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Bioaccumulation and toxicity tests using benthic invertebrates such as the estuarine amphipod Leptocheirus plumulosus are typically used to assess the ecological risk associated with contaminated sediments. Despite their ecological and regulatory importance, little is known about such species at the genetic level. To begin understanding cellular and genetic responses of L. plumulosus to contaminants, we isolated several of their genes and developed quantitative assays to measure the effects of water exposures to 2, 4, 6-trinitrotoluene and phenanthrene on gene expression. Real-time polymerase chain reaction (PCR) assays demonstrated that the expression of the genes for actin and a retrotransposon, hopper, was dependent on the exposure and tissue concentrations of those chemicals. Our data suggests that exposure to the explosive 2, 4, 6-trinitrotoluene and phenanthrene may induce movement of hopper resulting in unexpected genotoxic results.