Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1035448 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects.
2013-01-01 | GSE39169 | GEO
Project description:Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects. Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a NanodropM-BM-. ND-1000 spectrophotometer. Total RNA was stored at -80oC until analyzed with oligonucleotide microarrays. Zebrafish 44,000 gene arrays (Agilent Single Color 19161, Platform number GPL6457) were purchased from Agilent (Sta. Clara, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturerM-bM-^@M-^Ys protocol and recommendations. Four controls and four treated samples were analyzed, each sample consisting of a pool of embryos. One ug of total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturerM-bM-^@M-^Ys kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA). An Axon GenePixM-BM-. 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA) was used to scan microarray images at 5 M-NM-<m resolution. Data were resolved from microarray images using Agilent Feature Extraction software and analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA).
2013-01-01 | E-GEOD-39169 | biostudies-arrayexpress
Project description:Flame retardants are detected globally in the environment, and pose great risks to human health. The potential effects of these chemicals on the development of nervous system have raise public concerns. In this study, to explore the toxicity profiles of these chemicals in the early developmental stage of human nervous system, we induced neural ectoderm from human embryonic stem cells in the presence of individual or mixture of BDE-47, BDE-209, TBBPA, TBBPS, TCBPA. By analyzing the whole transcriptional changes in the samples treated with 1 μΜ of each chemical, we identified a set of neural development relative biological processes that response to these chemicals. Genes involved in the GO terms relative to neural development were further confirmed by qRT-PCR assay, with samples treated with various concentrations (10 nM, 100 nM, 1 μΜ, 5 μΜ) of these chemicals. We found out that axon guidance and synaptogenesis may be the major target of these chemicals. In addition, these flame retardants may dysregulate the WNT and AHR signaling pathways. BDE-209 showed similar toxicity with BDE-47, whereas TBBPS and TCBPA may not be safe alternatives to TBBPA.
2022-03-01 | GSE128431 | GEO
Project description:Polybrominated diphenyl ethers (PBDEs) are persistent organic chemicals implied as flame re-tardants. Humans are mainly exposed to BDE-47, -99 and -209 congeners by diet. PBDEs are metabolic disruptors with liver as main target organ. To investigate their mode of action at a human relevant concentration, we exposed HepG2 cells to these congeners and their mixture at 1 nM for 72h, analyzing their transcriptomic and proteomic profiles. KEGG pathways and GSEA Hallmarks enrichment analyses evidenced that BDE-47 disrupted the glucose metabolism and Hypoxia pathway; all the congeners and the MIX affected lipid metabolism and signaling Hallmarks regulating metabolism as mTORC1 and PI3K/AKT/MTOR. These results were confirmed by glucose secretion depletion and increased lipid accumulation, especially in BDE-47 and -209 treated cells. These congeners also affected the EGFR/MAPK signaling; further, BDE-47 enriched the Estrogen pathway. Interestingly, BDE-209 and the MIX increased ERα gene expression, whereas all the congeners and the MIX induced ERβ and PPARγ. We also found that PBDEs modulated several lncRNAs and that HNRNAP1 represented a central hub in all the four interaction networks. Overall, despite the low concentration used, the PBDEs investigated affected glucose and lipid metabolism with different underlying modes of action, as highlighted by the integrated omics analysis. These results may support the mechanism-based risk assessment of these compounds in relation to liver metabolism disruption.
2022-10-28 | GSE216590 | GEO
Project description:Assessing seagrass meadows fish diversity using eDNA
| PRJNA777404 | ENA