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Ontology highlight
ABSTRACT:
PROVIDER: PRJEB54929 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9981100_1.fastq.gz | Fastqsanger.gz | |||
| ERR9981100_2.fastq.gz | Fastqsanger.gz | |||
| ERR9981110_1.fastq.gz | Fastqsanger.gz | |||
| ERR9981110_2.fastq.gz | Fastqsanger.gz | |||
| ERR9981101_1.fastq.gz | Fastqsanger.gz |
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Project description:Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure
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Project description:Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. In particular, trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L-1) over a 72-hour time period. Copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis along with shifts in its microbiota. Unexpectedly, very few genes were differentially expressed in copper-treated copepods compared to controls, with most of the reported differences involving genes upregulated in males compared to females. In contrast, copper increased the taxonomic diversity indices of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in copper-treated copepods concurred with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, and Alkanindiges) and a higher relative abundance of the copA gene encoding a periplasmic inducible multi-copper oxidase. Overall, these results revealed very contrasting responses of E. affinis and its microbiota to copper exposure. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines here the need to follow the microbial component during the evaluation of the vulnerability of the zooplankton to the metallic stress.
2023-06-29 | GSE212602 | GEO
Project description:The in vitro and in vivo toxicity of copper oxide nanoparticles (CuO NPs) is attributed to both particle and dissolved copper ion species. However, a clear understanding of 1) the specific cellular responses that are modulated by the two species and 2) the temporal dynamics in toxicity, as the proportional amount of particulate and ionic forms change over time, is lacking. In the current study, in vitro responses to microparticulate CuO (CuO MPs), CuO NPs, and dissolved Cu2+ were characterized in order to elucidate particle and ion induced kinetic effects. Particle dissolution experiments were carried out in relevant cell culture medium, using CuO NPs and MPs. Mouse lung epithelial cells were exposed for 2 - 48 h with 1 - 25 µg/mL CuO MPs, CuO NPs, or 7 & 54 µg/mL CuCl2. Cellular viability and genome-wide transcriptional responses were assessed. Dose and time dependent cytotoxicity was observed in CuO NP exposed cells, which was delayed and subtle in CuCl2 and not observed in CuO MPs treated cells. Analyses of differentially expressed genes and associated pathway perturbations showed that dissolved ions released by CuO NPs in extracellular medium are insufficient to account for the observed potency and cytotoxicity. Further organization of gene expression results in an Adverse Outcome Pathway (AOP) framework revealed a series of key events potentially involved in CuO NPs toxicity. The AOP is applicable to soluble metal oxide nanoparticle induced toxicity in general, and thus, can facilitate the development of in vitro alternative strategies to screen their toxicity.
2022-11-03 | GSE161017 | GEO
Project description:In vivo and in vitro microbiota responses to three prebiotics
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Project description:Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism
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Project description:Microbiota response in the copepod eurytemora affinis to tebufenozide exposure
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Project description:Copper (Cu) is not only one of the essential trace elements for animal body, but also an important nutrient component for normal physiology and metabolism of animal reproductive system. Lack or excess of copper will directly or indirectly affect animal reproductive activities. However, the effect of copper on reproductive performance of boars and sows has not been studied and the effect of excessive Copper addition on reproductive performance of sows is even less, and the molecular mechanism is poorly understood. Here, we document that copper has the negative effects on the oocyte maturation and Organelle function. We show that copper exposure perturbs the porcine oocyte meiotic maturation and impair the spindle/chromosome structure, displaying an obviously defective spindle assembly, and abnormal distribution of actin dynamics and cortical granules. In addition, single-cell transcriptome analysis identifies target effectors of copper in porcine oocytes, which was further demonstrated that copper exposure affects the distribution and function of mitochondria, and high ROS levels, DNA damage, and early apoptosis in porcine oocytes. Collectively, we demonstrate that copper exposure causes abnormalities in mitochondrial function and distribution, resulting in increased oxidative stress ROS levels, DNA damage and apoptosis, ultimately leading to decreased quality of porcine oocytes.
2021-06-28 | GSE168867 | GEO
Project description:Epigenetic mechanisms are moving to the forefront of environmental sciences, especially because environmentally induced epigenetic changes shape biological responses to contamination of chemicals. Moreover, such marks can be inherited by subsequent generations through epigenetic transgenerational inheritance, thus having long-term implications. In this work, we focused on Daphnia as a representative of the potentially threatened freshwater biota aiming to gain an insight on the involvement of epigenetic mechanisms in their response, eventually adaptation, to metal contamination. Copper induced DNA methylation changes, their potential transgenerational inheritance, and life-history traits were assessed. Organisms differing in their history of past exposure to copper were exposed to toxic levels of the element for one-generation (F0) and then monitored for three subsequent unexposed generations (F1, F2, and F3). Overall, methylation changes targeted important genes for counteracting the effects of metals and oxidative stress, including dynein light chain, ribosomal kinase and nuclear fragile X mental retardation-interacting protein. Also, contrasting overall and gene-specific methylation responses were observed in organisms differing in their history of exposure to copper, with different transgenerational methylation responses being also identified among the two groups, without apparent life-history costs. Taken together, these results demonstrate the capacity of copper to promote epigenetic transgenerational inheritance in a specific manner concerning past history of exposure, thereby supporting the potential of developing and incorporating epigenetic biomarkers in risk assessment frameworks.
2023-03-14 | GSE201140 | GEO
Project description:Gene expression profiling revealed rapid activation of immunity, both local and systemic, which however did not provide protection of fish against the parasite. Major changes of transcriptome responses wwere observed between days 5 and 10 Atlantic salmon was challenged with L. salmonis at the copepod stage. Skin, spleen, and head kidney were sampled from challenged and control fish at 1, 3, 5 dpi (corresponding to the copepod stage); 10 and 15 dpi (chalimus stage). A total of forty samples of spleen and skin form infected salmon (4 individuals from the 5 time points) were used for microarray analyses.. Test samples were labeled with Cy5 and hybridized to pooled control samples labeled with Cy3 from the same time-points. Competitive hybridization to the arrays was followed by washing, scanning, image analysis, and data analysis. Selected genes were analyzed with RT-qPCR.
2011-02-03 | E-GEOD-26984 | biostudies-arrayexpress
Project description:Gene expression profiling revealed rapid activation of immunity, both local and systemic, which however did not provide protection of fish against the parasite. Major changes of transcriptome responses wwere observed between days 5 and 10 Atlantic salmon was challenged with L. salmonis at the copepod stage. Skin, spleen, and head kidney were sampled from challenged and control fish at 1, 3, 5 dpi (corresponding to the copepod stage); 10 and 15 dpi (chalimus stage). A total of forty samples of spleen and skin form infected salmon (4 individuals from the 5 time points) were used for microarray analyses.. Test samples were labeled with Cy5 and hybridized to pooled control samples labeled with Cy3 from the same time-points. Competitive hybridization to the arrays was followed by washing, scanning, image analysis, and data analysis. Selected genes were analyzed with RT-qPCR.
2011-02-03 | E-GEOD-26981 | biostudies-arrayexpress