GEO DataSets

(Submitter supplied) Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL6381

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

8 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL6381

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

8 Samples

Download data: TXT

(Submitter supplied) Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms such as springtails, supplement traditional ecotoxicological research, but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

62 Samples

Download data: TXT

(Submitter supplied) Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance is correlated with heritable increase of metal excretion efficiency; less pronounce cadmium induced growth reduction and, over-expression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and cadmium tolerant populations. more...

Organism:

Orchesella cincta

Type:

Expression profiling by array

Platform:

GPL7876

16 Samples

Download data: TXT

(Submitter supplied) Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

64 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL17934

21 Samples

Download data: TXT

(Submitter supplied) It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

112 Samples

Download data: TXT

(Submitter supplied) "Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins." Joseph.R.Shaw, John.K.Colbourne, Jennifer.C.Davey, Stephen.P.Glaholt, Thomas.H.Hampton, Celia.Y.Chen, Carol.L.Folt, Joshua.W.Hamilton (BMC Genomics 2007). Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. more...

Organism:

Daphnia pulex

Type:

Expression profiling by array

Platform:

GPL6195

3 Samples

Download data: GPR, TXT

(Submitter supplied) Metals at high concentrations can exert toxic effects on microorganisms. It has been widely reported that lowering environmental pH reduces effects of cadmium toxicity in bacteria. Understanding the effects of pH-mediated cadmium toxicity on bacteria would be useful for minimizing cadmium toxicity in the environment and gaining insight into the interactions between organic and inorganic components of life. more...

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL6540

8 Samples

Download data: MEV

(Submitter supplied) We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. more...

Organism:

Folsomia candida

Type:

Expression profiling by array

Platform:

GPL7150

32 Samples

Download data: TXT