Enchytraeus crypticus
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ABSTRACT:
PROVIDER: PRJNA286781 | ENA |
REPOSITORIES: ENA
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Project description:Exposure to different copper forms – nanoparticles, nanowires, salt and field aged: gene expression profiling in Enchytraeus crypticus
| PRJNA286782 | ENA
Project description:Exposure to UV radiation: gene expression profile in Enchytraeus crypticus
| PRJNA286780 | ENA
Project description:The effect of nanomaterials (NMs) is less understood in light of the implemented and existing methodologies for regular chemicals. To understand the mode of action of NMs is one of the alternatives to improve predictions and environmental risk assessment (ERA). In the present work the high-throughput gene expression tool (4x44K microarray for Enchytraeus crypticus) was used to investigate the mechanisms activated by Ni exposure. Ni nanoparticles (Ni-NPs) were investigated together with Ni-salt (NiNO3). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69793 | GEO
Project description:Negatives effects induced by exposure to ultra-violet (UV) radiation are well known. Nevertheless the modes of action of UV radiation are not well understood, in particular in soil invertebrates. In the present work, the effects of two UV doses (mimicking worst case scenarios in earth crust) on gene expression profile of Enchytraeus crypticus (Enchytraeidae, Oligochaeta) were investigated using the high-throughput 4 x 44K microarray developed for the species.
2017-06-13 | GSE69794 | GEO
Project description:Mechanisms of phenanthrene toxicity in the soil invertebrate Enchytraeus crypticus
| PRJNA299072 | ENA
Project description:The testing of NMs under the currently available standard toxicity tests does not cover many of the NMs specificities. One of the current recommended approaches forward lays on understanding the mechanisms of action as these can help predicting long term effects and safe-by-design production. Copper nanomaterials (Cu-NMs) usage has been highly increasing with the concern in terms of exposure, effect and associated risks. In the present study we used the high-throughput gene expression tool developed for Enchytraeus crypticus (44Kx4 Agilent microarray) to study to the effect of exposure to several copper forms. The copper treatments include two NMs (spherical and wires) and two copper-salt treatments (CuNO3 spiked and Cu field historical contamination). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69792 | GEO
Project description:The transcriptome of the ecotoxicological model Enchytraeus crypticus is well studied but the downstream changes at the protein level remained a gap. Changes in the protein regulation following exposure to CuO nanomaterial (NM) and Cu salt (CuCl2) were investigated. High performance liquid chromatography with tandem mass spectrometry using tandem mass tags was used. CuO NM elicited higher number of differentially expressed proteins compared to CuCl2 with little to no overlap of proteins. CuO NM caused more stress response mechanisms, with good agreement between differentially expressed proteins, genes and metabolites. CuCl2 caused higher impact in shorter time periods, but organisms have conserved mechanisms (constitutive genes) that allow Cu handling and detoxification. CuO NM caused higher impact after a longer exposure period, inducing regulation of facultative genes with a whole differentiated paradigm and cascade. This could be due to different issues: 1) the cell uptake route is different for Cu NM and Cu ions 2) internalized Cu NM can result in a “Trojan- horse” effect 3) the cascade of events occurs in a different time order 4) the organism uptake is different between life stages, i.e., cocoons thickened surface protects the entry of NM and juveniles have facilitated entry via tegument. Protein responses are of key importance when trying to understand the link between exposure and the related adverse biological effects. We here used advanced proteomic profiling techniques to describe how the protein responses differ when an organism is exposed to Copper (Cu) nanomaterial compared to when it is exposure to Cu ions. We observed that when organisms are exposed to the nano-form they have longer-term changes in protein patterns, patterns that are different from the responses following exposure to the ionic form. On the level of individual proteins we identified nano-specific mechanisms.
2018-08-16 | PXD010647 | Pride
Project description:The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity. An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed.
2014-05-01 | GSE51838 | GEO
Project description:Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus
| PRJNA322344 | ENA