Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
Project description:Metaproteomic data for Rodriguez-Ramos, et al. interrogating microbial and viral communities of hyporheic river sediments within the Columbia River. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.
Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerably extend be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Microarray analysis were performed with early life stages of zebrafish exposed to 2 sediment extracts from the Upper part of the River Rhine, Germany. The expression profile as then compared to the expression pattern of model toxicants, such as, 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, combining mechanism-specific bioassays as well as chemical analysis of the sediments to the gene expression data has contributed to a more comprehensive view on the hazard potential of the sediments.
