Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666055 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12727000_1.fastq.gz | Fastqsanger.gz | |||
| SRR12727000_2.fastq.gz | Fastqsanger.gz | |||
| SRR12727001_1.fastq.gz | Fastqsanger.gz | |||
| SRR12727001_2.fastq.gz | Fastqsanger.gz | |||
| SRR12726999_1.fastq.gz | Fastqsanger.gz |
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Project description:The increase in human population and urbanization are resulting in an increase in the volume of wastewater and urban runoff effluents entering natural ecosystems. These effluents may contain multiple pollutants to which the biological response of aquatic organisms is still poorly understood mainly due to mixture toxicity and interactions with other environmental factors. In this context, RNA sequencing was used to assess the impact of a chronic exposure to wastewater treatment plant and stormwater effluents at the whole-transcriptome level and evaluate the potential physiological outcomes in the Asian clam Corbicula fluminea. We de-novo assembled a transcriptome from C. fluminea digestive gland and identified a set of 3,181 transcripts with altered abundance in response to water quality. The largest differences in transcriptomic profiles were observed between C. fluminea from the reference site and those exposed to wastewater treatment plant effluents. On both anthropogenically impacted sites, most differentially expressed transcripts were involved in signaling pathways in relation to energy metabolism such as mTOR and FoxO, suggesting an energy/nutrient deficit and hypoxic conditions. These conditions were likely responsible for damages to proteins and transcripts in response to wastewater treatment effluents whereas exposure to urban runoff might result in immune and endocrine disruptions. In absence of comprehensive chemical characterization, the RNAseq approach could provide information regarding the mode of action of pollutants and then be useful for the identification of which parameters must be studied at higher integration level in order to diagnose sites where the presence of complex and variable mixtures of chemicals is suspected.
2018-08-28 | GSE104933 | GEO
Project description:Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures. Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures.
2020-08-19 | PXD013655 | Pride
Project description:Three surface waters in Gainesville, Florida were used in a 48 hour whole effluents exposure to assess gene expression profiles of male fathead minnow liver. Microarray analysis was used to determine changes in gene expression of exposed fish to waters from a site downstream of a wastewater treatment plant (streamwater), a wastewater treatment plant (wastewater), and a lake (stormwater). Differences in gene expression between fish exposed to collected waters and controls were observed. Number of altered genes and biological processes were 1028 and 18 for stormwater; 787 and 19 for streamwater; and: 575 and 12 for wastewater. In general, the effects observed in all exposed fish were related with fatty acid metabolism, DNA repair, oxidation-reduction process, cell wall catabolic process and apoptosis. All exposed fish showed altered expression of genes related with DNA damage repair. In particular fish exposed to stormwater and streamwater showed downregulation of several key intermediates transcripts of cholesterol. The presence and environmental persistence of perfluorinated chemicals (PFCs) in these waters, the resemblance in known effects on transcripts with those found in this study, suggest that the set of genes differentially regulated in fathead minnows after 48 hours of exposure may be attributed to exposure to PFCs. Three surface water sites were chosen for effluent collection in Gainesville, Florida: A lake (stormwater), surface water downstream of a wastewater treatment plant (streamwater), and a wastewater treatment plant effluent used for landscaping irrigation (wastewater). Water from each site was collected two days prior to the fish exposure experiment using Chemfluor ® tubing and a 120 liters steel barrels coated with polyester resin (gel coat) to avoid cross-contamination. Three barrels for each effluent were collected during day 1. Water from the barrel was transported to the laboratory and pumped into four fiberglass cylinders in the aquatic toxicology facility. Water from each cylinder was then pumped into four replicate aquariums per treatment and kept for 1 day without fish (pre-treatment). On day 2, four male fathead minnows from a common tank were transferred to each replicate aquarium and kept for 48 hours, with one 75% water change after first 24 hours. The exposure system consisted of 40 L glass aquaria. Each exposure was conducted in quadruplicate and each aquarium contained the four male fish in 25 L of treatment water . The water used in the control treatment was carbon filtered, dechlorinated tap water. The positions of the treatment tanks were randomized and test initiation times were staggered to ensure an exposure/sampling interval of 48 h. The fish were not fed during the experiment. The temperature range of the water was 24-26 °C with a photoperiod of 16 h light: 8 h dark. Liver was isolate from 4 males indviduals for each treatment except for control group (3 individuals).
2012-04-24 | E-GEOD-37550 | biostudies-arrayexpress
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2014-10-15 | GSE61830 | GEO
Project description:Evaluating the potential human health and ecological risks associated with exposures to complex chemical mixtures in the environment is one of the main challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrate chemical monitoring and biological effects data to evaluate risks associated with specific chemicals present in the environment. In the present study water samples from five locations near two wastewater treatment plants in the St. Croix River basin on the border of MN and WI, USA were analyzed for 127 contaminants including wastewater indicators, pharmaceuticals, and a number of natural and synthetic steroids. Prior knowledge about chemical-gene interactions was used to develop site-specific knowledge assembly models (KAMs) that were used to formulate hypothesis concerning possible biological effects of exposure to the chemicals detected at each location and suggest assays and endpoints for follow-up investigation. Additionally empirical hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location using a high density oligonucleotide microarray. Empirical gene expression data were analyzed to identify functional annotation terms enriched among the lists of differentially-expressed probes. However, the general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses, based on prior knowledge.
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Project description:Juvenile gilthead sea bream of 10-15 g initial body weight were randomly distributed in eight 500-L tanks in a seawater re-circulatory system equipped with physical and biological filters, and a heat-unit system that maintained water temperature above 18-19 ºC. Fish grew from July to December at a density of 8-10 kg/m3 with an overall daily growth index of 1.9 ± 0.01. Extruded pellets (47 % protein, 21% lipid; Proaqua, Palencia, Spain) were offered to visual satiety. Feeding was stopped one day before confinement exposure, and batches of 10 fish were then transferred from two 500-L tanks to cylinder net baskets of 10-L volume (117-123 Kg/m3), suspended each one in 90-L tanks with a high flow of seawater (10 L/min) to avoid water deterioration (Oxygen > 5 ppm; unionised ammonia < 0.02 mg/L). Fish from seven additional 500-L tanks were established as control groups, and remained undisturbed prior to sampling at zero and each sampling time. At each sampling time (1.5, 3, 6, 24, 72 and 120 h), eight fish from one control and one confinement tank were netted into a bucket to be anaesthetized with 0.1 g/L 3-aminobenzoic acid ethyl ester (MS-222). Fish were killed by cervical section and liver was taken, frozen immediately in liquid nitrogen and stored at -80 ºC until RNA isolation. Only 6h, 72h and 120h were analysed on the microarray. The experimental design was a reference design with the reference being prepared from a pool of all (confined and control) RNAs used in the microarray analysis. All samples were hybridised twice (except L72C5R, L120C2F, L120S4F, L24C4F) with one being the dye swap of the other. Keywords: Time Course
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Project description:Three surface waters in Gainesville, Florida were used in a 48 hour whole effluents exposure to assess gene expression profiles of male fathead minnow liver. Microarray analysis was used to determine changes in gene expression of exposed fish to waters from a site downstream of a wastewater treatment plant (streamwater), a wastewater treatment plant (wastewater), and a lake (stormwater). Differences in gene expression between fish exposed to collected waters and controls were observed. Number of altered genes and biological processes were 1028 and 18 for stormwater; 787 and 19 for streamwater; and: 575 and 12 for wastewater. In general, the effects observed in all exposed fish were related with fatty acid metabolism, DNA repair, oxidation-reduction process, cell wall catabolic process and apoptosis. All exposed fish showed altered expression of genes related with DNA damage repair. In particular fish exposed to stormwater and streamwater showed downregulation of several key intermediates transcripts of cholesterol. The presence and environmental persistence of perfluorinated chemicals (PFCs) in these waters, the resemblance in known effects on transcripts with those found in this study, suggest that the set of genes differentially regulated in fathead minnows after 48 hours of exposure may be attributed to exposure to PFCs.
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