Ceriodaphnia DNA Microarrays

Ceriodaphnia DNA 微阵列

• 批准号: 7681641
• 负责人: Owen Hughes
• 金额: $ 26.53万
• 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/7681641
• 关键词: Algae; Animals; Binding; Bioinformatics; Biological Assay; Biological Sciences; Chemicals; Chloride Ion; Chlorides; Chronic; Cladocera; Complementary DNA; Contracts; Copper; DNA Microarray Chip; DNA Sequence; Data; Databases; Development; Diazinon; Dose; Ecosystem; Elements; Environment; Environmental Monitoring; Exposure to; Gene Expression; Genes; Genomics; Goals; Growth; Health; Human; Label; Libraries; Measures; Methods; Molecular Profiling; Monitor; Oligonucleotide Microarrays; Oligonucleotides; Organism; Pathway interactions; Performance; Pharmacologic Substance; Phase; Printing; Process; Property; Protocols documentation; RNA; Reporting; Research Infrastructure; Reverse Transcriptase Polymerase Chain Reaction; Running; Sampling; Series; Software Design; Technology; Testing; Time; Toxic Environmental Substances; Toxic effect; Toxicity Tests; Toxin; Validation; Work; Zinc Chloride; base; biological systems; cDNA Library; chemical property; chemical release; data management; design; falls; 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特性。然而，迄今为止，尚未开发出针对最常用和接受的环境毒性监测生物之一的基因组基础设施 Ceriodaphnia dubia。在这个 II 期提案中，我们通过使用高通量测序对大量 C. dubia cDNA 进行测序来扩展我们的 I 期工作。序列组装和注释后，我们将打印一个 4x70,000 个元件的寡核苷酸微阵列，代表至少 10,000 个不同的基因。该阵列将用于对四种具有不同化学性质的参考毒素进行毒性测试。每种测试的化学物质都将以三种不同的浓度进行分析。我们将为每种毒素定义表达特征，并尝试将表达结果与已知的毒性机制相关联。此外，我们将在一种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，并记录表达谱如何随时间变化。最后，我们将组装一个高度注释的 Ceriodaphnia 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，用于识别和理解用于测试环境毒性的关键生物体之一——水蚤 Ceriodaphnia dubia 的环境毒性。 DNA 微阵列是一种识别和表征环境毒性的独特而强大的方法，因为它们能够结合许多特定的测试来实现对毒性效应的全球了解。 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化的微阵列，用于学术和商业环境。除了市售的 Ceriodaphnia 微阵列之外，Eon Corporation 将通过基于微阵列的测试的合同性能以及分发包含每个元件/基因的识别、功能和表达信息的表达分析数据库来促进这些阵列的使用。 环境毒性测试技术比目前常用的药物毒性测试技术落后了 15 年。如果没有新技术来识别和表征环境毒素，释放到环境中的化学物质的种类和数量不断增加，将对环境和人类健康造成难以估量的损失。