptomic changes during pseudorabies virus infection

    Directory of Open Access Journals (Sweden)

    Damarius S. Fleming

    2016-12-01

    Full Text Available Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO (GSE74473 database.

  9. Characterization of gonadal transcriptomes from the turbot (Scophthalmus maximus).

    Science.gov (United States)

    Hu, Yulong; Huang, Meng; Wang, Weiji; Guan, Jiantao; Kong, Jie

    2016-01-01

    The mechanisms underlying sexual reproduction and sex ratio determination remains unclear in turbot, a flatfish of great commercial value. And there is limited information in the turbot database regarding genes related to the reproductive system. Here, we conducted high-throughput transcriptome profiling of turbot gonad tissues to better understand their reproductive functions and to supply essential gene sequence information for marker-assisted selection programs in the turbot industry. In this study, two gonad libraries representing sex differences in Scophthalmus maximus yielded 453 818 high-quality reads that were assembled into 24 611 contigs and 33 713 singletons by using 454 pyrosequencing, 13 936 contigs and singletons (CS) of which were annotated using BLASTx. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that various biological functions and processes were associated with many of the annotated CS. Expression analyses showed that 510 genes were differentially expressed in males versus females; 80% of these genes were annotated. In addition, 6484 and 6036 single nucleotide polymorphisms (SNPs) were identified in male and female libraries, respectively. This transcriptome resource will serve as the foundation for cDNA or SNP microarray construction, gene expression characterization, and sex-specific linkage mapping in turbot.

  10. Application of transcriptomics in Chinese herbal medicine studies

    Directory of Open Access Journals (Sweden)

    Hsin-Yi Lo

    2012-04-01

    Full Text Available Transcriptomics using DNA microarray has become a practical and popular tool for herbal medicine study because of high throughput, sensitivity, accuracy, specificity, and reproducibility. Therefore, this article focuses on the overview of DNA microarray technology and the application of DNA microarray in Chinese herbal medicine study. To understand the number and the objectives of articles utilizing DNA microarray for herbal medicine study, we surveyed 297 frequently used Chinese medicinal herbs listed in Pharmacopoeia Commission of People’s Republic of China. We classified these medicinal herbs into 109 families and then applied PudMed search using “microarray” and individual herbal family as keywords. Although thousands of papers applying DNA microarray in Chinese herbal studies have been published since 1998, most of the articles focus on the elucidation of mechanisms of certain biological effects of herbs. Construction of the bioactivity database containing large-scaled gene expression profiles of quality control herbs can be applied in the future to analyze the biological events induced by herbs, predict the therapeutic potential of herbs, evaluate the safety of herbs, and identify the drug candidate of herbs. Moreover, the linkage of systems biology tools, such as functional genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics and toxicogenomics, will become a new translational platform between Western medicine and Chinese herbal medicine.

  11. Leading edge analysis of transcriptomic changes during pseudorabies virus infection.

    Science.gov (United States)

    Fleming, Damarius S; Miller, Laura C

    2016-12-01

    Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.

  12. Characterizing the transcriptome and molecular markers information ...

    Indian Academy of Sciences (India)

    2008). Analyses of the genetic structure .... The annotations and classifications for the transcriptome ... Based on the Pfam classification, the predic- ..... J. Lipid. Res. 33, 251–262. Eckert C. G., Samis K. E. and Lougheed S. C. 2008 Genetic vari-.

  13. The floral transcriptome of Eucalyptus grandis

    CSIR Research Space (South Africa)

    Vining, KJ

    2015-10-01

    Full Text Available As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages...

  14. Collecting Taxes Database

    Data.gov (United States)

    US Agency for International Development — The Collecting Taxes Database contains performance and structural indicators about national tax systems. The database contains quantitative revenue performance...

  15. USAID Anticorruption Projects Database

    Data.gov (United States)

    US Agency for International Development — The Anticorruption Projects Database (Database) includes information about USAID projects with anticorruption interventions implemented worldwide between 2007 and...

  16. NoSQL databases

    OpenAIRE

    Mrozek, Jakub

    2012-01-01

    This thesis deals with database systems referred to as NoSQL databases. In the second chapter, I explain basic terms and the theory of database systems. A short explanation is dedicated to database systems based on the relational data model and the SQL standardized query language. Chapter Three explains the concept and history of the NoSQL databases, and also presents database models, major features and the use of NoSQL databases in comparison with traditional database systems. In the fourth ...

  17. 3rd International Conference on Transcriptomics

    OpenAIRE

    John A Daniel

    2017-01-01

    Conference Series has been instrumental in conducting international Biochemistry meetings for seven years, and very excited to expand Europe, America and Asia Pacific continents. Previous meetings were held in major cities like Philadelphia, Orlando with success the meetings again scheduled in three continents. 3rd International Conference on Transcriptomics to be held during October 30 - November 01, 2017 at Bangkok, Thailand The Global Transcriptomics business sector to develop at a C...

  18. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

    Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

  19. Transcriptome datasets of oil palm pathogen Ganoderma boninense

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    Irene Liza Isaac

    2018-04-01

    Full Text Available Ganoderma boninense is known to be the causal agent for basal stem rot (BSR affecting the oil palm industry worldwide thus cumulating to high economic losses every year. Several reports have shown that a compatible monokaryon pair needs to mate; producing dikaryotic mycelia to initiate the infection towards the oil palm. However, the molecular events occurs during mating process are not well understood. We performed transcriptome sequencing using Illumina RNA-seq technology and de novo assembly of the transcripts from monokaryon, mating junction and dikaryon mycelia of G. boninense. Raw reads from these three libraries were deposited in the NCBI database with accession number SRR1745787, SRR1745773 and SRR1745777, respectively.

  20. Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models

    International Nuclear Information System (INIS)

    Rogers, Simon; Girolami, Mark; Kolch, Walter; Waters, Katrina M.; Liu, Tao; Thrall, Brian D.; Wiley, H. S.

    2008-01-01

    Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated. Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. By providing probabilistic assignments this approach sits between the two extremes of concatenating the data on the assumption that mRNA and protein clusters would have a one-to-one relationship, and independent clustering where the mRNA profile provides no information on the protein profile and vice-versa. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC) stimulated by epidermal growth factor (EGF) over a series of timepoints corresponding to one cell cycle. The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the gene ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding. Conclusions: The dynamic regulation of the transcriptome and proteome in mammalian cells in response to an acute mitogenic stimulus appears largely independent with very little

  1. Transcriptome analysis of the Chinese giant salamander (Andrias davidianus using RNA-sequencing

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    Yong Huang

    2017-12-01

    Full Text Available The Chinese giant salamander (Andrias davidianus is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases, a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.

  2. Insight into the transcriptome of Arthrobotrys conoides using high throughput sequencing.

    Science.gov (United States)

    Ramesh, Pandit; Reena, Patel; Amitbikram, Mohapatra; Chaitanya, Joshi; Anju, Kunjadia

    2015-12-01

    Arthrobotrys conoides is a nematode-trapping fungus belonging to Orbiliales, Ascomycota group, and traps prey nematodes by means of adhesive network. Fungus has a potential to be used as a biocontrol agent against plant parasitic nematodes. In the present study, we characterized the transcriptome of A. conoides using high-throughput sequencing technology and characterized its virulence unigenes. Total 7,255 cDNA contigs with an average length of 425 bp were generated and 6184 (61.81%) transcripts were functionally annotated and characterized. Majority of unigenes were found analogous to the genes of plant pathogenic fungi. A total of 1749 transcripts were found to be orthologous with eukaryotic proteins of KOG database. Several carbohydrate active enzymes and peptidases were identified. We also analyzed classically and nonclassically secreted proteins and confirmed by BLASTP against fungal secretome database. A total of 916 contigs were analogous to 556 unique proteins of Pathogen Host Interaction (PHI) database. Further, we identified 91 unigenes homologous to the database of fungal virulence factor (DFVF). A total of 104 putative protein kinases coding transcripts were identified by BLASTP against KinBase database, which are major players in signaling pathways. This study provides a comprehensive look at the transcriptome of A. conoides and the identified unigenes might have a role in catching and killing prey nematodes by A. conoides. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Analysis of the transcriptome of Isodon rubescens and key enzymes involved in terpenoid biosynthesis

    Directory of Open Access Journals (Sweden)

    Xiuhong Su

    2016-05-01

    Full Text Available Isodon rubescens is an important medicinal plant in China that has been shown to reduce tumour growth due to the presence of the compound oridonin. In an effort to facilitate molecular research on oridonin biosynthesis, we reported the use of next generation massively parallel sequencing technologies and de novo transcriptome assembly to gain a comprehensive overview of I. rubescens transcriptome. In our study, a total of 50,934,276 clean reads, 101,640 transcripts and 44,626 unigenes were generated through de novo transcriptome assembly. A number of unigenes – 23,987, 10,263, 7359, 18,245, 17,683, 19,485, 9361 – were annotated in the National Center for Biotechnology Information (NCBI non-redundant protein (Nr, NCBI nucleotide sequences (Nt, Kyoto Encyclopedia of Genes and Genomes (KEGG Orthology (KO, Swiss-Prot, protein family (Pfam, gene ontology (GO, eukaryotic ortholog groups (KOG databases, respectively. Furthermore, the annotated unigenes were functionally classified according to the GO, KOG and KEGG. Based on these results, candidate genes encoding enzymes involved in terpenoids backbone biosynthesis were detected. Our data provided the most comprehensive sequence resource available for the study on I. rubescens, as well as demonstrated the effective use of Illumina sequencing and de novo transcriptome assembly on a species lacking genomic information.

  4. Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence.

    Science.gov (United States)

    Houshyani, Benyamin; van der Krol, Alexander R; Bino, Raoul J; Bouwmeester, Harro J

    2014-06-19

    Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types. In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis. Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.

  5. De novo assembly of leaf transcriptome in the medicinal plant Andrographis paniculata

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    Neeraja Cherukupalli

    2016-08-01

    Full Text Available Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeqTM 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant nonredundant protein database, gene ontology and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts − using kyoto encyclopedia of genes and genomes database − revealed 5,606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6,767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs in 23,168 transcripts. Assembled sequences of transcriptome of A.paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analyses besides identification of key enzymes involved in the various pathways of secondary metabolism.

  6. Communication in palliative care: the applicability of the SAGE and THYME model in Singapore.

    Science.gov (United States)

    Martin, Ang Seng Hock; Costello, John; Griffiths, Jane

    2017-06-02

    Majority of the progress and development in palliative care in the last decade has been improvements in physical aspects of treatment, namely pain and symptom management. Psychosocial aspects of care have improved, although not enough to meet the needs of many patients and family members. This is evident in many parts of the world and notably in Singapore, where palliative care is seen as an emerging medical and nursing specialty. To discuss the implementation of the SAGE and THYME communication model in a palliative care context. The article examines the use of the model and how its implementation can improve communication between patients and nurses. The model works by reviewing contemporary developments made in relation to improving communication in palliative care. These include, highlighting the importance of meeting individual needs, therapeutic relationship building, and advanced communication training within a Singaporean context. The implementation of the SAGE and THYME model can be a useful way of enabling nurses to improve and maintain effective communication in a medically dominated health care system. The challenges and constraints in educating and training nurses with limited skills in palliative care, forms part of the review, including the cultural and attitude constraints specific to Singaporean palliative care.

  7. SAGE-VAR: AN INFRARED SURVEY OF VARIABILITY IN THE MAGELLANIC CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Riebel, D. [Department of Physics, United States Naval Academy, 572 C Holloway Road, Annapolis, MD 21402 (United States); Boyer, M. L. [Observational Cosmology Laboratory, Code 665, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Srinivasan, S. [Academia Sinica, Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 10617, Taiwan (China); Whitelock, P.; Feast, M. [Astrophysics, Cosmology and Gravity Centre, Astronomy Department, University of Cape Town, Rondebosch 7701 (South Africa); Meixner, M.; Shiao, B. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Babler, B.; Meade, M.; Whitney, B. [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States); Groenewegen, M. A. T. [Royal Observatory of Belgium, Ringlaan 3, B-1180 Brussels (Belgium); Ita, Y., E-mail: riebel.d@gmail.com [Astronomical Institute, Graduate School of Science, Tohoku University, 6-3 Aramaki Aoba, Aoba-ku, Sendai, Miyagi 980-8578 (Japan)

    2015-07-01

    We present the first results from the Surveying the Agents of Galaxy Evolution (SAGE)-Var program, a follow up to the Spitzer legacy program SAGE (Meixner et al.). We obtained four epochs of photometry at 3.6 and 4.5 μm covering the bar of the LMC and the central region of the SMC in order to probe the variability of extremely red sources missed by variability surveys conducted at shorter wavelengths, and to provide additional epochs of observation for known variables. Our six total epochs of observations allow us to probe infrared (IR) variability on 15 different timescales ranging from ∼20 days to ∼5 yr. Out of a full catalog of 1 717 554 (LMC) and 457 760 (SMC) objects, we find 10 (LMC) and 6 (SMC) large amplitude Asymptotic Giant Branch (AGB) variables without optically measured variability owing to circumstellar dust obscuration. The catalog also contains multiple observations of known AGB variables, type I and II Cepheids, eclipsing variables, R CrB stars, and young stellar objects, which will be discussed in following papers. Here we present IR Period–Luminosity (PL) relations for classical Cepheids in the Magellanic Clouds, as well as improved PL relationships for AGB stars pulsating in the fundamental mode using mean magnitudes constructed from six epochs of observations.

  8. SAGE aerosol measurements. Volume 1, February 21, 1979 to December 31, 1979

    International Nuclear Information System (INIS)

    Mccormick, M.P.

    1985-10-01

    The Stratospheric Aerosol and Gas Experiment (SAGE) satellite system, launched on February 18, 1979, provides profiles of aerosol extinction, ozone concentration, and nitrogen dioxide concentration between about 80 N and 80 S. Zonal averages, separated into sunrise and sunset events, and seasonal averages of the aerosol extinction at 1.00 microns and 0.45 microns ratios of the aerosol extinction to the molecular extinction at 1.00 microns, and ratios of the aerosol extinction at 0.45 microns to the aerosol extinction at 1.00 microns are given. The averages for 1979 are shown in tables and in profile and contour plots (as a function of altitude and latitude). In addition, temperature data provided by the National Oceanic and Atmospheric Administration (NOAA) for the time and location of each SAGE measurement are averaged and shown in a similar format. Typical values of the peak aerosol extinction were 0.0001 to 0.0002 km at 1.00 microns depth values for the 1.00 microns channel varied between 0.001 and 0.002 over all latitudes

  9. Control of the phytoplankton response during the SAGE experiment: A synthesis

    Science.gov (United States)

    Peloquin, Jill; Hall, Julie; Safi, Karl; Ellwood, Michael; Law, Cliff S.; Thompson, Karen; Kuparinen, Jorma; Harvey, Michael; Pickmere, Stuart

    2011-03-01

    The SOLAS Air-Sea Gas Exchange (SAGE) experiment was conducted in Sub-Antarctic waters off the east coast of the South Island of New Zealand in the late summer of 2004. This mesoscale iron enrichment experiment was unique in that chlorophyll a (chl a) and primary productivity were only 2× OUT stations values toward the end of the experiment and this enhancement was due to increased activity of non-diatomaceous species. In addition, this enhancement in activity appeared to occur without a significant build up of particulate organic carbon. Picoeukaryotes (statistically significant increase, a doubling in biomass. To better understand the controls of phytoplankton growth and biomass, we present results from a series of on-deck perturbation experiments conducted during SAGE. Results suggest that the pico-dominated phytoplankton assemblage was only weakly inhibited by iron. Diatoms with high growth rates comprised a small (food web. A primary implication of this study is that any iron-mediated gain in fixed carbon with this set of environmental conditions has a high probability of being recycled in surface waters.

  10. Can reliable sage-grouse lek counts be obtained using aerial infrared technology

    Science.gov (United States)

    Gillette, Gifford L.; Coates, Peter S.; Petersen, Steven; Romero, John P.

    2013-01-01

    More effective methods for counting greater sage-grouse (Centrocercus urophasianus) are needed to better assess population trends through enumeration or location of new leks. We describe an aerial infrared technique for conducting sage-grouse lek counts and compare this method with conventional ground-based lek count methods. During the breeding period in 2010 and 2011, we surveyed leks from fixed-winged aircraft using cryogenically cooled mid-wave infrared cameras and surveyed the same leks on the same day from the ground following a standard lek count protocol. We did not detect significant differences in lek counts between surveying techniques. These findings suggest that using a cryogenically cooled mid-wave infrared camera from an aerial platform to conduct lek surveys is an effective alternative technique to conventional ground-based methods, but further research is needed. We discuss multiple advantages to aerial infrared surveys, including counting in remote areas, representing greater spatial variation, and increasing the number of counted leks per season. Aerial infrared lek counts may be a valuable wildlife management tool that releases time and resources for other conservation efforts. Opportunities exist for wildlife professionals to refine and apply aerial infrared techniques to wildlife monitoring programs because of the increasing reliability and affordability of this technology.

  11. SAGE-VAR: AN INFRARED SURVEY OF VARIABILITY IN THE MAGELLANIC CLOUDS

    International Nuclear Information System (INIS)

    Riebel, D.; Boyer, M. L.; Srinivasan, S.; Whitelock, P.; Feast, M.; Meixner, M.; Shiao, B.; Babler, B.; Meade, M.; Whitney, B.; Groenewegen, M. A. T.; Ita, Y.

    2015-01-01

    We present the first results from the Surveying the Agents of Galaxy Evolution (SAGE)-Var program, a follow up to the Spitzer legacy program SAGE (Meixner et al.). We obtained four epochs of photometry at 3.6 and 4.5 μm covering the bar of the LMC and the central region of the SMC in order to probe the variability of extremely red sources missed by variability surveys conducted at shorter wavelengths, and to provide additional epochs of observation for known variables. Our six total epochs of observations allow us to probe infrared (IR) variability on 15 different timescales ranging from ∼20 days to ∼5 yr. Out of a full catalog of 1 717 554 (LMC) and 457 760 (SMC) objects, we find 10 (LMC) and 6 (SMC) large amplitude Asymptotic Giant Branch (AGB) variables without optically measured variability owing to circumstellar dust obscuration. The catalog also contains multiple observations of known AGB variables, type I and II Cepheids, eclipsing variables, R CrB stars, and young stellar objects, which will be discussed in following papers. Here we present IR Period–Luminosity (PL) relations for classical Cepheids in the Magellanic Clouds, as well as improved PL relationships for AGB stars pulsating in the fundamental mode using mean magnitudes constructed from six epochs of observations

  12. Dry fermented buffalo sausage with sage oil extract: Safety and quality

    Directory of Open Access Journals (Sweden)

    Ibrahim, Hayam M.

    2010-03-01

    Full Text Available Sage oil extract was added during the preparation of dry fermented buffalo meat sausage. Some chemical, microbial and sensory characteristics of sausages were evaluated during the ripening period. In particular, pH, lipid oxidation, biogenic amines and micro flora were analyzed. Results of this study pointed out that sage oil extract as natural antioxidant could be utilized in dry fermented sausage, prepared from buffalo meat, in order to obtain a final product within acceptable lipid oxidation and biogenic amine levels, as well as improved sensory quality.Extractos de aceite de salvia fueron añadidos a embutidos de carne de búfalo. Las características químicas, microbiológicas y sensoriales de los embutidos fueron evaluadas durante el periodo de maduración. En particular, pH, oxidación lipídica, aminas biogénicas y microflora fueron analizadas. Los resultados de este estudio indican que los extractos de aceite de salvia, como antioxidantes naturales, podrían ser utilizados en embutidos preparados con carnes de búfalo, con objeto de obtener un producto final con unos niveles de aminas biogénicas y de oxidación lipídica aceptable, así como con una calidad sensorial mejorada.

  13. Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana.

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    Yanan Liu

    Full Text Available The Eastern woodchuck (Marmota monax is a classical animal model for studying hepatitis B virus (HBV infection and hepatocellular carcinoma (HCC in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO. The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs and the simple sequence repeats (SSRs were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC

  14. Transcriptome of the freshwater amphipod Gammarus pulex hepatopancreas

    Directory of Open Access Journals (Sweden)

    E. Gismondi

    2016-06-01

    Full Text Available So far, ecotoxicological studies used biomarkers of exposure or of effects in order to investigate the impacts of contaminated areas on biota (Peakall, 1994 [6]. However, although these results are important in the ecotoxicological risk assessment, biomarkers are very specific and only provide information on the biological processes or physiological pathways targeted by the biomarkers experimenters choose to test (Monsinjon and Knigge, 2007 [5]. In recent years, proteomics have become a major tool in ecotoxicology, as they provide a global insight into the mechanism of action of pollutants without the need of hypothesis testing or any preconception on the biological processes likely impacted (Gismondi et al., 2015; Trapp et al., 2015 [7]; Truebano, 2016 [8]. However, the analysis of proteomic results is often limited due to the lack of database, especially for non-model organisms, such as Gammarus sp, commonly used as biological model in ecotoxicology (Sornom et al., 2012 [11]; Vellinger et al., 2013 [9]; Gismondi and Thomé, 2014 [1]; Lebrun et al., 2014 [3]. Here, we performed Illumina HiSeq sequencing to total RNA isolated from the hepatopancreas (i.e. detoxification tissue of Gammarus pulex males and females coming from uncontaminated river and contaminated river (e.g. PCB, benzo(apyrene. Approximately 290 M paired-end reads were assembled, filtered and sorted into 39,801 contigs whose 10.878 were similar of proteins available in databases. The assembled contigs could represent a reference hepatopancreas transcriptome for G. pulex, and constitute an important resource for future investigations on the impacts of pollutants on invertebrate biota, since it would improve the understanding of the mechanisms of action involved in toxicity. In addition, the hepatopancreas transcriptome will also allow the identification of new potential biomarkers for the ecotoxicological risk assessments. Assembled contigs were deposited in the European

  15. Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

    Directory of Open Access Journals (Sweden)

    Tingcai Cheng

    Full Text Available The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG and posterior silk gland (PSG. Three sericin genes (sericin 1, sericin 2, and sericin 3 were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25 were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs and 361 insertion-deletions (INDELs were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

  16. PrimateLit Database

    Science.gov (United States)

    Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

  17. A comparative gene expression database for invertebrates

    Directory of Open Access Journals (Sweden)

    Ormestad Mattias

    2011-08-01

    Full Text Available Abstract Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN projects.

  18. KALIMER database development

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwan Seong; Lee, Yong Bum; Jeong, Hae Yong; Ha, Kwi Seok

    2003-03-01

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment.

  19. KALIMER database development

    International Nuclear Information System (INIS)

    Jeong, Kwan Seong; Lee, Yong Bum; Jeong, Hae Yong; Ha, Kwi Seok

    2003-03-01

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment

  20. Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta.

    Science.gov (United States)

    Niu, Donghong; Wang, Fei; Xie, Shumei; Sun, Fanyue; Wang, Ze; Peng, Maoxiao; Li, Jiale

    2016-04-01

    The razor clam Sinonovacula constricta is an important commercial species. The deficiency of developmental transcriptomic data is becoming the bottleneck of further researches on the mechanisms underlying settlement and metamorphosis in early development. In this study, de novo transcriptome sequencing was performed for S. constricta at different early developmental stages by using Illumina HiSeq 2000 paired-end (PE) sequencing technology. A total of 112,209,077 PE clean reads were generated. De novo assembly generated 249,795 contigs with an average length of 585 bp. Gene annotation resulted in the identification of 22,870 unigene hits against the NCBI database. Eight unique sequences related to metamorphosis were identified and analyzed using real-time PCR. The razor clam reference transcriptome would provide useful information on early developmental and metamorphosis mechanisms and could be used in the genetic breeding of shellfish.

  1. Development of a quality assurance safety assessment database for near surface radioactive waste disposal

    International Nuclear Information System (INIS)

    Park, J. W.; Kim, C. L.; Park, J. B.; Lee, E. Y.; Lee, Y. M.; Kang, C. H.; Zhou, W.; Kozak, M. W.

    2003-01-01

    A quality assurance safety assessment database, called QUARK (QUality Assurance program for Radioactive waste management in Korea), has been developed to manage both analysis information and parameter database for safety assessment of Low- and Intermediate-Level radioactive Waste (LILW) disposal facility in Korea. QUARK is such a tool that serves QA purposes for managing safety assessment information properly and securely. In QUARK, the information is organized and linked to maximize the integrity of information and traceability. QUARK provides guidance to conduct safety assessment analysis, from scenario generation to result analysis, and provides a window to inspect and trace previous safety assessment analysis and parameter values. QUARK also provides default database for safety assessment staff who construct input data files using SAGE(Safety Assessment Groundwater Evaluation), a safety assessment computer code

  2. Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

    Directory of Open Access Journals (Sweden)

    Man-Li He

    2016-11-01

    Full Text Available Abstract Background Psoroptic mange is a chronic, refractory, contagious and infectious disease mainly caused by the mange mite Psoroptes ovis, which can infect horses, sheep, buffaloes, rabbits, other domestic animals, deer, wild camels, foxes, minks, lemurs, alpacas, elks and other wild animals. Features of the disease include intense pruritus and dermatitis, depilation and hyperkeratosis, which ultimately result in emaciation or death caused by secondary bacterial infections. The infestation is usually transmitted by close contact between animals. Psoroptic mange is widespread in the world. In this paper, the transcriptome of P. ovis is described following sequencing and analysis of transcripts from samples of larvae (i.e. the Pso_L group and nymphs and adults (i.e. the Pso_N_A group. The study describes differentially expressed genes (DEGs and genes encoding allergens, which help understanding the biology of P. ovis and lay foundations for the development of vaccine antigens and drug target screening. Methods The transcriptome of P. ovis was assembled and analyzed using bioinformatic tools. The unigenes of P. ovis from each developmental stage and the unigenes differentially between developmental stages were compared with allergen protein sequences contained in the allergen database website to predict potential allergens. Results We identified 38,836 unigenes, whose mean length was 825 bp. On the basis of sequence similarity with seven databases, a total of 17,366 unigenes were annotated. A total of 1,316 DEGs were identified, including 496 upregulated and 820 downregulated in the Pso_L group compared with the Pso_N_A group. We predicted 205 allergens genes in the two developmental stages similar to genes from other mites and ticks, of these, 14 were among the upregulated DEGs and 26 among the downregulated DEGs. Conclusion This study provides a reference transcriptome of P. ovis in absence of a reference genome. The analysis of DEGs and

  3. Logical database design principles

    CERN Document Server

    Garmany, John; Clark, Terry

    2005-01-01

    INTRODUCTION TO LOGICAL DATABASE DESIGNUnderstanding a Database Database Architectures Relational Databases Creating the Database System Development Life Cycle (SDLC)Systems Planning: Assessment and Feasibility System Analysis: RequirementsSystem Analysis: Requirements Checklist Models Tracking and Schedules Design Modeling Functional Decomposition DiagramData Flow Diagrams Data Dictionary Logical Structures and Decision Trees System Design: LogicalSYSTEM DESIGN AND IMPLEMENTATION The ER ApproachEntities and Entity Types Attribute Domains AttributesSet-Valued AttributesWeak Entities Constraint

  4. An Interoperable Cartographic Database

    OpenAIRE

    Slobodanka Ključanin; Zdravko Galić

    2007-01-01

    The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on t...

  5. Software listing: CHEMTOX database

    International Nuclear Information System (INIS)

    Moskowitz, P.D.

    1993-01-01

    Initially launched in 1983, the CHEMTOX Database was among the first microcomputer databases containing hazardous chemical information. The database is used in many industries and government agencies in more than 17 countries. Updated quarterly, the CHEMTOX Database provides detailed environmental and safety information on 7500-plus hazardous substances covered by dozens of regulatory and advisory sources. This brief listing describes the method of accessing data and provides ordering information for those wishing to obtain the CHEMTOX Database

  6. The genetic network of greater sage-grouse: Range-wide identification of keystone hubs of connectivity

    Science.gov (United States)

    Todd B. Cross; Michael K. Schwartz; David E. Naugle; Brad C. Fedy; Jeffrey R. Row; Sara J. Oyler-McCance

    2018-01-01

    Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage-grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on...

  7. Greater Sage-Grouse Habitat Use and Population Demographics at the Simpson Ridge Wind Resource Area, Carbon County, Wyoming

    Energy Technology Data Exchange (ETDEWEB)

    Gregory D. Johnson; Chad W. LeBeau; Ryan Nielsen; Troy Rintz; Jamey Eddy; Matt Holloran

    2012-03-27

    This study was conducted to obtain baseline data on use of the proposed Simpson Ridge Wind Resource Area (SRWRA) in Carbon County, Wyoming by greater sage-grouse. The first two study years were designed to determine pre-construction seasonally selected habitats and population-level vital rates (productivity and survival). The presence of an existing wind energy facility in the project area, the PacifiCorp Seven Mile Hill (SMH) project, allowed us to obtain some information on initial sage-grouse response to wind turbines the first two years following construction. To our knowledge these are the first quantitative data on sage-grouse response to an existing wind energy development. This report presents results of the first two study years (April 1, 2009 through March 30, 2011). This study was selected for continued funding by the National Wind Coordinating Collaborative Sage-Grouse Collaborative (NWCC-SGC) and has been ongoing since March 30, 2011. Future reports summarizing results of this research will be distributed through the NWCC-SGC. To investigate population trends through time, we determined the distribution and numbers of males using leks throughout the study area, which included a 4-mile radius buffer around the SRWRA. Over the 2-year study, 116 female greater sage-grouse were captured by spotlighting and use of hoop nets on roosts surrounding leks during the breeding period. Radio marked birds were located anywhere from twice a week to once a month, depending on season. All radio-locations were classified to season. We developed predictor variables used to predict success of fitness parameters and relative probability of habitat selection within the SRWRA and SMH study areas. Anthropogenic features included paved highways, overhead transmission lines, wind turbines and turbine access roads. Environmental variables included vegetation and topography features. Home ranges were estimated using a kernel density estimator. We developed resource selection

  8. Restoration handbook for sagebrush steppe ecosystems with emphasis on greater sage-grouse habitat - Part 3: Site level restoration decisions

    Science.gov (United States)

    David A. Pyke; Jeanne C. Chambers; Mike Pellant; Richard F. Miller; Jeffrey L. Beck; Paul S. Doescher; Bruce A. Roundy; Eugene W. Schupp; Steven T. Knick; Mark Brunson; James D. McIver

    2017-01-01

    Sagebrush steppe ecosystems in the United States currently (2016) occur on only about one-half of their historical land area because of changes in land use, urban growth, and degradation of land, including invasions of non-native plants. The existence of many animal species depends on the existence of sagebrush steppe habitat. The greater sage-grouse (Centrocercus...

  9. Forbs: Foundation for restoration of monarch butterflies, other pollinators, and greater sage-grouse in the western United States

    Science.gov (United States)

    Kas Dumroese; Tara Luna; Jeremy Pinto; Thomas D. Landis

    2016-01-01

    Monarch butterflies (Danaus plexippus), other pollinators, and Greater Sage-Grouse (Centrocercus urophasianus) are currently the focus of increased conservation efforts. Federal attention on these fauna is encouraging land managers to develop conservation strategies, often without corresponding financial resources. This could foster a myopic approach when...

  10. Nesting ecology of greater sage-grouse Centrocercus urophasianus at the eastern edge of their historic distribution

    Science.gov (United States)

    Katie M. Herman-Brunson; Kent C. Jensen; Nicholas W. Kaczor; Christopher C. Swanson; Mark A. Rumble; Robert W. Klaver

    2009-01-01

    Greater sage-grouse Centrocercus urophasianus populations in North Dakota declined approximately 67% between 1965 and 2003, and the species is listed as a Priority Level 1 Species of Special Concern by the North Dakota Game and Fish Department. The habitat and ecology of the species at the eastern edge of its historical range is largely unknown. We...

  11. Formulation of sage essential oil (Salvia officinalis, L.) monoterpenes into chitosan hydrogels and permeation study with GC-MS analysis.

    Science.gov (United States)

    Kodadová, Alexandra; Vitková, Zuzana; Herdová, Petra; Ťažký, Anton; Oremusová, Jarmila; Grančai, Daniel; Mikuš, Peter

    2015-01-01

    This study deals with the formulation of natural drugs into hydrogels. For the first time, compounds from the sage essential oil were formulated into chitosan hydrogels. A sample preparation procedure for hydrophobic volatile analytes present in a hydrophilic water matrix along with an analytical method based on the gas chromatography coupled with the mass spectrometry (GC-MS) was developed and applied for the evaluation of the identity and quantity of essential oil components in the hydrogels and saline samples. The experimental results revealed that the chitosan hydrogels are suitable for the formulation of sage essential oil. The monoterpene release can be effectively controlled by both chitosan and caffeine concentration in the hydrogels. Permeation experiment, based on a hydrogel with the optimized composition [3.5% (w/w) sage essential oil, 2.0% (w/w) caffeine, 2.5% (w/w) chitosan and 0.1% (w/w) Tween-80] in donor compartment, saline solution in acceptor compartment, and semi-permeable cellophane membrane, demonstrated the useful permeation selectivity. Here, (according to lipophilicity) an enhanced permeation of the bicyclic monoterpenes with antiflogistic and antiseptic properties (eucalyptol, camphor and borneol) and, at the same time, suppressed permeation of toxic thujone (not exceeding its permitted applicable concentration) was observed. These properties highlight the pharmaceutical importance of the developed chitosan hydrogel formulating sage essential oil in the dermal applications.

  12. The antibacterial effect of sage extract (Salvia officinalis) mouthwash against Streptococcus mutans in dental plaque: a randomized clinical trial.

    Science.gov (United States)

    Beheshti-Rouy, Maryam; Azarsina, Mohadese; Rezaie-Soufi, Loghman; Alikhani, Mohammad Yousef; Roshanaie, Ghodratollah; Komaki, Samira

    2015-06-01

    The aim of the study was to evaluate the clinical effects of a mouthwash containing Sage (Salvia officinalis) extracts on Streptococcus mutans (SM) causing dental plaque in school-aged children. A double blind clinical trial study was conducted in a dormitory on 70 girls aged 11-14 years having the same socioeconomic and oral hygiene conditions. These students were randomly divided into 2 groups; the first group (N=35) using Sage mouthwash, and the second group (N=35) using placebo mouthwash without active any ingredients. At the baseline, plaque samples obtained from the buccal surfaces of teeth were sent to laboratory to achieve SM colony count. These tests were reevaluated after 21 days of using the mouthwashes. Statistical data analysis was performed using t-student tests with pSage mouthwash significantly reduced the colony count (P=0.001). Average number of colonies in test group was 3900 per plaque sample at the baseline, and 300 after mouthwash application. In the control group, pre-test colony count was 4400 that was reduced to 4000; although this reduction wasn't significant. The Sage mouthwash effectively reduced the number of Streptococcus mutans in dental plaque.

  13. Quantifying restoration effectiveness using multi-scale habitat models: Implications for sage-grouse in the Great Basin

    Science.gov (United States)

    Robert S. Arkle; David S. Pilliod; Steven E. Hanser; Matthew L. Brooks; Jeanne C. Chambers; James B. Grace; Kevin C. Knutson; David A. Pyke; Justin L. Welty; Troy A. Wirth

    2014-01-01

    A recurrent challenge in the conservation of wide-ranging, imperiled species is understanding which habitats to protect and whether we are capable of restoring degraded landscapes. For Greater Sage-grouse (Centrocercus urophasianus), a species of conservation concern in the western United States, we approached this problem by developing multi-scale empirical models of...

  14. 78 FR 65700 - Notice of Availability of the Utah Greater Sage-Grouse Draft Land Use Plan Amendments and...

    Science.gov (United States)

    2013-11-01

    .../Garfield/Antimony, Pinyon, Warm Springs, House Range, Pony Express, Box Elder, Randolph, Park City, and...) Pinyon Management Framework Plan (MFP) (1978) Warm Springs RMP (1987) House Range RMP (1987) Pony Express... lands identified as having the highest value to maintaining sustainable Greater Sage-Grouse populations...

  15. Spitzer sage survey of the large magellanic cloud. II. Evolved stars and infrared color-magnitude diagrams

    NARCIS (Netherlands)

    Blum, R. D.; Mould, J. R.; Olsen, K. A.; Frogel, J. A.; Meixner, M.; Markwick-Kemper, F.; Indebetouw, R.; Whitney, B.; Meade, M.; Babler, B.; Churchwell, E. B.; Gordon, K.; Engelbracht, C.; For, B. -Q.; Misselt, K.; Vijh, U.; Leitherer, C.; Volk, K.; Points, S.; Reach, W.; Hora, J. L.; Bernard, J. -P.; Boulanger, F.; Bracker, S.; Cohen, M.; Fukui, Y.; Gallagher, J.; Gorjian, V.; Harris, J.; Kelly, D.; Kawamura, A.; Latter, W. B.; Madden, S.; Mizuno, A.; Mizuno, N.; Oey, M. S.; Onishi, T.; Paladini, R.; Panagia, N.; Perez-Gonzalez, P.; Shibai, H.; Sato, S.; Smith, L.; Staveley-Smith, L.; Tielens, A.G.G.M; Ueta, T.; Van Dyk, S.; Zaritsky, D.; Werner, M.J.

    Color-magnitude diagrams (CMDs) are presented for the Spitzer SAGE (Surveying the Agents of a Galaxy's Evolution) survey of the Large Magellanic Cloud (LMC). IRAC and MIPS 24 mu m epoch 1 data are presented. These data represent the deepest, widest mid-infrared CMDs of their kind ever produced in

  16. Antioxidant activity and sensory analysis of a rosmarinic acid-enriched extract of garden sage (Salvia officinalis)

    Science.gov (United States)

    A novel extract of S. officinalis (garden sage) was prepared using supercritical carbon dioxide (SC-CO2) extraction, followed by a Soxhlet hot water extraction. The resulting extract was enriched in polyphenols, including rosmarinic acid (RA), which has shown promising health benefits in animals. Th...

  17. OCT2, SSX and SAGE1 reveal the phenotypic heterogeneity of spermatocytic seminoma reflecting distinct subpopulations of spermatogonia

    DEFF Research Database (Denmark)

    Lim, Jasmine; Goriely, Anne; Turner, Gareth Dh

    2011-01-01

    in the normal adult testis. We analysed the expression pattern of OCT2, SSX2-4, and SAGE1 in 36 SS cases and four intratubular SS (ISS) as well as a series of normal testis samples throughout development. We describe for the first time two different types of SS characterized by OCT2 or SSX2-4 immunoexpression......, whilst SAGE1 was exclusively present in a subset of post-pubertal germ cells, most likely B spermatogonia. The presence of OCT2 and SSX2-4 in distinct subsets of germ cells implies that these markers represent germ cells at different maturation stages. Analysis of SAGE1 and SSX2-4 in ISS showed spatial...... differences suggesting ongoing maturation of germ cells during progression of SS tumourigenesis. We conclude that the expression pattern of OCT2, SSX2-4, and SAGE1 supports the origin of SS from spermatogonia and provides new evidence for heterogeneity of this tumour, potentially linked either to the cellular...

  18. DATABASES DEVELOPED IN INDIA FOR BIOLOGICAL SCIENCES

    Directory of Open Access Journals (Sweden)

    Gitanjali Yadav

    2017-09-01

    Full Text Available The complexity of biological systems requires use of a variety of experimental methods with ever increasing sophistication to probe various cellular processes at molecular and atomic resolution. The availability of technologies for determining nucleic acid sequences of genes and atomic resolution structures of biomolecules prompted development of major biological databases like GenBank and PDB almost four decades ago. India was one of the few countries to realize early, the utility of such databases for progress in modern biology/biotechnology. Department of Biotechnology (DBT, India established Biotechnology Information System (BTIS network in late eighties. Starting with the genome sequencing revolution at the turn of the century, application of high-throughput sequencing technologies in biology and medicine for analysis of genomes, transcriptomes, epigenomes and microbiomes have generated massive volumes of sequence data. BTIS network has not only provided state of the art computational infrastructure to research institutes and universities for utilizing various biological databases developed abroad in their research, it has also actively promoted research and development (R&D projects in Bioinformatics to develop a variety of biological databases in diverse areas. It is encouraging to note that, a large number of biological databases or data driven software tools developed in India, have been published in leading peer reviewed international journals like Nucleic Acids Research, Bioinformatics, Database, BMC, PLoS and NPG series publication. Some of these databases are not only unique, they are also highly accessed as reflected in number of citations. Apart from databases developed by individual research groups, BTIS has initiated consortium projects to develop major India centric databases on Mycobacterium tuberculosis, Rice and Mango, which can potentially have practical applications in health and agriculture. Many of these biological

  19. Modeling ecological minimum requirements for distribution of greater sage-grouse leks: implications for population connectivity across their western range, U.S.A.

    Science.gov (United States)

    Knick, Steven T; Hanser, Steven E; Preston, Kristine L

    2013-06-01

    Greater sage-grouse Centrocercus urophasianus (Bonaparte) currently occupy approximately half of their historical distribution across western North America. Sage-grouse are a candidate for endangered species listing due to habitat and population fragmentation coupled with inadequate regulation to control development in critical areas. Conservation planning would benefit from accurate maps delineating required habitats and movement corridors. However, developing a species distribution model that incorporates the diversity of habitats used by sage-grouse across their widespread distribution has statistical and logistical challenges. We first identified the ecological minimums limiting sage-grouse, mapped similarity to the multivariate set of minimums, and delineated connectivity across a 920,000 km(2) region. We partitioned a Mahalanobis D (2) model of habitat use into k separate additive components each representing independent combinations of species-habitat relationships to identify the ecological minimums required by sage-grouse. We constructed the model from abiotic, land cover, and anthropogenic variables measured at leks (breeding) and surrounding areas within 5 km. We evaluated model partitions using a random subset of leks and historic locations and selected D (2) (k = 10) for mapping a habitat similarity index (HSI). Finally, we delineated connectivity by converting the mapped HSI to a resistance surface. Sage-grouse required sagebrush-dominated landscapes containing minimal levels of human land use. Sage-grouse used relatively arid regions characterized by shallow slopes, even terrain, and low amounts of forest, grassland, and agriculture in the surrounding landscape. Most populations were interconnected although several outlying populations were isolated because of distance or lack of habitat corridors for exchange. Land management agencies currently are revising land-use plans and designating critical habitat to conserve sage-grouse and avoid endangered

  20. Modeling ecological minimum requirements for distribution of greater sage-grouse leks: implications for population connectivity across their western range, U.S.A.

    Science.gov (United States)

    Knick, Steven T.; Hanser, Steven E.; Preston, Kristine L.

    2013-01-01

    Greater sage-grouse Centrocercus urophasianus (Bonaparte) currently occupy approximately half of their historical distribution across western North America. Sage-grouse are a candidate for endangered species listing due to habitat and population fragmentation coupled with inadequate regulation to control development in critical areas. Conservation planning would benefit from accurate maps delineating required habitats and movement corridors. However, developing a species distribution model that incorporates the diversity of habitats used by sage-grouse across their widespread distribution has statistical and logistical challenges. We first identified the ecological minimums limiting sage-grouse, mapped similarity to the multivariate set of minimums, and delineated connectivity across a 920,000 km2 region. We partitioned a Mahalanobis D2 model of habitat use into k separate additive components each representing independent combinations of species–habitat relationships to identify the ecological minimums required by sage-grouse. We constructed the model from abiotic, land cover, and anthropogenic variables measured at leks (breeding) and surrounding areas within 5 km. We evaluated model partitions using a random subset of leks and historic locations and selected D2 (k = 10) for mapping a habitat similarity index (HSI). Finally, we delineated connectivity by converting the mapped HSI to a resistance surface. Sage-grouse required sagebrush-dominated landscapes containing minimal levels of human land use. Sage-grouse used relatively arid regions characterized by shallow slopes, even terrain, and low amounts of forest, grassland, and agriculture in the surrounding landscape. Most populations were interconnected although several outlying populations were isolated because of distance or lack of habitat corridors for exchange. Land management agencies currently are revising land-use plans and designating critical habitat to conserve sage-grouse and avoid endangered

  1. Determination of the biologically active flavour substances thujone and camphor in foods and medicines containing sage (Salvia officinalis L.

    Directory of Open Access Journals (Sweden)

    Stühlinger Wolf

    2011-07-01

    Full Text Available Abstract Background The sage plant Salvia officinalis L. is used as ingredient in foods and beverages as well as in herbal medicinal products. A major use is in the form of aqueous infusions as sage tea, which is legal to be sold as either food or medicine. Sage may contain two health relevant substances, thujone and camphor. The aim of this study was to develop and validate an analytical methodology to determine these active principles of sage and give a first overview of their concentrations in a wide variety of sage foods and medicines. Results A GC/MS procedure was applied for the analysis of α- and β-thujone and camphor with cyclodecanone as internal standard. The precision was between 0.8 and 12.6%, linearity was obtained from 0.1 - 80 mg/L. The recoveries of spiked samples were between 93.7 and 104.0% (average 99.1%. The time of infusion had a considerable influence on the content of analytes found in the teas. During the brewing time, thujone and camphor show an increase up to about 5 min, after which saturation is reached. No effect was found for preparation with or without a lid on the pot used for brewing the infusion. Compared to extracts with ethanol (60% vol, which provide a maximum yield, an average of 30% thujone are recovered in the aqueous tea preparations. The average thujone and camphor contents were 4.4 mg/L and 16.7 mg/L in food tea infusions and 11.3 mg/L and 25.4 mg/L in medicinal tea infusions. Conclusions The developed methodology allows the efficient determination of thujone and camphor in a wide variety of sage food and medicine matrices and can be applied to conduct surveys for exposure assessment. The current results suggest that on average between 3 and 6 cups of sage tea could be daily consumed without reaching toxicological thresholds.

  2. Interseasonal movements of greater sage-grouse, migratory behavior, and an assessment of the core regions concept in Wyoming

    Science.gov (United States)

    Fedy, Bradley C.; Aldridge, Cameron L.; Doherty, Kevin E.; O'Donnell, Michael S.; Beck, Jeffrey L.; Bedrosian, Bryan; Holloran, Matthew J.; Johnson, Gregory D.; Kaczor, Nicholas W.; Kirol, Christopher P.; Mandich, Cheryl A.; Marshall, David; McKee, Gwyn; Olson, Chad; Swanson, Christopher C.; Walker, Brett L.

    2012-01-01

    Animals can require different habitat types throughout their annual cycles. When considering habitat prioritization, we need to explicitly consider habitat requirements throughout the annual cycle, particularly for species of conservation concern. Understanding annual habitat requirements begins with quantifying how far individuals move across landscapes between key life stages to access required habitats. We quantified individual interseasonal movements for greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) using radio-telemetry spanning the majority of the species distribution in Wyoming. Sage-grouse are currently a candidate for listing under the United States Endangered Species Act and Wyoming is predicted to remain a stronghold for the species. Sage-grouse use distinct seasonal habitats throughout their annual cycle for breeding, brood rearing, and wintering. Average movement distances in Wyoming from nest sites to summer-late brood-rearing locations were 8.1 km (SE = 0.3 km; n = 828 individuals) and the average subsequent distances moved from summer sites to winter locations were 17.3 km (SE = 0.5 km; n = 607 individuals). Average nest-to-winter movements were 14.4 km (SE = 0.6 km; n = 434 individuals). We documented remarkable variation in the extent of movement distances both within and among sites across Wyoming, with some individuals remaining year-round in the same vicinity and others moving over 50 km between life stages. Our results suggest defining any of our populations as migratory or non-migratory is innappropriate as individual strategies vary widely. We compared movement distances of birds marked using Global Positioning System (GPS) and very high frequency (VHF) radio marking techniques and found no evidence that the heavier GPS radios limited movement. Furthermore, we examined the capacity of the sage-grouse core regions concept to capture seasonal locations. As expected, we found the core regions approach, which was

  3. Summary of science, activities, programs, and policies that influence the rangewide conservation of Greater Sage-Grouse (Centrocercus urophasianus)

    Science.gov (United States)

    Manier, D.J.; Wood, David J.A.; Bowen, Z.H.; Donovan, R.M.; Holloran, M.J.; Juliusson, L.M.; Mayne, K.S.; Oyler-McCance, S.J.; Quamen, F.R.; Saher, D.J.; Titolo, A.J.

    2013-01-01

    The Greater Sage-Grouse, has been observed, hunted, and counted for decades. The sagebrush biome, home to the Greater Sage-Grouse, includes sagebrush-steppe and Great Basin sagebrush communities, interspersed with grasslands, salt flats, badlands, mountain ranges, springs, intermittent creeks and washes, and major river systems, and is one of the most widespread and enigmatic components of Western U.S. landscapes. Over time, habitat conversion, degradation, and fragmentation have accumulated across the entire range such that local conditions as well as habitat distributions at local and regional scales are negatively affecting the long-term persistence of this species. Historic patterns of human use and settlement of the sagebrush ecosystem have contributed to the current condition and status of sage-grouse populations. The accumulation of habitat loss, persistent habitat degradation, and fragmentation by industry and urban infrastructure, as indicated by U.S. Fish and Wildlife Service (USFWS) findings, presents a significant challenge for conservation of this species and sustainable management of the sagebrush ecosystem. Because of the wide variations in natural and human history across these landscapes, no single prescription for management of sagebrush ecosystems (including sage-grouse habitats) will suffice to guide the collective efforts of public and private entities to conserve the species and its habitat. This report documents and summarizes several decades of work on sage-grouse populations, sagebrush as habitat, and sagebrush community and ecosystem functions based on the recent assessment and findings of the USFWS under consideration of the Endangered Species Act. As reflected here, some of these topics receive a greater depth of discussion because of the perceived importance of the issue for sagebrush ecosystems and sage-grouse populations. Drawing connections between the direct effects on sagebrush ecosystems and the effect of ecosystem condition on

  4. A conservation planning tool for Greater Sage-grouse using indices of species distribution, resilience, and resistance.

    Science.gov (United States)

    Ricca, Mark A; Coates, Peter S; Gustafson, K Benjamin; Brussee, Brianne E; Chambers, Jeanne C; Espinosa, Shawn P; Gardner, Scott C; Lisius, Sherri; Ziegler, Pilar; Delehanty, David J; Casazza, Michael L

    2018-06-01

    Managers require quantitative yet tractable tools that identify areas for restoration yielding effective benefits for targeted wildlife species and the ecosystems they inhabit. As a contemporary example of high national significance for conservation, the persistence of Greater Sage-grouse (Centrocercus urophasianus) in the Great Basin is compromised by strongly interacting stressors of conifer expansion, annual grass invasion, and more frequent wildfires occurring in sagebrush ecosystems. Associated restoration treatments to a sagebrush-dominated state are often costly and may yield relatively little ecological benefit to sage-grouse if implemented without estimating how Sage-grouse may respond to treatments, or do not consider underlying processes influencing sagebrush ecosystem resilience to disturbance and resistance to invasive species. Here, we describe example applications of a spatially explicit conservation planning tool (CPT) to inform prioritization of: (1) removal of conifers (i.e., pinyon-juniper); and (2) wildfire restoration aimed at improving habitat conditions for the Bi-State Distinct Population Segment of Sage-grouse along the California-Nevada state line. The CPT measures ecological benefits to sage-grouse for a given management action through a composite index comprised of resource selection functions and estimates of abundance and space use. For pinyon-juniper removal, we simulated changes in land-cover composition following the removal of sparse trees with intact understories, and ranked treatments on the basis of changes in ecological benefits per dollar-unit of cost. For wildfire restoration, we formulated a conditional model to simulate scenarios for land cover changes (e.g., sagebrush to annual grass) given estimated fire severity and underlying ecosystem processes influencing resilience to disturbance and resistance to invasion by annual grasses. For both applications, we compared CPT rankings to land cover changes along with sagebrush

  5. Transcriptome Profiling and In Silico Analysis of the Antimicrobial Peptides of the Grasshopper Oxya chinensis sinuosa.

    Science.gov (United States)

    Kim, In-Woo; Markkandan, Kesavan; Lee, Joon Ha; Subramaniyam, Sathiyamoorthy; Yoo, Seungil; Park, Junhyung; Hwang, Jae Sam

    2016-11-28

    Antimicrobial peptides/proteins (AMPs) are present in all types of organisms, from microbes and plants to vertebrates and invertebrates such as insects. The grasshopper Oxya chinensis sinuosa is an insect species that is widely consumed around the world for its broad medicinal value. However, the lack of available genetic information for this species is an obstacle to understanding the full potential of its AMPs. Analysis of the O. chinensis sinuosa transcriptome and expression profile is essential for extending the available genetic information resources. In this study, we determined the whole-body transcriptome of O. chinensis sinuosa and analyzed the potential AMPs induced by bacterial immunization. A high-throughput RNA-Seq approach generated 94,348 contigs and 66,555 unigenes. Of these unigenes, 36,032 (54.14%) matched known proteins in the NCBI database in a BLAST search. Functional analysis demonstrated that 38,219 unigenes were clustered into 5,499 gene ontology terms. In addition, 26 cDNAs encoding novel AMPs were identified by an in silico approach using public databases. Our transcriptome dataset and AMP profile greatly improve our understanding of O. chinensis sinuosa genetics and provide a huge number of gene sequences for further study, including genes of known importance and genes of unknown function.

  6. Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus

    Directory of Open Access Journals (Sweden)

    Yong Huang

    2017-06-01

    Full Text Available Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690 bp and N50 of 1263 bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.

  7. Plant transcriptomics and responses to environmental stress: an ...

    Indian Academy of Sciences (India)

    3Centre for Environmental Research, Near East University, 33010, Lefkosha, Turkish Republic of the Northern Cyprus. 4Department of ...... Transcriptomic analysis of sense and antisense strands of .... 2008 Stem cell transcriptome profiling via.

  8. Blood transcriptomics: applications in toxicology

    Science.gov (United States)

    Joseph, Pius; Umbright, Christina; Sellamuthu, Rajendran

    2015-01-01

    The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article. PMID:23456664

  9. Seasonal Habitat Use by Greater Sage-Grouse (Centrocercus urophasianus) on a Landscape with Low Density Oil and Gas Development.

    Science.gov (United States)

    Rice, Mindy B; Rossi, Liza G; Apa, Anthony D

    2016-01-01

    Fragmentation of the sagebrush (Artemisia spp.) ecosystem has led to concern about a variety of sagebrush obligates including the greater sage-grouse (Centrocercus urophasianus). Given the increase of energy development within greater sage-grouse habitats, mapping seasonal habitats in pre-development populations is critical. The North Park population in Colorado is one of the largest and most stable in the state and provides a unique case study for investigating resource selection at a relatively low level of energy development compared to other populations both within and outside the state. We used locations from 117 radio-marked female greater sage-grouse in North Park, Colorado to develop seasonal resource selection models. We then added energy development variables to the base models at both a landscape and local scale to determine if energy variables improved the fit of the seasonal models. The base models for breeding and winter resource selection predicted greater use in large expanses of sagebrush whereas the base summer model predicted greater use along the edge of riparian areas. Energy development variables did not improve the winter or the summer models at either scale of analysis, but distance to oil/gas roads slightly improved model fit at both scales in the breeding season, albeit in opposite ways. At the landscape scale, greater sage-grouse were closer to oil/gas roads whereas they were further from oil/gas roads at the local scale during the breeding season. Although we found limited effects from low level energy development in the breeding season, the scale of analysis can influence the interpretation of effects. The lack of strong effects from energy development may be indicative that energy development at current levels are not impacting greater sage-grouse in North Park. Our baseline seasonal resource selection maps can be used for conservation to help identify ways of minimizing the effects of energy development.

  10. Non-target effects on songbirds from habitat manipulation for Greater Sage-Grouse: Implications for the umbrella species concept

    Science.gov (United States)

    Carlisle, Jason D.; Chalfoun, Anna D.; Smith, Kurt T.; Beck, Jeffery L.

    2018-01-01

    The “umbrella species” concept is a conservation strategy in which creating and managing reserve areas to meet the needs of one species is thought to benefit other species indirectly. Broad-scale habitat protections on behalf of an umbrella species are assumed to benefit co-occurring taxa, but targeted management actions to improve local habitat suitability for the umbrella species may produce unintended effects on other species. Our objective was to quantify the effects of a common habitat treatment (mowing of big sagebrush [Artemisia tridentata]) intended to benefit a high-profile umbrella species (Greater Sage-Grouse [Centrocercus urophasianus]) on 3 sympatric songbird species of concern. We used a before–after control-impact experimental design spanning 3 yr in Wyoming, USA, to quantify the effect of mowing on the abundance, nest-site selection, nestling condition, and nest survival of 2 sagebrush-obligate songbirds (Brewer's Sparrow [Spizella breweri] and Sage Thrasher [Oreoscoptes montanus]) and one open-habitat generalist songbird (Vesper Sparrow [Pooecetes gramineus]). Mowing was associated with lower abundance of Brewer's Sparrows and Sage Thrashers but higher abundance of Vesper Sparrows. We found no Brewer's Sparrows or Sage Thrashers nesting in the mowed footprint posttreatment, which suggests complete loss of nesting habitat for these species. Mowing was associated with higher nestling condition and nest survival for Vesper Sparrows but not for the sagebrush-obligate species. Management prescriptions that remove woody biomass within a mosaic of intact habitat may be tolerated by sagebrush-obligate songbirds but are likely more beneficial for open-habitat generalist species. By definition, umbrella species conservation entails habitat protections at broad spatial scales. We caution that habitat manipulations to benefit Greater Sage-Grouse could negatively affect nontarget species of conservation concern if implemented across large spatial extents.

  11. Evaluation of the genetic distinctiveness of Greater Sage-grouse in the Bi-State Planning Area

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.

    2011-01-01

    The purpose of this study was to further characterize a distinct population of Greater Sage-grouse: the population located along the border between Nevada and California (Bi-State Planning Area) and centered around the Mono Basin. This population was previously determined to be genetically distinct from other Greater Sage-grouse populations across their range. Previous genetic work focused on characterizing genetic variation across the species' range and thereby used a coarse sampling approach for species characterization. The goal of this study was to investigate this population further by obtaining samples from breeding locations within the population and analyzing those samples with the same mitochondrial and microsatellite loci used in previous studies. Blood samples were collected in six locations within the Bi-State Planning Area. Genetic data from subpopulations were then compared with each other and also with two populations outside of the Bi-State Planning Area. Particular attention was paid to subpopulation boundaries and internal dynamics by drawing comparisons among particular regions within the Bi-State Planning Area and regions proximal to it. All newly sampled subpopulations contained mitochondrial haplotypes and allele frequencies that were consistent with the genetically unique Bi-State (Mono Basin) Greater Sage-grouse described previously. This reinforces the fact that this group of Greater Sage-grouse is genetically unique and warrants special attention. Maintaining the genetic integrity of this population could protect the evolutionary potential of this population of Greater Sage-grouse. Additionally, the White Mountains subpopulation was found to be significantly distinct from all other Bi-State subpopulations.

  12. The utility of transcriptomics in fish conservation.

    Science.gov (United States)

    Connon, Richard E; Jeffries, Ken M; Komoroske, Lisa M; Todgham, Anne E; Fangue, Nann A

    2018-01-29

    There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers. © 2018. Published by The Company of Biologists Ltd.

  13. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis

    OpenAIRE

    Jones, Beryl M.; Wcislo, William T.; Robinson, Gene E.

    2015-01-01

    Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome fo...

  14. The transcriptome of the Didelphis virginiana opossum kidney OK proximal tubule cell line.

    Science.gov (United States)

    Eshbach, Megan L; Sethi, Rahil; Avula, Raghunandan; Lamb, Janette; Hollingshead, Deborah J; Finegold, David N; Locker, Joseph D; Chandran, Uma R; Weisz, Ora A

    2017-09-01

    The OK cell line derived from the kidney of a female opossum Didelphis virginiana has proven to be a useful model in which to investigate the unique regulation of ion transport and membrane trafficking mechanisms in the proximal tubule (PT). Sequence data and comparison of the transcriptome of this cell line to eutherian mammal PTs would further broaden the utility of this culture model. However, the genomic sequence for D. virginiana is not available and although a draft genome sequence for the opossum Monodelphis domestica (sequenced in 2012 by the Broad Institute) exists, transcripts sequenced from both species show significant divergence. The M. domestica sequence is not highly annotated, and the majority of transcripts are predicted rather than experimentally validated. Using deep RNA sequencing of the D. virginiana OK cell line, we characterized its transcriptome via de novo transcriptome assembly and alignment to the M. domestica genome. The quality of the de novo assembled transcriptome was assessed by the extent of homology to sequences in nucleotide and protein databases. Gene expression levels in the OK cell line, from both the de novo transcriptome and genes aligned to the M. domestica genome, were compared with publicly available rat kidney nephron segment expression data. Our studies demonstrate the expression in OK cells of numerous PT-specific ion transporters and other key proteins relevant for rodent and human PT function. Additionally, the sequence and expression data reported here provide an important resource for genetic manipulation and other studies on PT cell function using these cells. Copyright © 2017 the American Physiological Society.

  15. Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation.

    Science.gov (United States)

    Ye, Wei; Wu, Hongqing; He, Xin; Wang, Lei; Zhang, Weimin; Li, Haohua; Fan, Yunfei; Tan, Guohui; Liu, Taomei; Gao, Xiaoxia

    2016-01-01

    Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation. A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant-pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation. The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of the transcriptome data of agarwood and A. sinensis lays the foundation

  16. Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis.

    Directory of Open Access Journals (Sweden)

    Raja Sekhar Nandety

    Full Text Available BACKGROUND: The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae, is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS: Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(-5 with known proteins. We assigned Gene Ontology (GO terms, Kyoto Encyclopedia of Genes and Genomes (KEGG annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS: Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that

  17. Comparative de novo transcriptome analysis of male and female Sea buckthorn.

    Science.gov (United States)

    Bansal, Ankush; Salaria, Mehul; Sharma, Tashil; Stobdan, Tsering; Kant, Anil

    2018-02-01

    Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE ( PKL ), phytochrome-associated serine/threonine-protein phosphatase ( FYPP ), protein TOPLESS ( TPL ), sensitive to freezing 6 ( SFR6 ), lysine-specific histone demethylase 1 homolog 1 ( LDL1 ), pre-mRNA-processing-splicing factor 8A ( PRP8A ), sucrose synthase 4 ( SUS4 ), ubiquitin carboxyl-terminal hydrolase 12 ( UBP12 ), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.

  18. De novo assembly of pen shell ( Atrina pectinata) transcriptome and screening of its genic microsatellites

    Science.gov (United States)

    Sun, Xiujun; Li, Dongming; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Yang, Aiguo

    2017-10-01

    The pen shell ( Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes (18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats (SSRs) were identified, of them the most abundant type was mono-nucleotide repeats (12902, 55.01%), which was followed by di-nucleotide (8132, 34.68%), tri-nucleotide (2010, 8.57%), tetra-nucleotide (401, 1.71%), and penta-nucleotide (7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.

  19. Visual analysis of transcriptome data in the context of anatomical structures and biological networks

    Directory of Open Access Journals (Sweden)

    Astrid eJunker

    2012-11-01

    Full Text Available The complexity and temporal as well as spatial resolution of transcriptome datasets is constantly increasing due to extensive technological developments. Here we present methods for advanced visualization and intuitive exploration of transcriptomics data as necessary prerequisites in order to facilitate the gain of biological knowledge. Color-coding of structural images based on the expression level enables a fast visual data analysis in the background of the examined biological system. The network-based exploration of these visualizations allows for comparative analysis of genes with specific transcript patterns and supports the extraction of functional relationships even from large datasets. In order to illustrate the presented methods, the tool HIVE was applied for visualization and exploration of database-retrieved expression data for master regulators of Arabidopsis thaliana flower and seed development in the context of corresponding tissue-specific regulatory networks.

  20. The de novo transcriptome and its analysis in the worldwide vegetable pest, Delia antiqua (Diptera: Anthomyiidae).

    Science.gov (United States)

    Zhang, Yu-Juan; Hao, Youjin; Si, Fengling; Ren, Shuang; Hu, Ganyu; Shen, Li; Chen, Bin

    2014-03-10

    The onion maggot Delia antiqua is a major insect pest of cultivated vegetables, especially the onion, and a good model to investigate the molecular mechanisms of diapause. To better understand the biology and diapause mechanism of the insect pest species, D. antiqua, the transcriptome was sequenced using Illumina paired-end sequencing technology. Approximately 54 million reads were obtained, trimmed, and assembled into 29,659 unigenes, with an average length of 607 bp and an N50 of 818 bp. Among these unigenes, 21,605 (72.8%) were annotated in the public databases. All unigenes were then compared against Drosophila melanogaster and Anopheles gambiae. Codon usage bias was analyzed and 332 simple sequence repeats (SSRs) were detected in this organism. These data represent the most comprehensive transcriptomic resource currently available for D. antiqua and will facilitate the study of genetics, genomics, diapause, and further pest control of D. antiqua. Copyright © 2014 Zhang et al.

  1. De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L..

    Directory of Open Access Journals (Sweden)

    Nan Fu

    Full Text Available BACKGROUND: Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding. PRINCIPAL FINDINGS: Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI non-redundant protein database (Nr and Swiss-Prot database respectively, and 10,473 (24.77% unigenes were assigned to Clusters of Orthologous Groups (COG. 21,126 (49.97% unigenes harboring Interpro domains were annotated, in which 15,409 (36.45% were assigned to Gene Ontology(GO categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG. Large numbers of simple sequence repeats (SSRs were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions. CONCLUSIONS: This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

  2. The testis and ovary transcriptomes of the rock bream (Oplegnathus fasciatus: A bony fish with a unique neo Y chromosome

    Directory of Open Access Journals (Sweden)

    Dongdong Xu

    2016-03-01

    Full Text Available The rock bream (Oplegnathus fasciatus is considerably one of the most economically important marine fish in East Asia and has a unique neo-Y chromosome system that is a good model to study the sex determination and differentiation in fish. In the present study, we used Illumina sequencing technology (HiSeq2000 to sequence, assemble and annotate the transcriptome of the testis and ovary tissues of rock bream. A total of 40,004,378 (NCBI SRA database SRX1406649 and 53,108,992 (NCBI SRA database SRX1406648 high quality reads were obtained from testis and ovary RNA sequencing, respectively, and 60,421 contigs (with average length of 1301 bp were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 14,036 contigs that show gender-enriched expressional profile with either testis-enriched (237 contigs or ovary-enriched (581 contigs with RPKM >100. There are 237 male- and 582 female-abundant expressed genes that show sex dimorphic expression. We hope that the gonad transcriptome and those gender-enriched transcripts of rock bream can provide some insight into the understanding of genome-wide transcriptome profile of teleost gonad tissue and give useful information in fish gonad development. Keywords: Gonad transcriptome, Testis, Ovary, Rock bream

  3. Database Description - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name PSCDB Alternative n...rial Science and Technology (AIST) Takayuki Amemiya E-mail: Database classification Structure Databases - Protein structure Database...554-D558. External Links: Original website information Database maintenance site Graduate School of Informat...available URL of Web services - Need for user registration Not available About This Database Database Descri...ption Download License Update History of This Database Site Policy | Contact Us Database Description - PSCDB | LSDB Archive ...

  4. Blood transcriptomics and metabolomics for personalized medicine.

    Science.gov (United States)

    Li, Shuzhao; Todor, Andrei; Luo, Ruiyan

    2016-01-01

    Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

  5. The Human Transcriptome: An Unfinished Story

    Directory of Open Access Journals (Sweden)

    Mihaela Pertea

    2012-06-01

    Full Text Available Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

  6. Transcriptome Analysis in Sheepgrass (Leymus chinensis). A Dominant Perennial Grass of the Eurasian Steppe

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shuangyan [Chinese Academy of Sciences (CAS), Institute of Botany (IB), Beijing; Huang, Xin [Chinese Academy of Sciences (CAS), Institute of Botany (IB), Beijing; Yang, Xiaohan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Gongshe [Chinese Academy of Sciences (CAS), Institute of Botany (IB), Beijing

    2013-07-04

    BACKGROUND: Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. RESULTS: The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. CONCLUSIONS: This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.

  7. Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.

    Science.gov (United States)

    Chen, Shuangyan; Huang, Xin; Yan, Xueqing; Liang, Ye; Wang, Yuezhu; Li, Xiaofeng; Peng, Xianjun; Ma, Xingyong; Zhang, Lexin; Cai, Yueyue; Ma, Tian; Cheng, Liqin; Qi, Dongmei; Zheng, Huajun; Yang, Xiaohan; Li, Xiaoxia; Liu, Gongshe

    2013-01-01

    Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.

  8. Transcriptome analysis and anthocyanin-related genes in red leaf lettuce.

    Science.gov (United States)

    Zhang, Y Z; Xu, S Z; Cheng, Y W; Ya, H Y; Han, J M

    2016-01-29

    This study aimed to analyze the transcriptome profile of red lettuce and identify the genes involved in anthocyanin accumulation. Red leaf lettuce is a popular vegetable and popular due to its high anthocyanin content. However, there is limited information available about the genes involved in anthocyanin biosynthesis in this species. In this study, transcriptomes of 15-day-old seedlings and 40-day-old red lettuce leaves were analyzed using an Illuminia HiseqTM 2500 platform. A total of 10.6 GB clean data were obtained and de novo assembled into 83,333 unigenes with an N50 of 1067. After annotation against public databases, 51,850 unigene sequences were identified, among which 46,087 were annotated in the NCBI non-redundant protein database, and 41,752 were annotated in the Swiss-Prot database. A total of 9125 unigenes were mapped into 163 pathways using the Kyoto Encyclopedia of Genes and Genomes database. Thirty-four structural genes were found to cover the main steps of the anthocyanin pathway, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase. Seven MYB, three bHLH, and two WD40 genes, considered anthocyanin regulatory genes, were also identified. In addition, 3607 simple sequence repeat (SSR) markers were identified from 2916 unigenes. This research uncovered the transcriptomic characteristics of red leaf lettuce seedlings and mature plants. The identified candidate genes related to anthocyanin biosynthesis and the detected SSRs provide useful tools for future molecular breeding studies.

  9. Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome

    Science.gov (United States)

    Yu, Guo-Jun; Wang, Man; Huang, Jie; Yin, Ya-Lin; Chen, Yi-Jie; Jiang, Shuai; Jin, Yan-Xia; Lan, Xian-Qing; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

    2012-01-01

    Background Ganoderma lucidum is a basidiomycete white rot fungus and is of medicinal importance in China, Japan and other countries in the Asiatic region. To date, much research has been performed in identifying the medicinal ingredients in Ganoderma lucidum. Despite its important therapeutic effects in disease, little is known about Ganoderma lucidum at the genomic level. In order to gain a molecular understanding of this fungus, we utilized Illumina high-throughput technology to sequence and analyze the transcriptome of Ganoderma lucidum. Methodology/Principal Findings We obtained 6,439,690 and 6,416,670 high-quality reads from the mycelium and fruiting body of Ganoderma lucidum, and these were assembled to form 18,892 and 27,408 unigenes, respectively. A similarity search was performed against the NCBI non-redundant nucleotide database and a customized database composed of five fungal genomes. 11,098 and 8, 775 unigenes were matched to the NCBI non-redundant nucleotide database and our customized database, respectively. All unigenes were subjected to annotation by Gene Ontology, Eukaryotic Orthologous Group terms and Kyoto Encyclopedia of Genes and Genomes. Differentially expressed genes from the Ganoderma lucidum mycelium and fruiting body stage were analyzed, resulting in the identification of 13 unigenes which are involved in the terpenoid backbone biosynthesis pathway. Quantitative real-time PCR was used to confirm the expression levels of these unigenes. Ganoderma lucidum was also studied for wood degrading activity and a total of 22 putative FOLymes (fungal oxidative lignin enzymes) and 120 CAZymes (carbohydrate-active enzymes) were predicted from our Ganoderma lucidum transcriptome. Conclusions Our study provides comprehensive gene expression information on Ganoderma lucidum at the transcriptional level, which will form the foundation for functional genomics studies in this fungus. The use of Illumina sequencing technology has made de novo transcriptome

  10. De novo sequencing, assembly and characterization of antennal transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae.

    Directory of Open Access Journals (Sweden)

    Haoliang Chen

    Full Text Available Anomala corpulenta is an important insect pest and can cause enormous economic losses in agriculture, horticulture and forestry. It is widely distributed in China, and both larvae and adults can cause serious damage. It is difficult to control this pest because the larvae live underground. Any new control strategy should exploit alternatives to heavily and frequently used chemical insecticides. However, little genetic research has been carried out on A. corpulenta due to the lack of genomic resources. Genomic resources could be produced by next generation sequencing technologies with low cost and in a short time. In this study, we performed de novo sequencing, assembly and characterization of the antennal transcriptome of A. corpulenta.Illumina sequencing technology was used to sequence the antennal transcriptome of A. corpulenta. Approximately 76.7 million total raw reads and about 68.9 million total clean reads were obtained, and then 35,656 unigenes were assembled. Of these unigenes, 21,463 of them could be annotated in the NCBI nr database, and, among the annotated unigenes, 11,154 and 6,625 unigenes could be assigned to GO and COG, respectively. Additionally, 16,350 unigenes could be annotated in the Swiss-Prot database, and 14,499 unigenes could map onto 258 pathways in the KEGG Pathway database. We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection. We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.We produced the first large-scale antennal transcriptome of A. corpulenta, which is a species that has little genomic information in public databases. The identified chemodetection unigenes can promote the molecular mechanistic study of behavior in A. corpulenta. These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

  11. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1991-11-01

    The first edition of the Directory of IAEA Databases is intended to describe the computerized information sources available to IAEA staff members. It contains a listing of all databases produced at the IAEA, together with information on their availability

  12. Native Health Research Database

    Science.gov (United States)

    ... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

  13. Cell Centred Database (CCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging.

  14. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  15. Household characteristics for older adults and study background from SAGE Ghana Wave 1

    Directory of Open Access Journals (Sweden)

    Richard B. Biritwum

    2013-06-01

    Full Text Available Background: Globally, the population aged 60 years and older is projected to reach 22% by 2050. In sub-Saharan Africa, this figure is projected to exceed 8%, while in Ghana, the older adult population will reach 12% by 2050. The living arrangements and household characteristics are fundamental determinants of the health and well-being of this population, data sources about which are increasingly available. Methods: The World Health Organization's Study on global AGEing and adult health (SAGE Wave 1 was conducted in China, Ghana, India, Russian Federation, Mexico, and South Africa between 2007 and 2010. SAGE Ghana Wave 1 was implemented in 2007/08 using face-to-face interviews in a nationally representative sample of persons aged 50-plus, along with a smaller cohort aged 18–49 years for comparison purposes. Household information included a household roster including questions about health insurance coverage for all household members, household and sociodemographic characteristics, status of the dwelling, and economic situation. Re-interviews were done in a random 10% of the sample and proxy interviews done where necessary. Verbal autopsies were conducted for deaths occurring in older adult household members in the 24 months prior to interview. Results: The total household population was 27,270 from 5,178 households. The overall household response rate was 86% and household cooperation rate was 98%. Thirty-four percent of household members were under 15 years of age while 8.3% were aged 65-plus years. Households with more than 11 members were more common in rural areas (57.2% and in the highest income quintile (30.6%. Household members with no formal education formed 24.7% of the sample, with Northern and Upper East regions reaching more than 50%. Only 26.8% of the household members had insurance coverage. Households with hard floors ranged from 25.7% in Upper West to 97.7% in Ashanti region. Overall, 84.9% of the households had access to

  16. Household characteristics for older adults and study background from SAGE Ghana Wave 1.

    Science.gov (United States)

    Biritwum, Richard B; Mensah, George; Minicuci, Nadia; Yawson, Alfred E; Naidoo, Nirmala; Chatterji, Somnath; Kowal, Paul

    2013-06-11

    Globally, the population aged 60 years and older is projected to reach 22% by 2050. In sub-Saharan Africa, this figure is projected to exceed 8%, while in Ghana, the older adult population will reach 12% by 2050. The living arrangements and household characteristics are fundamental determinants of the health and well-being of this population, data sources about which are increasingly available. The World Health Organization's Study on global AGEing and adult health (SAGE) Wave 1 was conducted in China, Ghana, India, Russian Federation, Mexico, and South Africa between 2007 and 2010. SAGE Ghana Wave 1 was implemented in 2007/08 using face-to-face interviews in a nationally representative sample of persons aged 50-plus, along with a smaller cohort aged 18-49 years for comparison purposes. Household information included a household roster including questions about health insurance coverage for all household members, household and sociodemographic characteristics, status of the dwelling, and economic situation. Re-interviews were done in a random 10% of the sample and proxy interviews done where necessary. Verbal autopsies were conducted for deaths occurring in older adult household members in the 24 months prior to interview. The total household population was 27,270 from 5,178 households. The overall household response rate was 86% and household cooperation rate was 98%. Thirty-four percent of household members were under 15 years of age while 8.3% were aged 65-plus years. Households with more than 11 members were more common in rural areas (57.2%) and in the highest income quintile (30.6%). Household members with no formal education formed 24.7% of the sample, with Northern and Upper East regions reaching more than 50%. Only 26.8% of the household members had insurance coverage. Households with hard floors ranged from 25.7% in Upper West to 97.7% in Ashanti region. Overall, 84.9% of the households had access to improved sources of drinking water, with the lowest at

  17. Person-centred communication for emotional support in district nursing: SAGE and THYME model.

    Science.gov (United States)

    Griffiths, Jane

    2017-12-02

    Patients on district nursing caseloads have multiple physical morbidities, and related emotional concerns. District nurses are ideally placed to assess and meet patients' emotional needs but in increasingly stretched workplaces, it is difficult to find time. There is also evidence that district nurses sometimes believe they lack skills to address patients' concerns. Traditional communication skills training is useful for encouraging patients to open up about their concerns, but less helpful at finding workable solutions. District nurses can be afraid to open a 'can of worms' of concerns that they are unable to deal with. SAGE and THYME is a person-centred, evidence-based communication skills model that addresses district nurses' concerns about time and skills. It provides a structure for conversations about concerns, and empowers patients to work with district nurses to find solutions. Research suggests that it is a promising model for district nursing practice.

  18. SAGE II Measurements of Stratospheric Aerosol Properties at Non-Volcanic Levels

    Science.gov (United States)

    Thomason, Larry W.; Burton, Sharon P.; Luo, Bei-Ping; Peter, Thomas

    2008-01-01

    Since 2000, stratospheric aerosol levels have been relatively stable and at the lowest levels observed in the historical record. Given the challenges of making satellite measurements of aerosol properties at these levels, we have performed a study of the sensitivity of the product to the major components of the processing algorithm used in the production of SAGE II aerosol extinction measurements and the retrieval process that produces the operational surface area density (SAD) product. We find that the aerosol extinction measurements, particularly at 1020 nm, remain robust and reliable at the observed aerosol levels. On the other hand, during background periods, the SAD operational product has an uncertainty of at least a factor of 2 during due to the lack of sensitivity to particles with radii less than 100 nm.

  19. In-beam study of {sup 253}No using the SAGE spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Mistry, A.K.; Herzberg, R.D.; Butler, P.A.; Cox, D.M.; Joss, D.T.; Page, R.D.; Seddon, D.; Thornhill, J.; Wells, D. [University of Liverpool, Oliver Lodge Laboratory, Liverpool (United Kingdom); Greenlees, P.T.; Papadakis, P.; Auranen, K.; Grahn, T.; Jakobsson, U.; Julin, R.; Konki, J.; Leino, M.; Pakarinen, J.; Peura, P.; Rahkila, P.; Sandzelius, M.; Scholey, C.; Sorri, J.; Stolze, S.; Uusitalo, J. [University of Jyvaskyla, Department of Physics, Jyvaskyla (Finland); Garnsworthy, A.B.; Ketelhut, S. [University of British Columbia, TRIUMF, Vancouver, British Columbia (Canada); Hauschild, K.; Lopez-Martens, A. [Universite Paris-Sud, CSNSM, CNRS, IN2P3, Orsay (France); Simpson, J. [STFC, Daresbury Laboratory, Daresbury, Warrington (United Kingdom)

    2017-02-15

    The heavy actinide nucleus {sup 253}No (Z = 102) was studied using the (S)ilicon (A)nd (Ge)rmanium (SAGE) spectrometer allowing simultaneous in-beam γ-ray and conversion electron spectroscopy at the accelerator laboratory of the University of Jyvaeskylae. Using the recoil-tagging technique, γ-electron coincidences have allowed for the extension of the level scheme in the lower-spin region of the yrast band. In addition, internal conversion coefficient (ICC) measurements to establish the multipolarity of transitions have been performed. Measurement of the interband-intraband branching ratios supports the assignment of the Nilsson band-head configuration 9/2{sup -}[734] assigned in previous studies. The study shows the viability of combined in-beam electron and γ-ray spectroscopy down to μb cross sections. (orig.)

  20. Solar neutrino oscillation parameters after SNO Phase-III and SAGE Part-III

    International Nuclear Information System (INIS)

    Yang Ping; Liu Qiuyu

    2009-01-01

    We analyse the recently published results from solar neutrino experiments SNO Phase-III and SAGE Part-III and show their constraints on solar neutrino oscillation parameters, especially for the mixing angle θ 12 . Through a global analysis using all existing data from SK, SNO, Ga and Cl radiochemical experiments and long base line reactor experiment KamLAND , we obtain the parameters Δm 12 2 =7.684 -0.208 +0.212 x 10 -5 eV 2 , tan 2 θ 12 =0.440 -0.057 +0.059 . We also find that the discrepancy between the KamLAND and solar neutrino results can be reduced by choosing a small non-zero value for the mixing angle θ 13 . (authors)

  1. Breeding of a new scarlet sage variety Shenzhouhong and its identification by SRAP

    International Nuclear Information System (INIS)

    Fu Qiaojuan; Shen Guozheng; Li Chunnan; Cui Hairui

    2012-01-01

    A new scarlet sage (Salvia splendens) variety Shenzhouhong was obtained by several generation selections from the progeny of the variety Diwang carried by the spacecraft Shenzhou No.4 for space mutagenesis. Shenzhouhong was approved to release by Non-major Crop Identification Committee of Zhejiang Province in December 2008. Compared with its original variety Diwang, Shenzhouhong was significantly improved in survival rate, flowering time and ornamental period of single flower branch. SRAP (sequence-related amplified polymorphism) analysis showed that 17 of 33 pairs of primer combinations tested in total were polymorphic and the genetic similarity coefficient between them was 0.945, suggesting that the genetic variation was happened after space mutagenesis. Our results proved that space mutagenesis was a kind of effective breeding approach for Salvia splendens and the SRAP was an efficient method for analysis of space-induced mutations. (authors)

  2. Discovery of a New Wolf-Rayet Star Using SAGE-LMC

    Science.gov (United States)

    Gvaramadze, V. V.; Chené, A.-N.; Kniazev, A. Y.; Schnurr, O.

    2012-12-01

    We report the first-ever discovery of an extragalactic Wolf-Rayet (WR) star with Spitzer. A new WR star in the Large Magellanic Cloud (LMC) was revealed via detection of its circumstellar shell using 24 μm images obtained in the framework of the Spitzer Survey of the Large Magellanic Cloud (SAGE-LMC). Subsequent spectroscopic observations with the Gemini South resolved the central star in two components, one of which is a WN3b+abs star, while the second one is a B0 V star. We consider the lopsided brightness distribution over the circumstellar shell as an indication that the WR star is a runaway and use this interpretation to identify a possible parent cluster of the star.

  3. Chemical composition of sage (Salvia officinalis L. essential oil from the Rio de Janeiro State (Brazil

    Directory of Open Access Journals (Sweden)

    A. Porte

    2013-01-01

    Full Text Available The purpose of this study was to investigate the chemical composition of the essential oil from fresh leaves of sage (Salvia officinalis L. from Petrópolis, Rio de Janeiro State, for international trade. The oil was isolated by hydrodistillation in a Clevenger-type apparatus and analyzed through a combination of GC-FID and GC-MS. The yield was 2.3 % on dry basis. Forty-seven constituents were identified according to their chromatographic retention indices and mass spectra, corresponding to 94.90 % of the compounds present. The major constituents of the oil were α-thujone (40.90 %, camphor (26.12 %, α-pinene (5.85 % and β-thujone (5.62 %. The essential oil studied was similar to those found in several European countries and can be a valuable product for the small farmers from the Petrópolis region in Rio de Janeiro State.

  4. Sage-femme ou gynécologue ? M.-A. Boivin (1773-1841)

    OpenAIRE

    Carol, Anne

    2011-01-01

    Marie-Anne Boivin a été en son temps une des sages-femmes françaises les plus célèbres. Son parcours professionnel et scientifique est présenté ici, illustrant l’espace laissé aux femmes dans les professions médicales. Reconnue d’abord pour ses ouvrages techniques concernant l’obstétrique, elle sort de son champ traditionnel de compétence pour aborder de façon novatrice la gynécologie naissante, à l’instar des médecins, avec son Traité pratique des maladies de l’utérus (1833), devenu un class...

  5. NIRS database of the original research database

    International Nuclear Information System (INIS)

    Morita, Kyoko

    1991-01-01

    Recently, library staffs arranged and compiled the original research papers that have been written by researchers for 33 years since National Institute of Radiological Sciences (NIRS) established. This papers describes how the internal database of original research papers has been created. This is a small sample of hand-made database. This has been cumulating by staffs who have any knowledge about computer machine or computer programming. (author)

  6. Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species.

    Directory of Open Access Journals (Sweden)

    Elsa Góngora-Castillo

    Full Text Available The natural diversity of plant metabolism has long been a source for human medicines. One group of plant-derived compounds, the monoterpene indole alkaloids (MIAs, includes well-documented therapeutic agents used in the treatment of cancer (vinblastine, vincristine, camptothecin, hypertension (reserpine, ajmalicine, malaria (quinine, and as analgesics (7-hydroxymitragynine. Our understanding of the biochemical pathways that synthesize these commercially relevant compounds is incomplete due in part to a lack of molecular, genetic, and genomic resources for the identification of the genes involved in these specialized metabolic pathways. To address these limitations, we generated large-scale transcriptome sequence and expression profiles for three species of Asterids that produce medicinally important MIAs: Camptotheca acuminata, Catharanthus roseus, and Rauvolfia serpentina. Using next generation sequencing technology, we sampled the transcriptomes of these species across a diverse set of developmental tissues, and in the case of C. roseus, in cultured cells and roots following elicitor treatment. Through an iterative assembly process, we generated robust transcriptome assemblies for all three species with a substantial number of the assembled transcripts being full or near-full length. The majority of transcripts had a related sequence in either UniRef100, the Arabidopsis thaliana predicted proteome, or the Pfam protein domain database; however, we also identified transcripts that lacked similarity with entries in either database and thereby lack a known function. Representation of known genes within the MIA biosynthetic pathway was robust. As a diverse set of tissues and treatments were surveyed, expression abundances of transcripts in the three species could be estimated to reveal transcripts associated with development and response to elicitor treatment. Together, these transcriptomes and expression abundance matrices provide a rich resource

  7. Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

    Science.gov (United States)

    Góngora-Castillo, Elsa; Childs, Kevin L.; Fedewa, Greg; Hamilton, John P.; Liscombe, David K.; Magallanes-Lundback, Maria; Mandadi, Kranthi K.; Nims, Ezekiel; Runguphan, Weerawat; Vaillancourt, Brieanne; Varbanova-Herde, Marina; DellaPenna, Dean; McKnight, Thomas D.; O’Connor, Sarah; Buell, C. Robin

    2012-01-01

    The natural diversity of plant metabolism has long been a source for human medicines. One group of plant-derived compounds, the monoterpene indole alkaloids (MIAs), includes well-documented therapeutic agents used in the treatment of cancer (vinblastine, vincristine, camptothecin), hypertension (reserpine, ajmalicine), malaria (quinine), and as analgesics (7-hydroxymitragynine). Our understanding of the biochemical pathways that synthesize these commercially relevant compounds is incomplete due in part to a lack of molecular, genetic, and genomic resources for the identification of the genes involved in these specialized metabolic pathways. To address these limitations, we generated large-scale transcriptome sequence and expression profiles for three species of Asterids that produce medicinally important MIAs: Camptotheca acuminata, Catharanthus roseus, and Rauvolfia serpentina. Using next generation sequencing technology, we sampled the transcriptomes of these species across a diverse set of developmental tissues, and in the case of C. roseus, in cultured cells and roots following elicitor treatment. Through an iterative assembly process, we generated robust transcriptome assemblies for all three species with a substantial number of the assembled transcripts being full or near-full length. The majority of transcripts had a related sequence in either UniRef100, the Arabidopsis thaliana predicted proteome, or the Pfam protein domain database; however, we also identified transcripts that lacked similarity with entries in either database and thereby lack a known function. Representation of known genes within the MIA biosynthetic pathway was robust. As a diverse set of tissues and treatments were surveyed, expression abundances of transcripts in the three species could be estimated to reveal transcripts associated with development and response to elicitor treatment. Together, these transcriptomes and expression abundance matrices provide a rich resource for

  8. De novo Assembly of Leaf Transcriptome in the Medicinal Plant Andrographis paniculata

    Science.gov (United States)

    Cherukupalli, Neeraja; Divate, Mayur; Mittapelli, Suresh R.; Khareedu, Venkateswara R.; Vudem, Dashavantha R.

    2016-01-01

    Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeq™ 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant non-redundant protein database, gene ontology, and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts—using kyoto encyclopedia of genes and genomes database—revealed 5606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs) in 23,168 transcripts. Assembled sequences of transcriptome of A. paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analysis besides identification of key enzymes involved in the various pathways of secondary metabolism. PMID:27582746

  9. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  10. Aviation Safety Issues Database

    Science.gov (United States)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  11. Combined effects of energy development and disease on greater sage-grouse.

    Directory of Open Access Journals (Sweden)

    Rebecca L Taylor

    Full Text Available Species of conservation concern are increasingly threatened by multiple, anthropogenic stressors which are outside their evolutionary experience. Greater sage-grouse are highly susceptible to the impacts of two such stressors: oil and gas (energy development and West Nile virus (WNv. However, the combined effects of these stressors and their potential interactions have not been quantified. We used lek (breeding ground counts across a landscape encompassing extensive local and regional variation in the intensity of energy development to quantify the effects of energy development on lek counts, in years with widespread WNv outbreaks and in years without widespread outbreaks. We then predicted the effects of well density and WNv outbreak years on sage-grouse in northeast Wyoming. Absent an outbreak year, drilling an undeveloped landscape to a high permitting level (3.1 wells/km² resulted in a 61% reduction in the total number of males counted in northeast Wyoming (total count. This was similar in magnitude to the 55% total count reduction that resulted from an outbreak year alone. However, energy-associated reductions in the total count resulted from a decrease in the mean count at active leks, whereas outbreak-associated reductions resulted from a near doubling of the lek inactivity rate (proportion of leks with a last count = 0. Lek inactivity quadrupled when 3.1 wells/km² was combined with an outbreak year, compared to no energy development and no outbreak. Conservation measures should maintain sagebrush landscapes large and intact enough so that leks are not chronically reduced in size due to energy development, and therefore vulnerable to becoming inactive due to additional stressors.

  12. Automated Oracle database testing

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    Ensuring database stability and steady performance in the modern world of agile computing is a major challenge. Various changes happening at any level of the computing infrastructure: OS parameters & packages, kernel versions, database parameters & patches, or even schema changes, all can potentially harm production services. This presentation shows how an automatic and regular testing of Oracle databases can be achieved in such agile environment.

  13. Inleiding database-systemen

    NARCIS (Netherlands)

    Pels, H.J.; Lans, van der R.F.; Pels, H.J.; Meersman, R.A.

    1993-01-01

    Dit artikel introduceert de voornaamste begrippen die een rol spelen rond databases en het geeft een overzicht van de doelstellingen, de functies en de componenten van database-systemen. Hoewel de functie van een database intuitief vrij duidelijk is, is het toch een in technologisch opzicht complex

  14. Tasakaalus tulemuskaardi sage viga on vääralt määratud näitajad / Mait Raava

    Index Scriptorium Estoniae

    Raava, Mait

    2003-01-01

    Tasakaalus tulemuskaart väljendab strateegiliste tulemusnäitajate põhjuslik-tagajärjelisi seoseid, kuid viga tuleb sageli nende tegurite määratlemisel, kirjutab autor. Skeem. Kommenteerib Sven Heil

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

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...19&lang=en Whole data download - Referenced database Rice Expression Database (RED) Rice full-length cDNA Database... (KOME) Rice Genome Integrated Map Database (INE) Rice Mutant Panel Database (Tos17) Rice Genome Annotation Database

  16. De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.

    Science.gov (United States)

    Tian, Xin-Jie; Long, Yan; Wang, Jiao; Zhang, Jing-Wen; Wang, Yan-Yan; Li, Wei-Min; Peng, Yu-Fa; Yuan, Qian-Hua; Pei, Xin-Wu

    2015-01-01

    The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

  17. Quantifying restoration effectiveness using multi-scale habitat models: implications for sage-grouse in the Great Basin

    Science.gov (United States)

    Arkle, Robert S.; Pilliod, David S.; Hanser, Steven E.; Brooks, Matthew L.; Chambers, Jeanne C.; Grace, James B.; Knutson, Kevin C.; Pyke, David A.; Welty, Justin L.

    2014-01-01

    A recurrent challenge in the conservation of wide-ranging, imperiled species is understanding which habitats to protect and whether we are capable of restoring degraded landscapes. For Greater Sage-grouse (Centrocercus urophasianus), a species of conservation concern in the western United States, we approached this problem by developing multi-scale empirical models of occupancy in 211 randomly located plots within a 40 million ha portion of the species' range. We then used these models to predict sage-grouse habitat quality at 826 plots associated with 101 post-wildfire seeding projects implemented from 1990 to 2003. We also compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe prevalence, and negatively associated with non-native plants and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.09) and not substantially different from burned areas that had not been treated. Restoration sites with quality habitat tended to occur at higher elevation locations with low annual temperatures, high spring precipitation, and high plant diversity. Of 313 plots seeded after fire, none met all sagebrush guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This pattern was similar for summer habitat. Less than 2% of treated plots met winter habitat guidelines. Restoration actions did not increase the probability of burned areas meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, climate, and topography. Our results suggest that sage-grouse are relatively unlikely to use many burned areas within 20 years of fire, regardless of treatment. Understory habitat conditions are more likely to be adequate than overstory

  18. An Interoperable Cartographic Database

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2007-05-01

    Full Text Available The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on the Internet. 

  19. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  20. Nuclear power economic database

    International Nuclear Information System (INIS)

    Ding Xiaoming; Li Lin; Zhao Shiping

    1996-01-01

    Nuclear power economic database (NPEDB), based on ORACLE V6.0, consists of three parts, i.e., economic data base of nuclear power station, economic data base of nuclear fuel cycle and economic database of nuclear power planning and nuclear environment. Economic database of nuclear power station includes data of general economics, technique, capital cost and benefit, etc. Economic database of nuclear fuel cycle includes data of technique and nuclear fuel price. Economic database of nuclear power planning and nuclear environment includes data of energy history, forecast, energy balance, electric power and energy facilities