Effects of soil properties and time of exposure on gene expression of Enchytraeus albidus (Oligochaeta).
Ontology highlight
ABSTRACT:
ORGANISM(S): Enchytraeus albidus
SUBMITTER: Susana Gomes
PROVIDER: E-GEOD-27700 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level, through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on gene expression in E. albidus during exposure periods of 2 days, 4 days and 3 weeks, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al., 2011) The main objectives of this study were: 1) to assess changes in gene expression of E. albidus over time, and 2) to identify molecular markers for natural and chemical exposures. Results showed a clear influence of exposure time in gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects at energy metabolism and cell growth level. Fluorescently labelled cDNA, from enchytraeids exposed during 4 days and 3 weeks to control soil (LUFA 2.2) and to the different exposure conditions 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).
2011-08-31 | E-GEOD-26896 | biostudies-arrayexpress
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).
2011-09-07 | E-GEOD-26331 | biostudies-arrayexpress
Project description:Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types. Hybridization onto the developed microarray revealed several genes with homology to known sequences. Genes of interest were confirmed through real-time polymerase chain reaction. It was possible to discriminate between natural and chemical stressors and chemical concentrations. Gene responses were detected under conditions known to have effects in the reproduction of individuals. It was confirmed that the integration of different endpoints improves the assessment process and enhances the understanding of the modes of action of stressors. The chemical stressM-bM-^@M-^Sinduced genes were related to factors such as immune response, stress response, metabolic processes, and/or signal transduction. The present study represents the first step of a gene-level study in the ecologically relevant and standard test species E. albidus. It demonstrates the usefulness of cDNA normalization in the production of cDNA libraries of ecotoxicological standard organisms that are not genome models like E. albidus. Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control LUFA 2.2 (Cy3) soil 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 Genepix software 5.0 (Axon Instruments). 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 M-bM-^@M-^S linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-HochbergM-bM-^@M-^Ys method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).
2011-03-30 | E-GEOD-18569 | biostudies-arrayexpress
Project description:Changes in soil properties (e.g. pH, organic matter content, granulometry) can influence chemical toxicity to organisms and act alone as stressors. Previous studies on Enchytraeus albidus showed that changes in soil properties caused effects on reproduction and avoidance behavior and also oxidative stress. In addition, results at the transcritptomic level indicated changes in gene expression profile due to soil properties changes. In this study, E. albidus was exposed to modified versions of the artificial standard OECD soil (different pH, OM and clay content) in different exposure times (2, 4 and 8 days). The gene expression profile was characterized using a class comparison statistical analysis. Results indicated that the transcriptional response was time dependent, with different genes being affected at different time points. Results also showed some genes (and biological functions) being affected in a soil specific way.
2011-09-07 | GSE27700 | GEO
Project description:The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses. In this study, gene expression and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction. Furthermore, genes involved in oxygen transport and heme metabolism (hemoglobin, δ-aminolevilunate synthase) were down-regulated. Applying a Partial Least Squares regression on nickel fingerprints and biochemical (sub)organismal parameters revealed a set of co-varying genes (hemoglobin, RNA terminal phosphate cyclase, a ribosomal protein and an âunknownâ gene fragment). An inverse relationship was seen between the mRNA expression levels of different cuticula proteins and available energy reserves. In addition to the nickel exposure, daphnids were exposed to binary mixtures of nickel and cadmium or nickel and lead. Using multivariate analysis techniques, the mixture gene expression fingerprints (Ni2++Cd2+, Ni2++Pb2+) were compared to those of the single metal treatments (Ni2+, Cd2+, Pb2+). It was hypothesized that the molecular fingerprints of the mixtures would be additive combinations of the gene expression profiles of the individual compounds present in the mixture. However, our results clearly showed additionally affected pathways after mixture treatment (e.g. additional affected genes involved in carbohydrate catabolic processes and proteolysis), indicating interactive molecular responses which are not merely the additive sum of the individual metals. These findings, although indicative of the complex nature of mixture toxicity evaluation, underline the potential of a toxicogenomics approach in gaining more mechanistic information on the effects of single compounds and mixtures. In general, a universal reference design was used. The following analysis (normalization and statistical analysis) was performed. Spots were identified and ratioâs quantified by means of the Genepix software 5.0 (Axon Instruments). Subsequently, a MIAME compliant platform, the BioArray Software Environment Database (BASE 1.2.12, http://www.islab.ua.ac.be/base/) was used for storage, further evaluation and succeeding statistical analysis of the microarray datasets. After a local background correction, spots with a foreground larger than the mean local background +2 standard deviations for one or both colours were selected for further analysis. The Log2 transformed Cy3/Cy5 ratio data were normalized by implementation of a Locally Weighed Scatterplot Smoothing (Lowess) (Yang et al., 2002) step, which is an intensity-based method. Significant vertical cut-off values of log -0.85 and 0.85 were determined through multiple self-self hybridizations. These were performed by labelling the same biological material with both Cy3 and Cy5 dyes and hybridizing them simultaneously on a microarray slide. To statistically evaluate the microarray results, Significance Analysis of Microarrays (SAM) described by Tusher et al. (2001) was applied on the Lowess normalized datasets. With this SAM approach a false discovery rate (FDR) below 5% was applied. As a result genes with log2 ratios outside the confidence interval of -0.85 and 0.85 were considered as differentially expressed gene fragments when FDR was below 5%.
2010-05-22 | E-GEOD-13866 | biostudies-arrayexpress
Project description:A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or downregulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F0 and F1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative. The experimental design used in the current study is as follows. A set of neonates (0-24h) taken from the laboratory culture was divided into two batches. One batch was transferred to modified standard M4 medium (Elendt and Bias, 1990) and cultured for three generations (CtrlF0–CtrlF2). A second batch of neonates was transferred into the same medium, with the Zn concentration adjusted to 388 µg/L. A group of F1 neonates born from this ZnF0 generation was then cultured in this Zn-contaminated medium [Zn(+)F1]. Another group of these F1 neonates was transferred back to the control medium [Zn(-)F1]. In this way, Zn(-)F1 daphnids were only briefly exposed to Zn during the first hours of their life-cycle. Offspring of the F1Zn(-) organisms were also cultured in the control medium [Zn(-/-)F2, which were named F2Zn(-) in Vandegehuchte et al. (2009))]. Offspring of the Zn(+)F1 daphnids were in turn divided in a similar manner into two batches, one of which was cultured further in Zn-contaminated medium [Zn(+)F2] while the other one was transferred to the control medium [Zn(+/-)F2]. Each combination of generation and exposure history is termed a ‘treatment’. Three replicates of ten adult daphnids each per treatment were sampled for RNA extraction on the day the next generation was started. In general, a universal reference design was used in which the reference sample was a pool composed of differently aged daphnids cultured in aerated carbon-filtered tap water, enriched with selenium (1 µg/L) and vitamins (7.5 mg/L thiamine, 100 µg/L cyanocobalamin and 75 µg/L biotin). Dye-bias effects were accounted for by regularly swapping Cy3 and Cy5 for labelling treatments/reference pool samples.
2010-07-23 | E-GEOD-22805 | biostudies-arrayexpress
Project description:Due to its antimicrobial activity, silver nanoparticles (Ag-NPs) are among the most used NPs worldwide, yet little information is available regarding their effects, particularly in soil dwelling organisms. Enchytraeids (Oligochaeta) are important members of the soil fauna which actively contribute to the acceleration of organic matter decomposition and nutrient recycling processes. Hence, for hazard and risk assessment it is important to provide toxicity data for these organisms and to understand more in regard to the mode of action of Ag-NPs within organism. To study this we conducted toxicity experiments using the OECD standard guideline, testing Ag-NPs and AgNO3, having assessed survival, reproduction and differential gene expression. Population toxicity responses were assessed showing higher toxicity for the AgNO3. In an attempt to understand the mode of action we performed transcription profiling using the microarray. Gene expression profile of Enchytraeus albidus was analysed after 2 days of exposure to 100 and 200 mg/kg of two silver forms (nanoparticles and salt_silver nitrate) in OECD soil. Three biological replicates per test treatment and control (clean OECD soil) were used.
2013-05-22 | E-GEOD-42431 | biostudies-arrayexpress
Project description:Daphnia are an important and widely studied model species in ecological and toxicological studies throughout the world and an official (OECD) recommended test organism. Their small size, wide distribution and easy growth conditions make this an organism ideal for functional genomics based studies, including metabolic profiling and transcriptomics. In this study we used an integrated systems approach in which transcriptomic, metabolomic and energetic responses of juvenile (4 days old) daphnids were evaluated in response to exposure to two poly aromatic hydrocarbons (pyrene and fluoranthene) and binary mixtures thereof. In addition, these responses were linked to responses measured during chronic experiments (21 days) assessing survival, growth and reproductive traits. Custom Daphnia magna microarrays were used to assess transcriptomic changes. Hierarchical cluster analysis did not result in a clear distinction between the single compounds suggesting similar molecular modes of action. Cluster analysis with both the single compounds and the binary mixture treatments resulted in a separation of treatments based on differences in toxic ratios rather than component differences. Changes in the metabolic profiles of the organisms were investigated using Nuclear Magnetic Resonance spectroscopy and Gas and Liquid Chromatography Mass Spectrometry. These multivariate metabolomic datasets were analysed with Principal Components Analysis and Partial Least Squares Discriminant Analysis. The major metabolite changes responsible for the differences observed indicated a disturbance in aminosugar metabolism in all cases. The study demonstrates the potential of âomicsâ to provide screening tools for monitoring of the freshwater environment â in invertebrate species - which is reasonably rapid, cost-effective and has the potential to greatly increase the amount of information obtained from aquatic toxicology testing. Two independent experiments were performed, each with two biological replicates. As a result, every treatment was measured four times with the exception of the two highest mixtures doses where we only had two available replicates. In general, a universal reference design was used in which the reference sample was a pool composed of aliquots from all samples. Dye-bias effects were accounted for by labeling two samples of every treatment with Cy3 and two with Cy5. Exp1Rep1 (reference Cy3, sample Cy5); Exp1Rep2 (reference Cy5, sample Cy3); Exp2Rep1 (reference Cy5, sample Cy3) and Exp2Rep2 (reference Cy3, sample Cy5)
2010-05-16 | E-GEOD-16869 | biostudies-arrayexpress
Project description:The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level, through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on gene expression in E. albidus during exposure periods of 2 days, 4 days and 3 weeks, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al., 2011) The main objectives of this study were: 1) to assess changes in gene expression of E. albidus over time, and 2) to identify molecular markers for natural and chemical exposures. Results showed a clear influence of exposure time in gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects at energy metabolism and cell growth level.
2011-09-01 | GSE26896 | GEO
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29864 | biostudies-arrayexpress