Ontology highlight
ABSTRACT:
PROVIDER: PRJNA749920 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR24202166_1.fastq.gz | Fastqsanger.gz | |||
| SRR24202166_2.fastq.gz | Fastqsanger.gz | |||
| SRR24202167_1.fastq.gz | Fastqsanger.gz | |||
| SRR24202167_2.fastq.gz | Fastqsanger.gz |
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Project description:Peptides and proteins were identified using a novel de novo-discovery approach in suspended and sinking organic particles from the eastern tropical North Pacific and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. De novo peptide sequencing, where the sequence of amino acids is determined directly from mass spectra rather than from comparison to theoretical spectra from a selected sequence database, was found to be a useful tool for discovery of peptides present in a sample but not initially included in the search database. Iterative de novo-informed database search results suggested the presence of fungal peptides and proteins in deep sinking particles, consistent with growing evidence that fungi play an important role in degradation of sinking material in the ocean. The de novo-discovery approach also allowed the tracking of modified autotrophic cyanobacterial peptides to the deep sea, where they contributed 0.63% of the phylum-level identifiable peptide pool in a bathymetric sediment trap sample. Overall, the amino acid composition of the peptides in the sinking material showed little change with depth, consistent with earlier observations of bulk organic matter and/or amino acid composition during the early stages of degradation. However, we identified an abundance of modified amino acids in sinking and suspended particles, including high levels of deamidation, suggesting that partial degradation of protein could potentially fuel observed anammox and contribute to observed pool of refractory organic nitrogen. We also observe methylation of arginine, which has previously been shown to slow degradation of peptides in seawater. Our results demonstrate several examples how de novo-discovery allows for a deeper evaluation of proteins and peptides in environmental systems undergoing degradation.
2022-01-10 | PXD023187 | Pride
Project description:suspended particulate matter Raw sequence reads
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Project description:The purpose of this study was to characterize global gene expression in human airway epithelial cells and identify cellular pathways associated with coarse, fine and ultrafine particulate matter (PM) exposures. Ambient PM was collected in 3 different size fractions from Chapel Hill air, particles were extracted from foam or filter matrices and lyophilized. Human primary airway epithelial cells were exposed to particles at 250μg/ml or vehicle control for 6h in culture. Following exposure, RNA was isolated and hybridized to human HG U133A affymetrix chips. Keywords: particle treatment
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Project description:Phytoplankton blooms represent hotspots of primary production and lead to the formation of particulate organic matter composed of living and dead algal cells. These particles are characterized by steep chemical gradients, for instance in oxygen concentration, that provide diverse ecological niches for specifically adapted microbes to thrive. Particulate fractions were collected at almost daily intervals between early March and late May in 2018. Amplicon sequencing and Meta-omics was used to asses microbial community composition and functionality at different time points.
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Project description:Particulate Organic Matter from filter samples (0.2um Supor, 3um Supor, 52 Nitex) in the oxygen deficient zone of the Eastern tropical Northern Pacific.
2023-06-21 | MSV000092225 | MassIVE
Project description:Suspended particulate matter from the North Pacific Gyre Metagenome
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Project description:We reported the gene expression profile of T47D cells treated with the organic extract of Particulate matter 2.5 (PM2.5) sampled next to the municipal solid waste incineration plant of Bologna city. Based on a air pollution distribution model that takes the incinaration plant as point source of emission, two sites were chosen to sample particulate matter near incineration plant: "FrulloEst" representing the maximum effect of the incineration plant, "Calamosco" representing the negative control of "FrulloEst" (minimun effect of incineration plant, same effect of other air pollution fonts). Another site, "Giardini Margherita", is chosen to sample the urban background air pollution. for each site sample collection was performed in winter and in summer season.
2018-01-31 | E-MEXP-3686 | biostudies-arrayexpress
Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 ± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 ± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 µmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287
2020-01-07 | GSE142805 | GEO