Abstract
Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics.
Highlights
The term “ecotoxicogenomics” has been introduced [1,2,3,4,5] to describe the toxicogenomic context into ecotoxicological field (Figure 1) [6]
The DNA microarrays applied to ecotoxicology have ranged from nylon membranes that are custom spotted with a couple dozen selected cDNAs [30,31,32] to commercially available, high-density arrays consisting of thousands of oligonucleotides synthesized directly onto a solid support such as a glass slide [33,34,35]
An ecotoxicogenomic assessment of D. magna with the use of expressed sequence tags (ESTs) and the database has been conducted [56]. Based on this sequence information, an oligonucleotide-based DNA microarray has been developed in order to determine the acute toxicogenomic profiling of D. magna in response to various types of chemical stressors, including copper sulfate (CuSO4), hydrogen peroxide (H2O2), pentachlorophenol (PCP), and β-naphthoflavone as testing substances exerting distinct toxicities
Summary
The term “ecotoxicogenomics” has been introduced [1,2,3,4,5] to describe the toxicogenomic context into ecotoxicological field (Figure 1) [6]. Genomic tools can facilitate ecology and evolutionary biology studies, allowing advance fundamental information and addressing the future issues related to chemical effects on environmental and human health. Purpose of this framework include: identification of ecological performance-regulated gene loci; functional analysis of ecological performance-related traits; evaluating individual, population, community, and ecosystem responses to the environment; examining the degree and significance of genetic variation among ecological performance-related traits [2]. The omic tools are useful for investigating important issues as follows: what are inducible genes and their functions; is there variation in gene expression in response to environmental change; is the variation adaptive; what are the consequences of the genetic variation-mediated molecular transformations at ecosystem-, community-, and population-level. We mainly discuss three aspects: the commonly used omic technologies, including genomic (or mRNA-transcriptomic), proteomic, metabolomic analyses, and more recently emerged epigenetic technology; collective technologies (i.e., cDNA microarray, high-density oligonucleotide arrays, suppression subtractive hybridization PCR or high-throughput pyrosequencing, two-dimensional gel electrophoresis, fluorescence difference gel electrophoresis, ProteinChip, surface-enhanced laser desorption ionization (SELDI) mass spectrometry, and nuclear magnetic resonance) in conjunction with statistical testing or multivariate analysis; as well as development of bioinformatics tools and their application to aquatic ecotoxicology studies
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