Modeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solvents

脱卤球菌基因网络建模和氯化溶剂生物修复生物指示剂测定的开发

• 批准号: 0731169
• 负责人: Ruth Richardson
• 金额: $ 32.46万
• 依托单位: Cornell University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2011-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0731169&HistoricalAwards=false
• 关键词: Modeling; gene; networks; Dehalococcoides; development

CBET-0731169Ruth RichardsonCornell UniversityModeling gene networks in Dehalococcoides and development of bioindicator assays for bioremediation of chlorinated solventsThis project will study how cultures of Dehalococcoides (DHC), the genus of bacteria involved in dechlorinating and degrading chlorinated hydrocarbon contaminants like TCE (trichloroethene) respond to environmental conditions. Based on this work, the investigators will develop appropriate dehalorespiration bioindicator assays that can be applied at contaminated field sites. The work will combine laboratory studies with field biomass sampling. In the first phase of work, two well-studied DHC-containing mixed cultures will be grown under a wide range of conditions and a subset of studies will include chemical stressors (O2, pH, chloroform). Heterogeneous datasets (genomics, chemical levels, dehalorespiration rates, populations) will be collected and incorporated into systems biology algorithms to generate gene network models. In the second phase, field biomass will be collected at bioaugmented sites to compare gene expression profiles of field-deployed DHC with those predicted from lab-derived models. In the final phase, genes highly correlated with dehalorespiration types and rates will be selected as bioindicators. Two types of bioindicator assays will be developed for field application?quantitative reverse transcription PCR (qRTPCR) and dipstick-style RNA-biosensors. The assays will be tested for robustness against other DHC strains and, ultimately, against field-sampled biomass.

CBET-0731169 Ruth Richardson Cornell University对脱卤球菌属中的基因网络进行建模，并开发用于氯化溶剂生物修复的生物指示剂试验本项目将研究脱卤球菌属(DHC)的培养如何对环境条件做出反应。在这项工作的基础上，研究人员将开发可应用于受污染现场的适当的脱卤素呼吸生物指示剂分析方法。这项工作将结合实验室研究和野外生物量采样。在第一阶段的工作中，将在广泛的条件下培养两种经过充分研究的含有DHC的混合培养物，并进行包括化学应激源(O2、pH、氯仿)的子集研究。将收集不同种类的数据集(基因组学、化学水平、脱卤素呼吸率、种群)，并将其纳入系统生物学算法，以生成基因网络模型。在第二阶段，将在生物增强地点收集田间生物量，以比较田间部署的DHC的基因表达谱与实验室衍生模型预测的基因表达谱。在最后阶段，与脱卤素呼吸类型和速率高度相关的基因将被选为生物指标。将开发两种用于现场应用的生物指示剂检测方法--定量逆转录聚合酶链式反应(QRTPCR)和试纸杆式RNA生物传感器。这些检测将测试对其他DHC菌株的稳健性，最终测试对野外采样的生物量的稳健性。