Identification of circular RNAs expression pattern in caprine fetal fibroblast cells exposed to a chronic noncytotoxic dose of graphene oxide-silver nanoparticle nanocomposites
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA820774 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18506213_1.fastq.gz | Fastqsanger.gz | |||
| SRR18506213_2.fastq.gz | Fastqsanger.gz | |||
| SRR18506214_1.fastq.gz | Fastqsanger.gz | |||
| SRR18506214_2.fastq.gz | Fastqsanger.gz | |||
| SRR18506215_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:circRNA sequencing for 6 samples.The increasing use of graphene oxide-silver nanoparticle nanocomposites (GO-AgNPs) in biomedical sciences and research also increases the chances of human and animal exposure to its chronic non-toxic doses. However, the available information is truly little for profound understanding of the effect of low-dose chronic exposure to GO-AgNPs on the epigenetic modification of the organism. In this research, we have investigated the impact of non-toxic doses of GO-AgNPs (0.5 µg/mL for 10 weeks, this dose does not interfere cell viability and ROS level) on the differential expression of circular RNAs (circRNAs) in caprine fetal fibroblast cells (CFFCs). In addition, using bioinformatics tools we have predicted the functions of those differentially expressed circRNAs on CFFCs. Furthermore, we have validated the expression of ten circRNAs using qRT-PCR to ensure the reliability of the sequencing data. The results showed that the differentially expressed circRNAs potentially regulates the GO-AgNPs induced epigenetic toxicity through a regulatory network consisted of circRNAs, miRNAs and mRNAs. Therefore, the inclusion of epigenetics approaches is essential to assess the biosafety level of GO-AgNPs nanomaterials.
2022-03-31 | GSE199594 | GEO
Project description:Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to sublethal concentrations of silver nanoparticles in order to gain insight into phytotoxicity caused by these nanomaterials. Methods: mRNA was extracted from non-treated and silver nanoparticle-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were single-end sequenced (100-nt read length) on an Illumina HiSeq2500 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 7.0.40, Qiagen). Results: Chronic exposure of A. thaliana plants to silver nanoparticles caused a change in abundance of transcripts involved in cell wall synhtesis and response to oxidative and biotic stress-related genes. Conclusions: While exposure to silver nanoparticle lead to gene expression changes, the reduction in chlorophyll concentration and carbon assimilation rate measured in exposed plants cannot be attributed to a shift in photosynthesis-related gene regulation.
2020-12-22 | GSE163583 | GEO
Project description:This study investigates transcriptomic differences in the lung and liver after pulmonary exposure to two Graphene based materials with similar physical properties, but different surface chemistry. Female C57BL/6 mouse were exposed by a single intratracheal instillation of 0, 18, 54 or 162 μg/mouse of graphene oxide (GO) or reduced graphene oxide (rGO). Pulmonary and hepatic transcriptional changes were compared to identify commonly and uniquely perturbed functions and pathways by GO and rGO. These changes were then related to previously analyzed endpoints. GO exposure induced more differentially expressed genes, affected more functions, and perturbed more pathways compared to rGO, both in the lung and liver.
2020-10-21 | GSE159707 | GEO
Project description:Background: The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms are not yet fully understood. Results: In this study, we show that Cupriavidus metallidurans is able to adapt to toxic silver concentrations and explicate the genetic circuit responsible for this adaptation. None of the known silver resistant determinants present in C. metallidurans are involved in the adapted response. Instead, increased silver resistance is achieved by the concerted action of a two-component system AgrR-AgrS, previously not associated with metal resistance, and two intrinsically disordered proteins PrsQ1 and PrsQ2. Both belong to an unique group of small, uncharacterized, extracellular proteins restricted to the genera Cupriavidus and Ralstonia. This system seems to be much more efficient as it gives C. metallidurans the ability to withstand much higher silver concentrations. The latter could be facilitated by the accumulation of silver ions and the formation of silver nanoparticles. Conclusions: Detailed knowledge and exploitation of this protein family could result in novel routes for metal nanoparticle formation and metal processing relevant for biotechnical and biomedical applications.
2018-12-31 | GSE107669 | GEO
Project description:Breast cancer is one of the fatal diseases, Graphene has a property that can be used for Imaging and Therapy. Global gene expression changes leading to these changes were investigated presently in Breast cancer subtypes. The pathological staging of the cancers is compared to global gene expression profiles. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
2021-03-31 | GSE104939 | 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: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:As antimicrobials, graphene materials (GMs) may have advantages over traditional antibiotics due to their physical mechanisms of action which ensure less chance of development of microbial resistance. However, the fundamental question as to whether the antibacterial mechanism of GMs originates from penetration by their sharp edges or wrapping of the cell membrane, or from a combination of these and other mechanisms, remains controversial. In this study, we show both experimentally and theoretically that GMs with high surface oxygen content (SOC) predominantly attach in parallel to the bacterial cell surface when in the suspension phase. The interaction mode shifts to perpendicular interaction when the SOC reaches a threshold of ~ 0.3 (the atomic percent of O in the total atoms). However, neither mode necessarily kills bacteria. Rather, bactericidal activity depends on the interaction of GMs with surrounding biomolecules. Proteomic study shows that protein corona forms on the surface graphene oxide in LB medium, thus explain the different antibacterial activity in different culture medium.
2023-05-10 | PXD027909 | Pride
Project description:A series of graphene oxide (GO) suspensions with different particle sizes (<100 nm, ~100 nm, ~1 µm and >1 µm) were successfully fabricated after 0, 30, 60 and 120 min of sonication, respectively. The antibacterial properties of GO suspensions showed that >1 µm GO size resulted in a loss of nearly 50% of bacterial viability, which was higher than treatment by ~100 nm GO size (25%) towards Escherichia coli (E. coli). Complete entrapment of bacteria by the larger GO was observed in transmission electron microscopy (TEM). Silver nanoparticles (Ag NPs) were doped onto GO samples with different lateral sizes to form GO-Ag NP composites. Resulting larger GO-Ag NPs showed higher antibacterial activity than smaller GO-Ag NPs. As observed by Fourier transform infrared spectroscopy (FTIR), the interaction between E. coli and GO occurred mainly at the outer membrane, where membrane amino acids interact with hydroxyl and epoxy groups. The reactive oxygen species (ROS) and the considerable penetration of released Ag+ into the inner bacterial cell membrane result in loss of membrane integrity and damaged morphology. The present work improves the combined action of GO size effect with constant Ag loadings for potential antibacterial activity.
| S-EPMC7353109 | biostudies-literature
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