Ceriodaphnia DNA Microarrays

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，基因组学基础设施尚未开发用于最常用和公认的环境毒性监测生物之一 模糊网纹蚤在这个第二阶段的提案中，我们通过对大量的C进行测序来扩展我们的第一阶段工作。dubia cDNA的高通量测序。在序列组装和注释后，我们将打印一个4x 70，000个元件的寡核苷酸微阵列，代表至少10，000个不同的基因。该阵列将用于对具有不同化学性质的四种参考毒素进行毒性测试。将在三种不同浓度下对每种受试化学品进行分析。我们将定义每种毒素的表达特征，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效应的低浓度毒素下进行一次为期7天的暴露，并注意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，可以轻松解释和共享杂交数据。本项目旨在开发用于鉴定和理解环境毒性的关键生物之一的DNA微阵列，用于测试环境毒性 水蚤Ceriodaphnia dubia。DNA微阵列是鉴定和表征环境毒性的独特的强有力的方法，因为它们能够联合收割机许多特定的测试，以实现对毒性效应的全面理解。 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，Eon Corporation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布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常用的药物毒性测试技术15年。如果没有识别和表征环境毒素的新技术，释放到环境中的化学物质的种类和数量不断增加，将造成难以估量的环境和人类健康损失。

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.