Dataset Information

Exposure to different copper forms – nanoparticles, nanowires, salt and field aged: gene expression profiling in Enchytraeus crypticus

ABSTRACT: The testing of NMs under the currently available standard toxicity tests does not cover many of the NMs specificities. One of the current recommended approaches forward lays on understanding the mechanisms of action as these can help predicting long term effects and safe-by-design production. Copper nanomaterials (Cu-NMs) usage has been highly increasing with the concern in terms of exposure, effect and associated risks. In the present study we used the high-throughput gene expression tool developed for Enchytraeus crypticus (44Kx4 Agilent microarray) to study to the effect of exposure to several copper forms. The copper treatments include two NMs (spherical and wires) and two copper-salt treatments (CuNO3 spiked and Cu field historical contamination). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.

ORGANISM(S): Enchytraeus crypticus

PROVIDER: GSE69792 | GEO | 2017/06/13

SECONDARY ACCESSION(S): PRJNA286782

REPOSITORIES: GEO

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Project description:Despite the increased utilization of nanoparticles, the behavior and effect in the environment is largely unknown and few resources are available for health and environmental effect studies. Enchytraeids are extensively used in studies of soil ecotoxicology and recently, a cDNA microarray for Enchytraeus albidus was developed, allowing also toxicogenomic studies in this species. These organisms are ecologically relevant small worms that indirectly contribute to the regulation and degradation of organic matter. In this study we compared the gene expression profiles of E. albidus when exposed to copper-salt (CuCl2) and copper nanoparticles (Cu-NP) spiked soil. The worms were exposed for 48 hours in soil to a range of concentrations. Microarray hybridizations revealed different response patterns between copper-salt and copper nanoparticles exposed organisms, these differences are mainly related with transcripts involved in the energy metabolism of the organisms. Despite unknown gene function in the data-set there are indications that Cu-salt and Cu-NP exposure induced specific gene level responses. Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control soil (from Hygum site in Denmark) and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).