Folsomia candida
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA120385 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Folsomia candida exposed to soil containing different phenanthrene concentrations
| PRJNA111333 | ENA
Project description: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. We used the uncorrelated shrunken centroid (USC) method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants. Gene expression was measured in springtails after exposure of 2 days to soil containing either EC10 or EC50 of 6 different metals. The exposure experiment was performed in two separate series (1 and 2), both containing a separate non-spiked (LUFA 2.2) soil control. Also, two field soil samples were tested. The samples were divided into a separate training set and a validation set for USC classifier analysis.
2010-02-04 | E-GEOD-19353 | biostudies-arrayexpress
Project description:Combined transcriptomics classifier analysis reveals a set of adverse effect genes for use as potential endpoint in effect based screening
| PRJNA289752 | ENA
Project description: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. We used the uncorrelated shrunken centroid (USC) method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants.
2010-02-05 | GSE19353 | GEO
Project description:Transcriptional plasticity of a soil arthropod across different ecological conditions
| PRJNA126307 | ENA
Project description:Folsomia candida exposed to different 2-phenylethyl isothiocyanate concentrations in soil
| PRJNA139951 | ENA
Project description:Folsomia candida exposed to different 2-phenylethyl isothiocyanate concentrations in soil
| PRJNA136369 | ENA
Project description:Multiple cryptic species of Folsomia candida from different geographic localities. Genome sequencing and assembly
| PRJNA909015 | ENA
Project description:The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation
| PRJNA141225 | ENA
Project description: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. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida’s tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil,and provides a mechanistic basis for the development of a gene expression soil quality test. Keywords: cadmium, soil, Collembola, environmental genomics
2008-08-08 | GSE11122 | GEO