Ceriodaphnia DNA Microarrays

描述（由申请人提供）：基因组方法同时报告了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的最常用的和公认的环境毒性监测生物之一的Ceriodaphnia dubia。在这个II期提案中，我们通过使用高通量测序对大量双歧杆菌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4x7万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。每一种被测试的化学物质都将以三种不同的浓度进行分析。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联系起来。此外，我们将对已知具有慢性影响的低浓度毒素进行为期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，这将使杂交数据的解释和共享变得容易。本项目旨在开发DNA微阵列技术，用于鉴定和了解环境毒性测试的关键生物之一，水蚤Ceriodaphnia dubia。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作用的全球理解。

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.