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Pilot application of hepatic cDNA microarray of the sentinel fish striped sea bream as environmental biomarker

ABSTRACT: Feral organisms are affected by adverse environmental factors present in their habitat. It was hypothesized that transcript expression pattern in a suitable target organ of a sentinel feral organism compared to a reference transcript population may serve as a comprehensive biomarker of these adverse effects. This study was aimed at inquiring the applicability of such biomarker and establishing a procedure for its appropriate utilization. The examined system contains dual-labeled microarray-based evaluation of the hepatic transcript expression pattern in a sentinel fish sampled in two habitats, a polluted (Haifa Bay) and a clean (Dor) site, respectively, for two years. The hepatic expression patterns were compared to a reference RNA assumed to represent specimens that have no exposure history to pollution. The sentinel fish is Lithognathus mormyrus, which inhabits a marine coastal habitat along the Mediterranean coast of Israel. The hepatic transcript expression patterns were evaluated using a 1152-clone cDNA microarray, biased towards pollution-affected genes. The LIMMA software was used to calculate the log2 ratios of expressions (M) and to identify the differentially expressed genes in each sample (adjusted P<0.01). Keywords: Response of fish hepatic gene expression pattern to environmental conditions.

ORGANISM(S): Lithognathus mormyrus

PROVIDER: GSE14673 | GEO | 2009/12/01

SECONDARY ACCESSION(S): PRJNA112371

REPOSITORIES: GEO

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Project description:Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp. Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels. The experiment contains a time serial sampling: T0 = before sampling; T1 = after 3 days of exposure; T2=after 15 days of exposure. In addition, caged eels were placed in 2 sites, Upstream (Up) and Downstream (Do) of the hotspot. 6 samples were dissected per sampling group (5 groups= ToUP; T1UP; T1Do; T2Up; T2Do), 30 samples in total

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Pilot application of hepatic cDNA microarray of the sentinel fish striped sea bream as environmental biomarker

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