The Experts below are selected from a list of 2259 Experts worldwide ranked by ideXlab platform

Daniel L Villeneuve - One of the best experts on this subject based on the ideXlab platform.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow. Environ Toxicol Chem 2016;35:212–217. © 2015 SETAC

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.

  • the fathead minnow in Aquatic Toxicology past present and future
    Aquatic Toxicology, 2006
    Co-Authors: Gerald T. Ankley, Daniel L Villeneuve
    Abstract:

    Abstract This paper reviews the roles of the fathead minnow ( Pimephales promelas ) as a small fish model in the field of Aquatic Toxicology. The species has been (and is) extensively used both for regulatory testing and research, especially in North America. For example, tests with the fathead minnow, ranging from 48-h lethality through partial and full life-cycle assays, are routinely used for regulatory programs aimed at assessing potential risks of new chemicals such as high-production volume materials and pesticides, as well as impacts of complex mixtures like effluents. The species also has been used for a wide variety of research applications focused on topics like the development of quantitative structure–activity relationship models, mixture toxicity, extrapolation of the effects of chemicals across species, and understanding the results of laboratory assays relative to impacts in the field. Attributes of the fathead minnow also make it an excellent model for addressing new challenges in Aquatic Toxicology, including identification of sensitive life-stages/endpoints for chemicals with differing modes/mechanisms of action, predicting population-level effects based on data collected from lower levels of biological organization, and exploring/understanding the emerging role of genomics in research and regulation.

Robert A Hoke - One of the best experts on this subject based on the ideXlab platform.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow. Environ Toxicol Chem 2016;35:212–217. © 2015 SETAC

Gerald T. Ankley - One of the best experts on this subject based on the ideXlab platform.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow. Environ Toxicol Chem 2016;35:212–217. © 2015 SETAC

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.

  • the fathead minnow in Aquatic Toxicology past present and future
    Aquatic Toxicology, 2006
    Co-Authors: Gerald T. Ankley, Daniel L Villeneuve
    Abstract:

    Abstract This paper reviews the roles of the fathead minnow ( Pimephales promelas ) as a small fish model in the field of Aquatic Toxicology. The species has been (and is) extensively used both for regulatory testing and research, especially in North America. For example, tests with the fathead minnow, ranging from 48-h lethality through partial and full life-cycle assays, are routinely used for regulatory programs aimed at assessing potential risks of new chemicals such as high-production volume materials and pesticides, as well as impacts of complex mixtures like effluents. The species also has been used for a wide variety of research applications focused on topics like the development of quantitative structure–activity relationship models, mixture toxicity, extrapolation of the effects of chemicals across species, and understanding the results of laboratory assays relative to impacts in the field. Attributes of the fathead minnow also make it an excellent model for addressing new challenges in Aquatic Toxicology, including identification of sensitive life-stages/endpoints for chemicals with differing modes/mechanisms of action, predicting population-level effects based on data collected from lower levels of biological organization, and exploring/understanding the emerging role of genomics in research and regulation.

Frank R Burns - One of the best experts on this subject based on the ideXlab platform.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.

  • sequencing and de novo draft assemblies of a fathead minnow pimephales promelas reference genome
    Environmental Toxicology and Chemistry, 2016
    Co-Authors: Frank R Burns, Daniel L Villeneuve, Gerald T. Ankley, Amarin L Cogburn, Eric R Waits, Yunjuan Chang, Victor Llaca, Stephane Deschamps, Raymond E Jackson, Robert A Hoke
    Abstract:

    The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both Aquatic Toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow. Environ Toxicol Chem 2016;35:212–217. © 2015 SETAC

Xuefang Liang - One of the best experts on this subject based on the ideXlab platform.

  • toxicogenomic applications of chinese rare minnow gobiocypris rarus in Aquatic Toxicology
    Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2016
    Co-Authors: Xuefang Liang
    Abstract:

    Abstract Rare minnow (Gobiocypris rarus), a Chinese native species, are an excellent emerging model organism for Aquatic toxicity testing and chemical safety assessment. “Big data” omics approaches (i.e., genomics, proteomics, and metabolomics) to inform mechanistic Toxicology are now applied to studies in rare minnows to better understand toxicity and molecular pathways perturbed by chemicals. This review highlights recent applications of toxicogenomics to study changes in the gene and protein expression profiles in rare minnows in response to chemicals. Here we briefly describe studies that utilized cDNA microarrays in characterization of the cellular effects of rare minnows in single and mixed chemical exposures. Then we compare gel-based proteomics studies in liver of rare minnows following treatment with endocrine disrupting chemicals including 17β-estradiol, 17α-methyltestosterone, pentachlorophenol, and perfluorooctanoic acid. A total of 90 proteins identified in these studies were functionally annotated and categorized. These responsive proteins have roles in biological processes that include metabolism (37.8%), response to oxidation/chemicals (16.7%), signal transduction (11.1%), transport (10%), cytoskeleton (6.7%) and others (17.8%). In addition, recent investigations of endocrine disrupting effects and neurotoxicity of benzotriazole, an emerging contaminant, are summarized. The objective is to continue to enrich genome and protein databases for this species and to integrate molecular datasets to consider temporal effects and complex regulation at the level of the genome and proteome.