Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589080 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.
2009-12-15 | GSE19483 | GEO
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils. Two channel experiment; control versus exposed (samples were time matched). 3 biological replicates, three technical replicates for both exposed and control fish. Samples were paired at random. One replicate per array
2010-05-18 | E-GEOD-19483 | biostudies-arrayexpress
Project description:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
Project description:Microbial community diversity in petroleum reservoirs
| PRJNA246768 | ENA
Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.
2023-06-06 | GSE234088 | GEO
Project description:The use of high levels of marine fish oil in aquafeeds is a non-sustainable practice. However, more sustainable oils sources from terrestrial plants do not contain long-chain polyunsaturated fatty acids (LC-PUFA). Consequently, feeds based on conventional vegetable oils reduce n-3 LC-PUFA levels in farmed fish. Therefore, the aquaculture industry desperately requires new, sustainable oil sources that contain high levels of n-3 LC-PUFA in order to supply the increasing demand for fish and seafood while maintaining the high nutritional quality of the farmed product. One approach to the renewable supply of n-3 LC-PUFA is metabolic engineering oilseed crops with the capacity to synthesize these essential fatty acids in seeds. In the present study, the oilseed Camelina sativa has been transformed with algal genes encoding the n-3 biosynthetic pathway and expression restricted to the seeds via seed-specific promoters to produce an oil containing > 20% eicosapentaenoic acid (EPA). This oil was investigated as a replacement for marine fish oil in feeds for post-smolt Atlantic salmon. In addition, this study with EPA-rich oil will contribute to our understanding of the biochemical and molecular mechanisms involved in the control and regulation of docosahexaenoic acid (DHA) production from EPA, and will thus better inform our understanding of this key part of the LC-PUFA biosynthetic pathway.
2015-12-21 | E-MTAB-2855 | biostudies-arrayexpress
Project description:The arctic ecosystems are increasingly exposed to pollution particularly from offshore petroleum extraction-related activities. The objective of the study is to map transcriptome responses in copepods of the arctic region in response to PAHs phenanthrene (Phe) and benzo[a]pyrene (BaP) found in crude-oil contaminants.
2021-10-01 | E-MTAB-10911 | biostudies-arrayexpress
Project description:The arctic ecosystems are increasingly exposed to pollution particularly from offshore petroleum extraction-related activities. The objective of the study is to map transcriptome responses in copepods of the arctic region in response to PAHs phenanthrene (Phe) and benzo[a]pyrene (BaP) found in crude-oil contaminants.
2021-10-01 | E-MTAB-10917 | biostudies-arrayexpress