Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna

Quantification of differentially expressed genes in Daphnia magna exposed to rubber wastewater

In this study, differentially expressed genes (DEGs) were investigated in Daphnia magna exposed to rubber wastewater using an annealing control primer (ACP)-based polymerase chain reaction (PCR) and real-time PCR. Among three identified DEGs, two genes (DEG1 and DEG2) were up-regulated, and DEG1 expression was well-correlated to a logarithm of rubber wastewater concentration (r2=0.971, p<0.0001). In addition, DEG1 expression in D. magna exposed to rubber wastewater was strongly correlated with that of D. magna exposed to Zn (r2=0.9513, p<0.05), suggesting that the induction of DEG1 was caused by Zn, which is the dominant toxicant in rubber wastewater. In addition, DEG1 expression was more sensitive to toxicants than immobility, which is the conventional endpoint in toxicity tests using D. magna. The lowest observed effect concentrations (LOEC) determined using immobility tests were 2.5% for rubber wastewater and 1.6mgl(-1) for Zn. In contrast, a significant increase in DEG1 expression was observed at exposure concentrations of as low as 0.6% rubber wastewater and 0.2mgl(-1) Zn. These results indicate that DEG1 is a sensitive and quantitative biomarker of water and wastewater containing Zn.

Fluorescent RNA arbitrarily primed polymerase chain reaction. A new differential display approach to detect contaminant-induced alterations of gene expression in wildlife species

Differential display polymerase chain reaction (PCR) can facilitate the identification of novel molecular end points related to contaminant exposure in a wide range of species. To date, various differential display methodologies have been described in detail. Herein, we describe a modification of the RNA arbitrarily primed PCR (RAP-PCR) method that involves the fluorescent labeling of cDNA transcripts via 5' rhodamine-labeled 18-mer arbitrary primers. These arbitrary primers typically bind to the coding regions of cDNA, which simplifies the downstream identification of contaminant-responsive genes. The technique has been aptly named fluorescent RNA arbitrarily primed PCR, FRAP-PCR, and has been successfully utilized with several avian species and RNA sources (e.g., cultured cells, tissue). This straightforward, safe, and cost-effective approach represents a useful alternative to the radiometric-based RAP-PCR method.

Recent applications of DNA microarray technology to toxicology and ecotoxicology

Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be used both to provide information about the mechanism of action of the toxicant and to form a sort of "genetic signature" for the identification of toxic products. The development of high-quality, commercially available gene arrays has allowed this technology to become a standard tool in molecular toxicology. Several national and international initiatives have provided the proof-of-principle tests for the application of gene expression for the study of the toxicity of new and existing chemical compounds. In the last few years the field has progressed from evaluating the potential of the technology to illustrating the practical use of gene expression profiling in toxicology. The application of gene expression profiling to ecotoxicology is at an earlier stage, mainly because of the the many variables involved in analyzing the status of natural populations. Nevertheless, significant studies have been carried out on the response to environmental stressors both in model and in nonmodel organisms. It can be easily predicted that the development of stressor-specific signatures in gene expression profiling in ecotoxicology will have a major impact on the ecotoxicology field in the near future. International collaborations could play an important role in accelerating the application of genomic approaches in ecotoxicology.

Identification of a gene induced in conjugation-promoted cells of toxic marine dinoflagellatesAlexandrium tamarenseandAlexandrium catenellausing differential display analysis

Marine dinoflagellates Alexandrium tamarense and Alexandrium catenella produce toxins that cause paralytic shellfish poisoning (PSP). A detailed mechanism of encystment is necessary for a better understanding of bloom dynamics and the toxic effect of these organisms. In this study, a cDNA that was up-regulated in conjugation-promoted cells at encystment was identified using differential display. It encoded a polypeptide of 195 amino acids with a molecular weight of 20,900 Da. The deduced amino acid sequence of this cDNA showed 62% similarity with the polypeptide encoded by SPS19, a gene that is activated specifically during spore maturation and spore wall formation in Saccharomyces cerevisiae. Therefore, the cDNA obtained was termed an SPS19 homolog in this study. The expression levels of the SPS19 homolog were highest immediately after the promotion of conjugation and decreased sequentially later, a pattern similar to that of SPS19 in the sporulation of S. cerevisiae in terms of the time of induction and the duration of expression. These similarities between the SPS19 homolog and SPS19 suggested that the putative function of the SPS19 homolog might be an involvement in encystment. RT-PCR showed that the expression of the SPS19 homolog was highest in conjugation-promoted cells but low in vegetative cells. The SPS19 homolog was believed to be expressed constantly in order for cells to respond rapidly to environmental changes and ensure encystment. Characterization of the identified gene might help in understanding the mechanism of encystment.