Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1219498 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32236744_1.fastq.gz | Fastqsanger.gz | |||
| SRR32236744_2.fastq.gz | Fastqsanger.gz | |||
| SRR32236745_1.fastq.gz | Fastqsanger.gz | |||
| SRR32236745_2.fastq.gz | Fastqsanger.gz | |||
| SRR32236746_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 78 |
Similar Datasets
Project description:The consistent cold temperatures and large amount of precipitation in the Olympic and Cascade ranges of Washington State are thought to increase atmospheric deposition of contaminants in these high elevation locations. Total mercury and 28 organochlorine compounds were measured in composite, whole fish samples collected from 14 remote lakes in the Olympic, Mt. Rainer, and North Cascades National Parks. Mercury was detected in fish from all lakes sampled and ranged in concentration from 17 to 262 ug/kg wet weight. Only two organochlorines, total polychlorinated biphenyls (tPCB) and dichlorodiphenyldichloroethylene (DDE), were detected in fish tissues (concentrations <25 ug/kg wet weight). No organochlorines were detected in sediments (MRL ≈1-5 ug/kg), while median total and methyl mercury in sediments were 30.4 and 0.34 ug/kg (dry weight), respectively. Using a targeted rainbow trout cDNA microarray with known genes, we detected significant differences in liver transcriptional responses, including metabolic, endocrine, and immune-related genes, in fish collected from a contaminated lake compared to a lake with a lower contaminant load. Overall, our results suggest that local urban areas are contributing to the observed contaminant patterns, while the transcriptional changes point to a biological response associated with exposure to these contaminants in fish. Specifically, the gene expression pattern leads us to hypothesize a role for mercury in disrupting the metabolic and reproductive pathways in fish from high elevation lakes in western Washington. Keywords: High altitude lakes, mercury, salmonids, organochlorines
2007-05-01 | GSE6886 | GEO
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoA-carrying AOA within these sediments.
2013-08-24 | GSE50163 | GEO
Project description:In this study, we investigated Mn3+-cycling microbial populations enriched from Lake Matano, Indonesia using metagenomics and metaproteomics. Lake Matano contains an active Mn cycle that links the oxic-anoxic interface with anoxic deep waters that are enriched in iron and manganese, and depleted in sulfate, phosphate, and oxidized nitrogen (Crowe et al., 2008; Jones et al., 2011). Sediments were incubated with sequential transfers for ~1 year with Mn3+ as the sole electron acceptor and methane as organic carbon until achieving sediment-free conditions. Here we investigate this novel species of Dechloromonas (Betaproteobacteria), “Candidatus Dechloromonas occultata,” which was the dominant population in enrichment cultures with active Mn3+ reduction. “Ca. D. occultata” expressed electron conduits related to those involved in Fe2+ oxidation (Mto-like), as well as a novel cytochrome c-rich gene cluster putatively involved in extracellular electron transfer, and an atypical nitrous oxide reductase. According to ribosomal counts, Dechloromonas outnumber Geobacter. In terms of functional genes, Dechloromonas expresses a wider variety and number of genes. Dechloromonas therefore seems to have a (selective?) advantage over Geobacter. Previous experiments revealed that Dechloromonas express nitrogen regulators, reductases and scavenging genes, as well as many carbon central metabolic pathways, and aromatic carbon degradation pathways. Dechloromonas is a beta proteobacteria, and these are "experts" in nitrogen metabolism. Geobacter, on the other hand, is well known for carbon degradation. Our previous experiments lead to our hypothesis that Dechloromonas is more active because they are more successful at acquiring nitrogen, a limiting nutrient for Geobacter. This would further suggest that carbon is not the limiting nutrient. We will test 2 hypotheses with the next suite of experiments 1) pyrophosphate supports the community, by allowing carbon fixation , 2)Dechloromonas has a (selective?) advantage over Geobacter. To test this hypothesis, bioreactors will be used to grow biotriplicate cultures of (1)- CH4 vs. pyrophosphate and (2)-CH4 vs. Mn(III) pyrophosphate. Here we have analyzed whole cell pellets using gas phase fractionations on the Q Exactive. Are Dechloromonas capable of out-competing Geobacter when grown in media with methane as the only carbon source bioreactors because they are capable of acquiring more nitrogen? Source of inoculum. Lake Matano is a metal-rich, ancient ocean analog (Crowe et al. 2011, Jones et al. 2011). Organic carbon in Lake Matano is mostly mineralized via methanogenesis before reaching the iron-rich sediments, limiting organic matter bioavailability for metal-reducers (Kuntz et al. 2015). A 15-cm sediment core from 200 m water depth in Lake Matano, Sulawesi Island, Indonesia (02°26′27.1′′S, 121°15′12.3′′E; in situ sediment temperature ~27°C) was sampled in November 2014 and sub-sampled at 5 cm increments. Sediments were sealed in gas-tight Mylar bags with no headspace (Hansen et al. 2000) and stored at 4°C until incubations began in December 2015.
2020-06-30 | PXD011642 | Pride
Project description:The aim of this study is to determine the molecular mechanism by which indoxyl sulfate acts on endothelial cells. Endothelial cells (HUVECs) were incubated with medium containing indoxyl sulfate at concentration found in chronic kidney disease patients (1mM). Since indoxyl sulfate is a potassium salt, control medium contains KCl at 1mM. Cells were incubated during four hours in presence of indoxyl sulfate or KCl. Seven biological replicates were obtained for these two conditions.
2014-01-01 | GSE34259 | GEO
Project description:Dimitry Y. Sorokin et al., (2021, Russian Academy of Sciences, Russia and Delft University of Technology, The Netherlands) describe the isolation and physiological and genomic properties of a fifth functional group of sulfur-respiring haloarchaea enriched from hypersaline lake sediments with CO as the electron donor. Additional shotgun proteomic profiling of the described strains has been performed.
2022-12-25 | PXD028241 | Pride
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoAÂ-carrying AOA within these sediments. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50163 | biostudies-arrayexpress
Project description:Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic planktonic bacteria, dwelling in freshwater systems (lakes, ponds, and streams) across all climatic zones and across all continents. This includes habitats characterised by strongly fluctuating environmental conditions. So the experiments were designed to mimick winter and summer scenarios with additional impact of UV irradiation. Comparative transcriptomic studies were conducted to analyse gene-expression levels in contrasting experimental conditions. Overall, molecular candidates were revealed that may contribute in rapid acclimatisation of this strain in their immediate environment.
2017-10-31 | GSE98129 | GEO