Ecotoxicogenomic assessment of diclofenac toxicity in soil
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ABSTRACT:
ORGANISM(S): Folsomia candida
PROVIDER: GSE59589 | GEO | 2014/10/01
SECONDARY ACCESSION(S): PRJNA255666
REPOSITORIES: GEO
Similar Datasets
Project description:This study investigates transcriptional responses of the springtail Folsomia candida to two relevant concentrations of diclofenac A direct design was used where springtails were exposed to 3two concentrations of diclofenac (EC10 and EC50 on reproduction) and microarrays were directly contrased to those from animals exposed to clean LUFA2.2 soil. 4 biological replicates were used with each containing 25 grams of soil and 30 adult, randomly selected, age sychronized springtails
2014-10-01 | E-GEOD-59589 | biostudies-arrayexpress
Project description:The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile.
2014-07-19 | GSE59588 | GEO
Project description:Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism. Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level.
2011-05-12 | GSE29239 | GEO
Project description:Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism. Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level.
2011-12-29 | GSE26698 | GEO
Project description:The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile. A direct design was used where springtails were exposed to 3 field soils (2 polluted and 1 clean) and cadium and microarrays were directly contrased to those from animals exposed to clean LUFA2.2 soil. 4 biological replicates were used with each containing 25 grams of soil and 30 adult, randomly selected, age sychronized springtails
2014-07-19 | E-GEOD-59588 | biostudies-arrayexpress
Project description:Ecotoxicological tests may be biased by the use of laboratory strains that usually contain very limited genetic diversity. It is therefore essential to study how genetic variation influences stress tolerance relevant for toxicity outcomes. To that end we studied sensitivity to cadmium in two distinct genotypes of the parthogenetic soil ecotoxicological model organism Folsomia candida. Clonal lines of both genotypes (TO1 and TO2) showed divergent fitness responses to cadmium exposure; TO2 reproduction was 20% less affected by cadmium. Statistical analyses revealed significant differences between the cadmium-affected transcriptomes; i) the number of genes affected by cadmium in TO2 was only minor (~22%) compared to TO1; ii) 97 genes showed a genotype M-CM-^W cadmium interaction and their response to cadmium showed globally larger fold changes in TO1 when compared to TO2; iii) the interaction genes showed a concerted manner of expression in TO1 while a less coordinated pattern was observed in TO2. We conclude that (1) there is genetic variation in parthenogenetic populations of F. candida, and (2) this variation affects life-history and molecular endpoints relative to cadmium toxicity. This sheds new light on the sources of biological variability in test results, even when the test organisms are thought to be genetically homogeneous because of their parthenogenetic reproduction. Gene expression was measured in two different clones (TO1 and TO2) of the springtail Folsomia candida, after exposure of 2 days to soil containing cadmium (Cd+) and non-spiked (Cd-) soil. A 2 x 2 factorial analysis was performed, to examine the effect of clone (TO1, TO2), of treatment (Cd+, Cd-), and the clone x treatment interaction.
2012-12-21 | E-GEOD-34167 | biostudies-arrayexpress
Project description:Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism. Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level. Four-exposure experiment; Control vs. Acetone control vs.EC10 vs.EC50 exposed animals. Biological replicates: 4 replicates for each exposure.
2011-12-29 | E-GEOD-26698 | biostudies-arrayexpress
Project description:Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism. Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level. Four-exposure experiment; Control vs. Acetone control vs.EC10 vs.EC50 exposed animals. Biological replicates: 4 replicates for each exposure.
2011-05-12 | E-GEOD-29239 | biostudies-arrayexpress
Project description:Gene expression analysis of diclofenac-treated rat cardiomyocytes vs non-treated rat cardiomyocytes. Goal of study is to identify changes on genes expression induced by diclofenac. The data analysis focused on genes that might be related to cardiotoxicity; genes expression ion channels and pathways. two control samples vs 6 diclofenac-treated samples. Variables of treatment included two time points (6h or 24h) and three reference concentrations (1, 1/5 and 1/25). Each group had 3 replicates.
2016-02-13 | E-GEOD-77880 | biostudies-arrayexpress
Project description:This study examined how transcriptomics tools can be included in a Triad-based soil quality assessment to assess the toxicity of soils from river banks polluted by metals. To that end we measured chemical soil properties and used the standardized ISO guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod, Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher tier testing in soil quality. One of the least polluted soils showed toxicity in the bioassay that could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that another factor than metals (most likely of biological origin) caused the toxicity. This study demonstrates the feasibility and advantages of integrating transcriptomics into Triad-based soil quality assessment. Combining molecular and organismal life-history trait’s stress responses helps identifying causes of adverse effect in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress.
2014-02-01 | GSE52393 | GEO