Ontology highlight
ABSTRACT:
PROVIDER: PRJNA819558 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18483522_1.fastq.gz | Fastqsanger.gz | |||
| SRR18483522_2.fastq.gz | Fastqsanger.gz | |||
| SRR18483523_1.fastq.gz | Fastqsanger.gz | |||
| SRR18483523_2.fastq.gz | Fastqsanger.gz | |||
| SRR18483524_1.fastq.gz | Fastqsanger.gz |
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Project description:To assess the impact of a municiple effluent across different environments, a gradient design (upstream, downstream, and at effluent) was set up across three waste water treatment plant outflows in three different regions of MN. These three sites represents vastly different land use and contamination profiles. The upstream location at each site was used as a point of comparison to reduce site specific differences in water. Fish were exposed at three sites in three locations for 4 days. The objectives of the study were to 1). determine if biological impact of the effluent could be detected at the downstream site; 2). If the use of the upstream site would allow point source influence to be detected over the ambient level of biological activity; 3). if using functional analyses of transcriptomic results would show similarities between effleunt and downstream sites. The current series contains n=53 microarrays associated with fish exposed at three locations (upstream, effluent, downstream) at 3 different site R, H, E for 4 days until tissues were collected
2013-12-13 | GSE53204 | GEO
Project description:Despite recent knowledge of the potential environmental impact that compounds present in municipal wastewater effluents, including contaminants of emerging concern (CECs), may have, the implications of fish exposure to this contaminant mixtures are not completely understood. The effects caused by effluent CECs may be subtle and diverse, thus the need for sensitive and comprehensive tools such as gene expression to detect such responses. In this study, we conducted laboratory exposures that examined plasma concentrations of vitellogenin (VTG), changes in secondary sexual characteristics and gene expression in sexually mature male fathead minnows (Pimephales promelas) exposed to environmentally realistic (0.5%) and higher (5%) concentrations of municipal wastewater effluents. Secondary and primary treated effluents were used. Several of the 32 CECs investigated were detected, including pharmaceuticals, personal care products, hormones, current use pesticides and industrial compounds. The percent of males with detectable levels of VTG was higher in fish exposed to effluent treatments. An increased number of males with changes in secondary sexual characteristics (e.g. development of ovipositors), was observed in fish exposed to 5% effluent treatments. Gene expression data indicated that overall expression patterns were characteristic to each effluent. Higher numbers of differentially expressed genes were observed in fish exposed to primary treated effluent when compared to controls. Differentially expressed genes belonged to several functional categories, including xenobiotic metabolism, estogenicity and energy/metabolism processes. Gene expression data provided information to understand some of the mechanisms behind the effects observed at higher biological levels. To investigate gene expression responses resulting from exposure to POTW effluents, two laboratory experiments were conducted using effluent from San Diego (Point Loma; SD) and Los Angeles (Hyperion; LA). The LA effluent received secondary treatment and the SD effluent received advanced primary treatment. Treatments used during exposures consisted of negative controls (moderately hard water), positive controls (E2), and 0.5% and 5% effluent concentrations. The 0.5% concentration of effluent represented an environmentally realistic exposure level. The 5% effluent concentration represented a higher level at which we expected biological responses. The exposures lasted 14 days. Treatments: EFFHa = 5% primary treated effluent EFFHb = 5% secondary treated effluent EFFLa = 0.5% primary treated effluent E2a = Estradiol, positive control for primary effluent E2b = Estradiol, positive control for secondary effluent CTRLa = Moderately hard water, negative control for primary effluent CTRLb = Moderately hard water, negative control for secondary effluent
2011-05-18 | E-GEOD-29350 | biostudies-arrayexpress
Project description:Assessment of fecal DNA extraction protocols for metagenomic study
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Project description:The microRNA biogenesis enzyme Drosha was found to be important for DNA repair and this function appears to be distinct to its role in miRNA-mediated repression. Novel small RNAs were reported previously to be produced from the sequences around a DNA break. Utilising an endonuclease system (AsiSI) we were unable to detect such small RNA around 100 cuts within the endogenous genome. Sequencing of R-loops (DNA:RNA hybrids) was performed and an increase in R-loop formation was observed around many DNA break sites. Loss of Drosha appears to perturb this damage dependent formation of R-loops. RNase H1 over-expression appears to reduce repair at these break sites. Drosha appears to be important for facilitating R-loop formation at DNA break sites to aid in the repair process.
2018-02-18 | GSE97648 | GEO
Project description:Contaminants of emerging concern (CECs) in treated municipal effluents have the potential to adversely impact exposed organisms prompting elevated public concern. Using transcriptomic tools, we investigated changes in gene expression and cellular pathways in the liver of male fathead minnows (Pimephales promelas) exposed to 5% concentrations of full secondary-treated (HTP) or advanced primary-treated (PL) municipal wastewater effluents containing CECs. Gene expression changes were associated with apical endpoints (plasma vitellogenin and changes in secondary sexual characteristics). Of 32 effluent CECs analyzed, 28 were detected including pharmaceuticals, personal care products, hormones, and industrial compounds. Transcript patterns differed between effluents, however < 10% of these had agreement in the detected response (e.g. transcrips involved in xenobiotic detoxification, oxidative stress and apoptosis) in both effluents. Exposure to PL effluent caused changes in transcript levels of genes involved in metabolic pathways (e.g., lipid transport and steroid metabolism). Exposure to HTP effluent affected transcripts involved in signaling pathways (e.g., focal adhesion assembly and extracellular matrix). Exposure to both effluents produced significantly higher levels of plasma VTG and changes in secondary sexual characteristics (e.g., ovipositor development). Taken together the results suggest, a potential association between some transcriptomic changes and higher biological responses following effluent exposure; and a potential adverse outcome pathway following exposure to complex chemical mixtures containing CECs -. Furthermore, this study identified responses in key genes and pathways not previously implicated in exposure to CECS, , which could be consistent with effluent exposure (e.g., oxidative stress) in addition to other pathway responses specific to the effluent type. This may be useful for assessing the adverse health effects of fish by effluents exposure to CECs.
2011-05-18 | GSE29350 | GEO