Project description:The potential of an hepatic transcriptome expression profile, evaluated in a sentinel feral fish, to serve as an environmental biomarker was examined. Gene expression profiles of individuals of Lithognathus mormyrus were examined using a cDNA microarray and were correlated to the set of environmental exposure conditions at their site and date of collection. The clusters of individual gene expression profiles were reasonably related to the fish samples and several sample-specific clusters of genes, designated gene signatures of the sample, were determined. The relationship between transcriptome expression and the fish samples indicated a potential for their utilization as an environmental biomarker.
Project description:The potential of an hepatic transcriptome expression profile, evaluated in a sentinel feral fish, to serve as an environmental biomarker was examined. Gene expression profiles of individuals of Lithognathus mormyrus were examined using a cDNA microarray and were correlated to the set of environmental exposure conditions at their site and date of collection. The clusters of individual gene expression profiles were reasonably related to the fish samples and several sample-specific clusters of genes, designated gene signatures of the sample, were determined. The relationship between transcriptome expression and the fish samples indicated a potential for their utilization as an environmental biomarker. Ten fish were sampled at each of two sites (Dor, Israel and Haifa, Israel) each of two years (2007 and 2008) for a total of 40 fish. All fish were hybridized to a common reference RNA population using a dye-swap design. Hence, each fish was hybridized twice vs. the reference RNA. The reference RNA was an equalized pool of the RNAs from all 10 fish comprising sample D7.
Project description:Changes in hepatic gene expression profiles upon exposures to cadmium applied by feeding or intra-peritoneal injections were identified in the striped sea bream (Lithognathus mormyrus) using cDNA microarray platform. Two groups of four fish were exposed to fed and injected CdCl2, respectively. Additional eight untreated fish were used as a reference group, pooled into 4 hepatic RNA preparations. The isolated hepatic mRNAs were hybridized, after conversion to labeled cDNAs, onto the microarray followed by slide scanning, imaging and analysis. Four parameters: M, meanA, P-value and B were calculated for each unique spot, for both cadmium-fed vs. reference fish (sample1) and cadmium-injected vs. reference fish (sample2). These parameters enable evaluation of hybridization intensity as well as statistical testing of differential expression. Keywords: Response to exposure to cadmium
Project description:The study was aimed at examining the effect of the model organic oxygen reactive species (ROS) tert-Butyl Hydroperoxide (tBHP) on hepatic multi-gene expression patterns of the fish Lithognathus mormyrus. Fish were exposed to injected tBHP followed by extraction of RNA from their livers. The corresponding labeled cDNAs of treated versus control fish were applied onto a cDNA microarray of ~1500 unique sequences and differentially expressed genes were identified. The hepatic profile of the in individual fish versus a reference RNA was the basic biomarker parameter. M, the log2 ratio of gene expression (M) was calculated from the imaged hybridization results by the LIMMA software (R environment) used also to statistically determine the differentially expressed genes in the various treatments. EXPANDER4.1 software was used to hierarchically cluster M profiles of individual fish across genes. This clustering was used as a preliminary step aimed at distinguishing groups of similarly expressed genes across the treatments. Gene annotation was aimed at more educated interpretation of the results.
