Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA167302 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR499864.fastq.gz | Fastqsanger.gz | |||
| SRR499865.fastq.gz | Fastqsanger.gz | |||
| SRR499866.fastq.gz | Fastqsanger.gz | |||
| SRR499867.fastq.gz | Fastqsanger.gz | |||
| SRR499868.fastq.gz | Fastqsanger.gz |
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Project description:Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. mRNA profiles of whole zebrafish embryos at 24 and 48 hours post-fertilisation (hpf) exposed to silver in nano, bulk and ionic forms were generated by deep sequencing using HT-SuperSAGE (Illumina GA2).
2013-06-17 | E-GEOD-38125 | biostudies-arrayexpress
Project description:Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.
2013-06-17 | GSE38125 | GEO
Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .
2018-02-01 | E-MTAB-5734 | biostudies-arrayexpress
Project description:Waterborne exposure of adult zebrafish to silver nanoparticles and ionic silver results in silver accumulation and effects at cellular and molecular levels
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Project description:Acute toxicity, bioaccumulation and effects of dietary transfer of silver from brine shrimps exposed to PVP/PEI-coated silver nanoparticles to zebrafish
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Project description:We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes.
2010-10-01 | GSE20682 | GEO
Project description:Silver nanoparticles (AgNPs), one of the most common nanomaterials in use today, have been shown to enter the aquatic environment from use of commercially obtained products. Although acute toxicity has been shown in vitro and in vivo, there is still a great deal of uncertainty surrounding the molecular mechanism of AgNP-induced toxicity. Much of the current literature centres on the question of whether toxicity is induced by the AgNPs themselves or by ionic silver released from the nanoparticle surface. Here, I present research investigating AgNP toxicity to Daphnia magna, a keystone species of freshwater ecosystems the world over, using a multi-omics platform of transcriptomics and metabolomics techniques. Initially, the AgNPs were fully characterised and the exposure conditions optimised to accurately assess the impact of AgNP exposure to D. magna. This allowed for the design of sub-lethal AgNP exposures that had been fully controlled for the fraction of dissolved silver ions. Secondly, using this multi-omics platform, the role of Ag+ ions in AgNP toxicity to D. magna was determined. Finally a metabolic pathway perturbed by AgNP exposure was identified, as well as two constituent metabolites of key importance. Overall, this research advances the mechanistic understanding of AgNP toxicity to aquatic organisms, and further highlights the need for greater consideration of the nanoscale in regulative legislature.
2017-05-08 | MTBLS260 | MetaboLights
Project description:Silver nanoparticles are used in consumer products like food contact materials, drinking water technologies and supplements, due to their antimicrobial properties. This leads to an oral uptake and exposure of intestinal cells. In contrast to other studies we found no apoptosis induction by surfactant coated silver nanoparticles in the intestinal cell model Caco-2 in a previous study, although the particles induced oxidative stress, morphological changes and cell death. Therefore, this study aimed to analyze the molecular mechanism of silver nanoparticles in Caco-2 cells. We used global gene expression profiling in differentiated Caco-2 cells, supported by verification of the microarray data by quantitative real time RT-PCR and microscopic analysis, impedance measurements and assays for apoptosis and oxidative stress. Our results revealed that the majority of surfactant coated silver nanoparticles are not taken up into differentiated Caco-2 cells. and probably affect the cells by outside-in signaling. They induce oxidative stress and have an influence on canonical pathways related to FAK, ILK, ERK, MAPK, integrins and adherence and tight junctions, thereby inducing transcription factors like AP1, NFĸB and NRF2, which mediate cellular reactions in response to oxidative stress and metal ions and induce changes in the cytoskeleton and cell-cell and cell-matrix contacts. The present data confirm the absence of apoptotic cell death. Non-apoptotic, necrotic cell death, especially in the intestine, can cause inflammation and influence the mucosal immune response.
2015-11-13 | GSE62253 | GEO
Project description:The current study deals to decipher the antibacterial mechanism of lysozyme coated silver nanoparticles (L-Ag NPs) (coated with lysozyme) against a Gram negative modal organism Escherichia coli K12 (MTCC 1302). Hence, the whole transcriptome profiling of E. coli K12 was done by exposing it to the MIC75 concentration of L-Ag NPs for 5 and 30 min., by RNA sequencing (RNAseq) analysis. The obtained results were utilized to understand all the metabolic pathways, signaling and molecular functions in bacterial cells under the stress of L-Ag NPs. RNAseq showed a high number of total reads along with significant ratio of high-quality reads, which confirmed the excellent quality and quantity of the obtained RNAseq data. Controlled release of ions from the surface of L-Ag NPs allowed the bacterial cells to function normally till the accumulation of threshold amount of silver ions which triggered the action of defence system, thus, reducing the chances of resistance development in bacteria. In long term, such treatment may force the bacterial machinery to induce changes in their genome to counteract the situation and develop resistance against silver ions, similar to the well-known antibiotic resistance problem. The obtained results advocate that L-Ag NPs can be used as effective antibacterial agent.
2022-06-15 | GSE151954 | GEO
Project description:Digital gene expression analysis by Ht-SuperSAGE (Matsumura et al. 2011. High-Throughput SuperSAGE. Methods Mol Biol.) was carried out to compare gene expression between wild type and mutant cell lines of the green algae Dunaliella tertiolecta under different light levels.
2020-06-30 | GSE129614 | GEO