Transcriptional responses of Folsomia candida exposed to polar and apolar narcotizing compounds.
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ABSTRACT:
ORGANISM(S): Folsomia candida
SUBMITTER: Dick Roelofs
PROVIDER: E-GEOD-19929 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Narcosis or baseline toxicity is the inert toxicity of hydrophobic compounds, supposed to take place at the level of the cellular membranes. Based on the linear relationship between the toxicity (logEC50) and the hydrophobicity (logKow), class I and II narcotizing compounds are recognized, in which the latter group is assumed to exert additional toxic mechanisms by hydrogen bond donor acidity by their polar groups. Chlorinated anilines, which occur often in the environment as degradation products of certain pesticides , are considered to be narcotizing compounds. In this study the transcriptional responses of the soil arthropod Folsomia candida are investigated upon exposure to a series of anilines with increasing chlorination. A discrimination between class1 and class2 narcotizing compound is being made.
2010-02-03 | GSE19929 | 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. 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:Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites. Folsomia candida was exposed to phenanthrene spiked soil or untreated (reference/control) soil for 2 days. Two different concentrations of phenanthrene were used, 24.95 and 45.80 mg/kg soil which represent the EC10 and EC50 on reproduction, respectively. For each concentration treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or phenanthrene spiked soil. Phenanthrene treated samples were always hybridized to reference samples in an evenly distributed dye-swap manner, which resulted in total in 8 hybridizations of 16 samples.
2010-05-18 | E-GEOD-14207 | 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: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:Temperature is an important ecological condition, and sudden temperature changes in soil can induce stress in soil-dwelling invertebrates. Soil animals can move to more favorable habitats and/or adapt physiologically to a stressful environment. Hyperthermic conditions will impact gene expression as one of the first steps. We use a transcriptomics approach to identify the transcripts of which expression changed in response to heat stress in the springtail Folsomia candida using a 5,131 probe microarray. A temperature shift from 20°C to 30°C for 30 minutes significantly altered the expression of 142 genes, of which 116 were upregulated, and 26 downregulated. Many upregulated genes encoded heat shock proteins (Hsps) or enzymes involved in the synthesis of ATP, such as members of the electron transport chain. Furthermore, genes involved in oxidative stress and anion-transporting ATPases were upregulated. Downregulated were glycoside hydrolases, involved in catalysis of certain disaccharides, which indicate an accumulation of stress-protective disaccharides. The microarray results from this study, which were validated using quantitative RT PCR, reveal a mild response to heat shock in this soil invertebrate, relative to other organisms. This may be due to specific ecological factors during evolution of soil invertebrates, such as the relatively stable temperatures in the soil habitat. This study presents potential candidate genes for future functional studies concerning thermal stress in soil-dwelling invertebrates, like e.g., the investigation of the heat hardening process. Folsomia candida was first acclimated to LUFA 2.2 soil at 20 C for two days. Then animals were either exposed to 30 C for 30 minutes (heat shock treated), or were not heat shocked (reference). For each treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or heat shock. Each unique heat shock treated sample was hybridized to a unique reference sample. In total in 4 hybridizations of 8 samples, was performed. The dyes were evenly distributed, which means that for each treatment two samples were labeled with cy3 and the other two with cy5.
2010-06-24 | E-GEOD-17024 | 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 traitM-bM-^@M-^Ys 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. We used a one-color microarray design where each sample was hybridized to a single array
2014-02-01 | E-GEOD-52393 | biostudies-arrayexpress
Project description:Genetic and molecular evidence to support the hypothesis that fungal secondary metabolites play a significant role in protecting the fungi against fungivory is scarce. We investigated the impact of fungal secondary metabolites on transcript regulation of stress related expressed sequence tags (ESTs) of the Collembola Folsomia candida feeding on mixed vs. single diets. Aspergillus nidulans wildtype (WT; Ascomycota) able to produce secondary metabolites including sterigmatocystin (ST) and a knockout mutant with reduced secondary metabolism (A. nidulans ?LaeA) were combined with the high quality fungus Cladosporium cladosporioides as mixed diets or offered as single diets. We hypothesized that (i) A. nidulans WT triggers more genes associated with stress responses compared to the A. nidulans ?laeA strain with suppressed secondary metabolism, (ii) C. cladosporioides causes significantly different transcript regulation than the A. nidulans strains ?laeA and WT, and (iii) mixed diets will cause significantly different transcript expression levels than single diets. All three hypotheses are generally supported despite the fact that many functions of the affected ESTs are unknown. The results bring molecular evidence for the existence of a link between fungal secondary metabolites and responses in springtails supporting the hypothesis that fungal secondary metabolites act as a shield against fungivory. Twenty-three day old Folsomia candida were fed ad libitum for five days to fungal cuts respectively Cladosporium cladosporoides, Aspergillus nidulans WT, Aspergillus nidulans ?LaeA and two mixed diets of C.cladosporoides/A. nidulans WT (mix 1) and C. cladosporoides/A. nudlans ?LaeA (mix2) respectively. Four biological replicates were used for every treatment and a dye swap was used with the Cy3/Cy5 labels. This resulted in 20 samples which were analysed in 10 hybridisations executed in an interwoven loop design. The C. cladosporoides diet was used as the reference in the data analysis.
2010-02-02 | E-GEOD-19930 | biostudies-arrayexpress