Unknown,Transcriptomics,Genomics,Proteomics

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The effects of different concentrations of phenanthrene on FHM liver

ABSTRACT: FHMs were exposed to three concentrations of phenanthrene (average measured 29, 287, 1006 ng/L) and fish were sampled after 48hr. There were 20 samples analyzed 5) control liver tissues 5) 29 ng/L phenanthrene exposed liver tissues 5) 287 ng/L phenanthrene exposed liver tissues 5)1006 ng/L phenanthrene exposed liver tissues. There was a total of 20 microarrays processed. In this study, gene expression to a 'dose-response' was investigated after in vivo exposure of fish to phenanthrene.

ORGANISM(S): Pimephales promelas

SUBMITTER: Christopher Martyniuk

PROVIDER: E-GEOD-44839 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the effects of the combination of two PAHs, benzo[a]pyrene (0.5M-NM-<g/L) and phenanthrene (50M-NM-<g/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48h of exposure. The cDNA libraries were constructed according to the SOLiDTM SAGETM protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program (AmiGO v.1.8). The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and a greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated genes (46%), in the experimental group compared to the control group. Out of this total, 327 genes were successfully categorized, 174 down-regulated and 153 up-regulated genes, using gene ontology tool. The final confidence gene network, analyzed in STRING, was composed by 199 nodes of proteins, 124 of them resulted in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, changes in oxidation-reduction processes, disturbances of intracellular signaling and changes in the immune response of discus fish. Also the gene network interactions have showed no central interplay cluster, exhibiting interconnected clusters interactions and sparsely connected sub-networks. These findings highlight that even an acute and sublethal exposure of PAHs can cause metabolism changes that may affect this fish species survival rates. Our findings using the SAGE-method and the SOLiD sequencer showed that this is a powerful tool for gene expression analysis in discus fish, a non-model organism. Transcriptome analysis of differentially expressed genes in liver in benzo[a]pyrene and phenanthrene-exposed and non-exposed fish (N=6 per treatment)

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The effects of different concentrations of phenanthrene on FHM liver

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