Project description:Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.
Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals.
Project description:Analyses of transcriptomic responses to heavy metal exposure in Manila clam collected in Venice lagoon areas characterized by different anthropogenic impact
Project description:We examined gene expression profiling of native mussels that were sampled in early summer 2003 from sites of the Venice lagoon area known to be differently affected by chemical pollution: Sites 1 and 2 close to the industrial district of Marghera and Site 3 close to the Lido lagoon outlet. Site 4, a current mussel farm located offshore, has been chosen as source of reference targets for microarray hybridizations. We have limited the preliminary assessment to the digestive gland. Digestive gland total RNA of each Site was hybridized in competition with the offshore mussels (Site 4 - Reference) and the relative abundance of each gene was measured by directly comparing fluorescent signals for each probe. We carried out two separate hybridizations for each site of the Venice lagoon area.. Keywords = digestive gland Keywords = Venice lagoon Keywords = chemical pollution Keywords = native mussels Keywords = transcriptional profiling Keywords: ordered
Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals. In this study, we analyzed 64 samples (pools of 5 digestive gland). Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
Project description:A Ruditapes philippinarum microarray platform was developed to assess variations on transcritpomic response to copper exposures in Manila clam colelctted in Venice lagoon areas subjected to different anthropogenic impact
Project description:DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact. A comparative analysis of gene expression was conducted between Manila clam from lowly-polluted Chioggia and Colmata area and polluted Marghera site.
Project description:To access the nutritional quality of the Ruditapes philippinarum, a comprehensive quality evaluation procedure is always important to be established. In this study, fifteen nutritional quality evaluation indicators of R. philippinarum from 7 months were analyzed, and the most important indicators were determined using a combination of multiple chemometric methods such as correlation analysis (CA), principal component analysis (PCA), and system cluster analysis (SCA). Significant differences in nutritional quality were observed across the 7 months, as per the ANOVA results (P < 0.05). The coefficient of variation values for the fifteen evaluation indicators for R. philippinarum across 7 months was 1.67-43.47%. The CA results revealed that some indicators were correlated to each other within a certain range. Four principal components with eigen-values > 1 were obtained with PCA, and a cumulative contribution of 92.11% was achieved. In addition, four essential quality indicators were extracted using SCA. Using these four indicators, a simple and efficient procedure can be applied for quality control in aquaculture.
