Gene expression data from yeast exposure to alachlor
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE28677 | GEO | 2011/08/28
SECONDARY ACCESSION(S): PRJNA138931
REPOSITORIES: GEO
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Project description:The world-wide used herbicide alachlor is among the priority substances listed in the European Water Framework Directive. We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to alachlor at concentrations exerting slight to moderate levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the lowest observed effect concentration (LOEC; ~8% growth inhibition) and the 20%-inhibitory concentration (IC20), compared to control cells not exposed to the herbicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 110 or 200 mg/L of ALA (corresponding to the LOEC and the IC20, respectively, of alachlor) or in medium non-supplemented with the herbicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with each concentration of alachlor versus controls were carried out independently. For each exposure condition, independent biological triplicates were processed and analysed.
2011-08-27 | E-GEOD-28677 | biostudies-arrayexpress
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Project description:Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 20 and 110 mg/L of PYR (corresponding to the PYR IC20 and IC50, respectively), or in medium non-supplemented with the fungicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with both concentrations of PYR and with control cells were carried out together. For each exposure condition, independent biological triplicates were processed and analysed.
2014-05-23 | E-GEOD-53126 | biostudies-arrayexpress
Project description:This study focus a comparative toxicogenomic analysis of the effects of four herbicides (alachlor, ALA, S-metolachlor, S-MET, diuron, DIU, and MCPA-methyl ester, MCPA-ME), one insecticide (carbofuran, CAB), and one fungicide (pyrimethanil, PYR), in the model yeast Saccharomyces cerevisiae, to predict potential cytotoxic effects of these xenobiotics while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. The six model pesticides selected have been used worldwide in agricultural activities, at the present time or in the past, and have different modes of action on their target-organisms. Moreover, some of them are currently in Annex 1 of EC Directive 1107/2009 (repealing 91/414), that is they are in use in the EU, but having some ecotoxicological concerns (e.g. S-MET, PYR, MCPA-ME), others have their use restricted and/or are priority substances under the Water Framework Directive (e.g. ALA, DIU), and one was banned (e.g. CAB). We used genome microarrays to obtain gene expression profiles in S. cerevisiae strain BY4741 upon 2 hours exposure to pesticide concentrations exerting a moderate inhibition of yeast growth rate. To obtain comparable gene expression profiles representing yeast response to the six different pesticides, all exposure treatments were performed with equitoxic pesticide concentrations that generated equivalent responses at the phenotypic level (namely, 20% growth-inhibitory concentrations, hereafter designated as the pesticide IC20).
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Project description:Transcriptonal profiling of BEAS-2B cells: Control versus skin sensitizers; Control versus respiratory sensitizers; Control versus non-sensitizing irritants Replicates: 3 biological replicates; Exposure: 10 different chemicals versus solvent, 1 exposure concentration (IC20); Exposure time: 3 different exposure time points;
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Project description:We analyzed genome-wide transcriptional changes in the S. cerevisiae strain BY4742 upon exposure to NP to identify differentially expressed genes, biological processes, metabolic pathways, and cellular compartments affected by this compound. For these analyses, we focused on two NP exposure scenarios: (1) exposure to a low inhibitory concentration (resulting in <15% reduction in cell number), and (2) exposure to a high inhibitory concentration (resulting in >65% reduction in cell number).
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Project description:Carbon source is the basic nutrition and is essential for yeast growth. We grew the yeast cells (BY4741 strain) under different carbon sources including glucose with different concentration, galactose and raffinose. We generated bulk-cell RNA-seq data and investigated the dynamics of gene expression profiles under different growth conditions. We also generated single-cell RNA-seq data for yeast cells under 2% glucose, and explored the heterogeneity of gene expression within a cell population.
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Project description:We analyzed genome-wide transcriptional profiles of Saccharomyces cerevisiae BY4742 strain in response to BPA, focusing on two exposure scenarios: (i) low-observed-effect concentration (<10% inhibition) to examine chronic effect of BPA on yeast population, and (ii) high-inhibitory concentration (>70% inhibition) to study acute effect. Initially, yeast cells were exposed to various concentrations of BPA. 50 mg/L and 300 mg/L BPA were determined as low-observed-effect concentration and the high-inhibitory concentration, respectively. Transcriptional profiles indicated that 81 genes were repressed and 104 genes were induced in response to 50 mg/L BPA. On the other hand, in 300 mg/L BPA exposure, 378 genes were down-regulated, while 606 genes were significantly up-regulated. Our data showed that there were similar processes affected by both concentrations such as mitochondria, nucleobase-containing small molecule metabolic process, transcription from RNA polymerase II promoter, and mitotic cell cycle and associated processes. However, different modes of actions of the BPA were found between two concentrations. 300 mg/L BPA exposure showed severe effects on the processes by repressing or inducing several genes or total mechanisms with high level of expression changes, while 50 mg/L BPA exposure changed the expression of some important genes with low level of expression changes in the processes. These results suggest that yeast cells respond via different ways to the different concentrations of BPA at transcriptomic level.
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Project description:The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of round up (CAS; 40465-66-5), the exposure dose was decided as 1500 times dilution by growth curve with continuously diluted exposure. Roundup is the brand name of a systemic, broad-spectrum herbicide contains the active ingredient glyphosate. Glyphosate is classed as a moderately toxic herbicide and in EPA toxicity class III. // Genomic profile of roundup treatment of yeast using DNA microarray analysis: The herbicide Roundup, which contains glyphosate as the active ingredient, was first introduced in 1974 and has enjoyed widespread use in Japan and elsewhere in the world. Roundup-induced reactions occurring in the yeast Saccharomyces cerevisiae may have a predictive value for understanding responses in higher eukaryotes, and we applied yeast DNA microarray analysis for this purpose. Functional characterization of up-regulated open reading frames (ORFs) following Roundup treatment suggests that Roundup affects membrane structures and cellular organelles. Expression profiles induced by treatments with detergents, oils and hydrostatic pressure were similar to those following Roundup treatment based on cluster analysis. Glyphosate alone was not found to inhibit yeast growth at the concentration contained in the Roundup treatment used for microarray analysis. The toxicity of Roundup appeared to be due to detergent in the product. Keywords: stress response
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