Ontology highlight
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PROVIDER: PRJNA484694 | ENA |
REPOSITORIES: ENA
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Project description:Chemical analysis of the compounds present in sediment, although informative, often is not indicative of the downstream biological effects that these contaminants exert on resident aquatic organisms. More direct molecular methods are needed to determine if marine life is affected by exposure to sediments. In this study, we used an aquatic multispecies microarray and q-PCR to investigate the effects on gene expression in juvenile sea bream (Sparus aurata) of two contaminated sediments defined as sediment 1 and 2 respectively, from marine areas in Northern Italy.
2011-01-01 | E-TABM-1146 | biostudies-arrayexpress
Project description:Gas hydrates, also known as clathrates, are cages of ice-like water crystals encasing gas molecules such as methane (CH4). Despite the global importance of gas hydrates, their microbiomes remain mysterious. Microbial cells are physically associated with hydrates, and the taxonomy of these hydrate-associated microbiomes is distinct from non-hydrate-bearing sites. Global 16S rRNA gene surveys show that members of sub-clade JS-1 of the uncultivated bacterial candidate phylum Atribacteria are the dominant taxa in gas hydrates. The Atribacteria phylogeny is highly diverse, suggesting the potential for wide functional variation and niche specialization. Here, we examined the distribution, phylogeny, and metabolic potential of uncultivated Atribacteria in cold, salty, and high-pressure sediments beneath Hydrate Ridge, off the coast of Oregon, USA, using a combination of 16S rRNA gene amplicon, metagenomic, and metaproteomic analysis. Methods were developed to extract bacterial cellular protein from these sediments, as outlined below. Sample Description Three sediments samples were collected from beneath Hydrate Ridge, off the coast of Oregon, USA. Sediments were cored at ODP site 1244 (44°35.1784´N; 125°7.1902´W; 895 m water depth) on the eastern flank of Hydrate Ridge ~3 km northeast of the southern summit on ODP Leg 204 in 2002 and stored at -80°C at the IODP Gulf Coast Repository. E10H5 sediment is from 68.5 meters below sediment surface interface C1H2 sediment is from 2 meters below sediment surface interface. C3H4 sediment is from 21 meters below sediment surface interface.
2020-01-22 | PXD012479 | Pride
Project description:Variations in prokaryotic community assembly and predicted metabolic potential of surface sediments with geography in the coastal northern Zhejiang, East China Sea
| PRJDB4762 | ENA
Project description:A/Zhejiang/DTID-ZJU02/2009(H1N1) is a strain of the swine-origin influenza A(H1N1) virus isolated during the human swine flu outbreak of 2009. To analyze the miRNA expression profiles of A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) at 0, 24, 48, and 72 h post-infection (hpi) and investigate the relation between the miRNA expression profile and its pathogenesis, Human MicroRNA Array v2.0 was applied. At 24 hpi, 174 miRNAs were detected to change their expression compared with 0 hpi, 28 of them increased and 146 decreased. At 48 hpi, 214 changed miRNAs were detected, 21 of them increased and 193 decreased. At 72 hpi, 282 changed miRNAs were detected, 19 of them increased and 263 decreased. Targets of the 21 significantly differentially expressed miRNAs were analyzed by bioinformatics technology. The function categories of the predicted targets were analyzed by GO(Gene ontology) annotation. The signaling pathways involving the changed miRNAs were analyzed by KEGG(Kyoto Encyclopedia of Genes and Genomes) and GO annotation. Four key signaling pathways were identified, namely, the MAPK, apoptosis, JAK_STAT, and toll-like receptor signaling pathways. The apoptosis and MAPK signaling pathways were activated by all miRNAs, whereas the JAK_STAT and toll-like receptor signaling pathways were activated by some miRNAs but inhibited by the others, suggesting balance in the host–virus interaction. We also constructed and analyzed the protein-protein interaction network of all the predicted targets and found some key nodes. This finding provides a picture of miRNA expression in A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) as complete as possible, which may provide important information for investigation of H1N1 pathogenesis and therapeutic method. the miRNA expression profiles of A549 cells infected with A/Zhejiang/DTID-ZJU02/2009(H1N1) at 0, 24, 48, and 72 h post-infection (hpi) were analyzed and the relation between the miRNA expression profile and its pathogenesis was investigated.
2013-11-06 | E-GEOD-52105 | biostudies-arrayexpress
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
2010-11-13 | GSE25227 | 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:Sediments and faeces 16S secuences Metagenome
| PRJNA381212 | ENA