Ceriodaphnia DNA Microarrays

Ceriodaphnia DNA 微阵列

• 批准号: 7407595
• 负责人: Owen Hughes
• 金额: $ 28.78万
• 依托单位: EON CORPORATION
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-03 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7407595
• 关键词: Algae; Animals; Binding; Bioinformatics; Biological; Biological Assay; Biological Sciences; Chemicals; Chloride Ion; Chlorides; Chronic; Cladocera; Complementary DNA; Contracts; Copper; DNA Microarray Chip; DNA Microarray format; DNA Sequence; Data; Databases; Development; Diazinon; Dose; Ecosystem; Elements; Environment; Environmental Monitoring; Exposure to; Facility Construction Funding Category; Gene Expression; Genes; Genomics; Goals; Growth; Health; Human; Label; Libraries; Measures; Methods; Molecular Profiling; Monitor; Numbers; Oligonucleotide Microarrays; Oligonucleotides; Organism; Pathway interactions; Performance; Pharmacologic Substance; Phase; Polymerase Chain Reaction; Printing; Process; Property; Protocols documentation; RNA; Range; Reporting; Research Infrastructure; Reverse Transcriptase Polymerase Chain Reaction; Running; Sampling; Series; Software Design; Standards of Weights and Measures; System; Technology; Testing; Time; Toxic Environmental Substances; Toxic effect; Toxicity Tests; Toxin; Validation; Work; Zinc Chloride; base; cDNA Library; chemical property; chemical release; data management; day; design; falls; fenoxycarb; interest; new technology; reproductive; research study; response; vector

DESCRIPTION (provided by applicant): Genomic methods simultaneously report both specific and holistic assessments of biological systems an ideal property when assessing the potential impact of chemicals on ecosystems and the environment. To date, however, genomics infrastructures have not been developed for one of the most commonly used and accepted environmental toxicity monitoring organisms Ceriodaphnia dubia. In this Phase II proposal, we expand on our Phase I work by sequencing a large number of C. dubia cDNAs using high-throughput sequencing. After sequence assembly and annotation, we will print a 4x70,000-element oligonucleotide microarray representing at least 10,000 distinct genes. This array will be used to perform toxicity tests on four reference toxins with different chemical properties. Each of the chemicals tested will be assayed at three different concentrations. We will define expression signatures for each of the toxins and attempt to correlate expression results with known toxicity mechanisms. In addition, we will perform one 7-day exposure at a low concentration of a toxin known to have chronic effects and note how the expression profile changes over time. Finally, we will assemble a highly annotated Ceriodaphnia database that has been integrated into a bioinformatics infrastructure that will allow easy interpretation and sharing of hybridization data.This project aims to develop DNA microarrays for the identification and understanding of environmental toxicity in the one of the key organisms used for testing environmental toxicity the water flea Ceriodaphnia dubia. DNA microarrays are a uniquely powerful method of identifying and characterizing environmental toxicity due to their ability to combine many specific tests to achieve a global understanding of toxic effects. High throughput DNA sequencing and NimbleGen based array synthesis will be used to produce fully annotated and commercial ready microarrays for use both in academic and commercial settings. In addition to commercially available Ceriodaphnia microarrays, Eon Corporation will facilitate use of these arrays through contracted performance of microarray based tests, and distribution of an expression analysis database that incorporates identification, function, and expression information for each element/gene. Technologies for environmental toxicity testing have fallen 15 years behind those now commonly used in pharmaceutical toxicity testing. Without new technologies for identifying and characterizing environmental toxins, the increasing variety and quantity of chemicals released into the environment will mount untold environmental and human health tolls.

描述(由申请人提供)：基因组方法同时报告对生物系统的具体和整体评估，这是评估化学品对生态系统和环境的潜在影响时的理想属性。然而，到目前为止，基因组学基础设施还没有为最常用和最被接受的环境毒性监测生物之一--杜氏沼虾开发出来。在这个第二阶段的提案中，我们通过使用高通量测序对大量的杜氏隐翅虫cDNA进行测序，来扩展我们的第一阶段工作。在序列组装和注释之后，我们将打印一个4x70,000个元素的寡核苷酸微阵列，代表至少10,000个不同的基因。该阵列将用于对四种不同化学性质的参考毒素进行毒性测试。每种被测试的化学物质都将在三种不同的浓度下进行检测。我们将为每种毒素定义表达签名，并试图将表达结果与已知的毒性机制相关联。此外，我们将在已知具有慢性影响的低浓度毒素下进行一次为期7天的暴露，并注意表达谱随时间的变化。最后，我们将组装一个高度注释的Cerodaphnia数据库，该数据库已集成到生物信息学基础设施中，以便轻松解释和共享杂交数据。该项目旨在开发DNA微阵列，用于识别和了解用于测试环境毒性的关键生物之一-水蚤的环境毒性。DNA微阵列是识别和表征环境毒性的一种独特而强大的方法，因为它们能够结合许多特定的测试来实现对毒性影响的全球了解。 高通量DNA测序和基于NimbleGen的阵列合成将用于生产完全注释和商业就绪的微阵列，用于学术和商业环境。除了商业上可用的Cerodaphnia微阵列，意昂公司还将通过基于微阵列的测试的合同性能和包含每个元件/基因的识别、功能和表达信息的表达分析数据库的分发，来促进这些阵列的使用。 环境毒性测试技术已经落后于现在通常用于药物毒性测试的技术15年。如果没有识别和表征环境毒素的新技术，排放到环境中的化学物质的种类和数量越来越多，将会给环境和人类健康带来难以估量的代价。