RNASeq of C. elegans exposed to silver (Ag) or silicon dioxide (SiO2) nanoparticles
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA506107 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8208610.fastq.gz | Fastqsanger.gz | |||
| SRR8208611.fastq.gz | Fastqsanger.gz | |||
| SRR8208602.fastq.gz | Fastqsanger.gz | |||
| SRR8208612.fastq.gz | Fastqsanger.gz | |||
| SRR8208603.fastq.gz | Fastqsanger.gz |
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Project description:RNAseq was carried out to compare the gene expression profiles underlying the Ag and SiO2 toxicities on C. elegans.
2018-11-20 | GSE122728 | GEO
Project description:Effects of silver nanoparticles (Ag NPs) on freshwater species have been reported in several studies, but there is not information on the potential long-term consequences of a previous exposure. In this work, we investigated the long-term effects of maltose-coated Ag NPs (20 nm) and of ionic silver (10 µg/L) after 21 days of exposure and at 6 months post-exposure (mpe) in adult zebrafish. Exposure resulted in significant silver accumulation in the whole body of fish exposed to ionic silver, but not in those exposed to Ag NPs. However, autometallography revealed metal accumulation in the liver and intestine of fish treated with the two silver forms and especially in the intestine of fish exposed to Ag NPs. X-ray microanalysis showed the presence of silver in gills, liver and intestine and of Ag NPs in gill and liver cells. Inflammation and hyperplasia were evident in the gills after both treatments and these histopathological conditions remained at 6 mpe. According to the hepatic transcriptome analysis, at 3 days ionic silver regulated a larger number of transcripts (410) than Ag NPs (129), while at 21 days Ag NPs provoked a stronger effect (799 vs 165 regulated sequences). Gene ontology terms such as “metabolic processes” and “response to stimulus” appeared enriched after all treatments, while “immune system” or “reproductive processes” were specifically enriched after the exposure to Ag NPs. This suggests that the toxicity of Ag NPs may not be solely related to the release of Ag ions, but also to the NP form. No evident effects were found on protein oxidation or on hepatocyte lysosomal membrane stability during exposure, but effects recorded on liver lysosomes and persistent damage on gill tissue at 6 mpe could indicate potential for long-term effects in exposed fish.
2018-06-12 | GSE89653 | GEO
Project description:From the result of the gene expression analyses of human hepatoma cell line, HepG2, a number of genes associated with cell proliferation and DNA repair were distinctively up-regulated by Ag-nanoparticle exposure, suggesting that Ag-nanoparticles might stimulate cell proliferation and DNA damage, which are considered to be mechanisms playing an important role for carcinogenesis and tumor progression. The inductions of these genes involved in cell proliferation were also observed in PS-nanoparticles and Ag2CO3-exposed cells. In addition, the inductions of DNA repair-associated genes were also observed in Ag2CO3-exposure. These results suggest that both “nanoshape” and “silver” can cause the inductions of these gene expression patterns. Furthermore, cysteine, a strong ionic silver ligand partially abolished these gene expressions induced by silver nanoparticles. Ionic silver sourced from Ag-nanoparticles could not fully explain these gene expressions.
2009-06-01 | GSE14452 | GEO
Project description:The widespread use of silver nanoparticles (Ag NPs) has raised substantial health risks to environmental and human beings. Although various negative effects had been reported, little is known about the epigenetic toxicity induced by Ag+ and Ag NPs. This study characterized physiological and lncRNA profiles to explore the toxic effects and epigenetic mechanisms in Tetrahymena thermophila on exposure to Ag+ and three types of Ag NPs. We found that both of Ag+ and Ag NPs exhibited strong growth-inhibiting effects on T. thermophila. The toxicity was mainly caused by high levels of reactive oxygen species (ROS), which subsequently led to lipid peroxidation and mitochondrial dysfunction. As a defense mechanism against oxidative stress, the protist elicited an antioxidant response. Importantly, 1250 lncRNAs were differentially expressed under Ag+ or Ag NPs exposure relative to the non-exposure control, which were clustered into 15 expression modules in weighted gene co-expression network analysis. These gene modules exhibited toxicant-specific expression patterns, indicating that they play various regulatory roles, including cell growth inhibition, cell membrane cation channel activation, and oxidoreductase activity promotion. Taken together, this research illuminates how post-transcriptional mechanisms of a ciliated protozoa regulate responses to Ag+ and Ag NPs toxicities.
2021-09-10 | GSE157616 | GEO
Project description:The release of silver nanoparticles (SNPs) in the environment has raised concerns about their effects on living organisms, including plants. In this study, changes in gene expression in Arabidopsis thaliana exposed to SNPs and silver ions (Ag+) were analyzed using Affymetrix expression microarrays. Exposure to 5 mg SNPs L-1 (20 nm) for 10 days resulted in up-regulation of 286 genes and down-regulation of 81 genes by reference to non-exposed plants. Exposure to 5 mg Ag+ L-1 for 10 days resulted in up-regulation of 84 genes and down-regulation of 53 genes by reference to non-exposed plants. Many genes differentially expressed by SNPs and Ag+ were found to be involved in plant response to various stresses: up-regulated genes were primarily associated with response to metals and oxidative stress (e.g., vacuolar cation/proton exchanger, superoxide dismutase, cytochrome P-450-dependent oxidase, and peroxidase), while down-regulated genes were more associated with response to pathogens and hormonal stimuli (e.g., auxin-regulated gene involved in organ size (ARGOS), ethylene signaling pathway, and systemic acquired resistance (SAR) against fungi and bacteria). A significant overlap was observed between genes differentially expressed in response to SNPs and Ag+ (13% and 21% of total up- and down-regulated genes, respectively), suggesting that SNP-induced stress originates partly from silver toxicity and partly from nanoparticle-specific effects. Three highly up-regulated genes in the presence of SNPs, but not Ag+, belong to the thalianol biosynthetic pathway, which is thought to be involved in plant defense system. Results from this study provide insights into the molecular mechanisms of plant response to SNPs and Ag+.
2014-02-12 | E-MEXP-3950 | biostudies-arrayexpress
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:Silver nanoparticles (NPs) are extensively used due to their antimicrobial activity and, therefore, their input into the ecosystem will increase. Silver can be bioaccumulated by low trophic level organisms and, then, incorporated into the food chain, reaching high level predators. The objectives of this study were to test the acute toxicity of N-vynil-2-pirrolidone/polyethylenimine (PVP-PEI) coated Ag NPs of 5 nm to brine shrimp (Artemia sp) larvae and to assess bioaccumulation and effects of silver transferred by the diet. For the later, brine shrimps were exposed to two different concentrations of Ag NPs, 100 ng/L as an environmentally relevant concentration and 100 µg/L as a likely effective concentration, in parallel with an unexposed control group and, then, used to feed zebrafish during 21 days in order to simulate two trophic levels of a simplified food web. For brine shrimp larvae, EC50 values ranged from 7.39 mg Ag/L (48 h post hatch larvae (hph) exposed for 48 h) to 19.63 mg Ag/L (24 hph larvae exposed for 24 h. Silver accumulation was measured in brine shrimps exposed to 0.1 and 1 mg/L of Ag NPs for 24 h. In zebrafish fed with brine shrimps exposed to Ag NPs, intestine showed higher metal accumulation than liver, although both organs presented the same pattern of dose and time-dependent metal accumulation as revealed by autometallography. Feeding of zebrafish for 3 days with brine shrimps exposed to 100 ng/L of Ag NPs was enough to impair fish health as reflected by the significant reduction of the lysosomal membrane stability and the presence of several histopathological conditions in the liver. Overall, results showed that Ag NPs were able to exert toxic effects on zebrafish through dietary exposure, even at an environmentally relevant concentration, which should act as concern of the need of studies in further detail about real impact of nanomaterials in the environment.
2017-03-21 | GSE90457 | GEO
Project description:RNA-Seq analysis was used for deep sequencing of transcriptome to detected molecular mechanisms of silver nanoparticles (AgNPs) and distinguish the effects of Arabidopsis thaliana exposure to AgNPs and Ag+.We identified 626 and 767 differentially expressed genes (DEGs) influenced by AgNPs and Ag+ respectively.302 genes were specifically regulated by the AgNPs treatment indicates that the nanoparticle-specific effects.This study provide a valuable resource for the discovery of genes related to special toxicity mechanism of AgNPs.
2021-08-03 | GSE118143 | GEO
Project description:Infections associated with antimicrobial-resistant bacteria now represent a significant threat to human health using conventional therapy, necessitating the development of alternate and more effective antibacterial compounds. Silver nanoparticles (Ag NPs) have been proposed as potential antimicrobial agents to combat infections. A complete understanding of their antimicrobial activity is required before these molecules can be used in therapy. Lysozyme coated Ag NPs were synthesized and characterized by TEMEDS, XRD, UV-vis, FTIR spectroscopy, zeta potential, and oxidative potential assay. Biochemical assays and deep level transcriptional analysis using RNA sequencing were used to decipher how Ag NPs exert their antibacterial action against multi-drug resistant Klebsiella pneumoniae MGH78578. RNAseq data revealed that Ag NPs induced a triclosan-like bactericidal mechanism responsible for the inhibition of the type II fatty acid biosynthesis. Additionally, released AgC generated oxidative stress both extra and intracellularly in K. pneumoniae. The data showed that triclosan-like activity and oxidative stress cumulatively underpinned the antibacterial activity of Ag NPs. This result was confirmed by the analysis of the bactericidal effect of Ag NPs against the isogenic K. pneumoniae MGH78578 1soxS mutant, which exhibits a compromised oxidative stress response compared to the wild type. Silver nanoparticles induce a triclosan like antibacterial action mechanism in multi-drug resistant K. pneumoniae. This study extends our understanding of anti-Klebsiella mechanisms associated with exposure to Ag NPs. This allowed us to model how bacteria might develop resistance against silver nanoparticles, should the latter be used in therapy.
2021-01-31 | GSE151953 | GEO
Project description:Applications for silver nanomaterials in consumer products are rapidly expanding, creating an urgent need for toxicological examination of the exposure potential and ecological effects of silver nanoparticles (AgNPs). The integration of genomic techniques into environmental toxicology has presented new avenues to develop exposure biomarkers and investigate the mode of toxicity of novel chemicals. In the present study we used a 15k oligonucleotide microarray for Daphnia magna, a freshwater crustacean and common indicator species for toxicity, to differentiate between particle specific and ionic silver toxicity and to develop exposure biomarkers for citrate-coated and PVP-coated AgNPs. Gene expression profiles revealed that AgNO3 and AgNPs have distinct expression profiles suggesting different modes of toxicity. However, the gene expression profiles of the different coated AgNPs were similar revealing similarities in the cellular effects of these two particles. Major biological processes disrupted by the AgNPs include protein metabolism and signal transduction. In contrast, AgNO3 caused a downregulation of developmental processes, particularly in sensory development. Metal responsive and DNA damage repair genes were induced by the PVP AgNPs, but not the other treatments. In addition, two specific biomarkers were developed for the environmental detection of PVP AgNPs; although further verification under different environmental conditions is needed. We exposed Daphnia magna to the 1/10 LC50 and LC25 of citrate coated and PVP-coated Ag nanoparticles and Ag+ as AgNO3 for 24-h. For each exposure condition, we performed 6 replicate exposures with 5 individuals in each. All exposures were compared to a unexposed laboratory control.
2012-08-04 | E-GEOD-35150 | biostudies-arrayexpress