Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microbial remineralization of particulate organic carbon in the ocean’s twilight zone

ABSTRACT: we characterized the microbial communities and proteomes of POC collected from the twilight zone at three contrasting sites in the northwest Pacific Ocean using a metaproteomic approach.Particle-attached bacteria, Alteromonadales, Rhodobacterales and Enterobacteriales, were the major remineralizers of POC in the twilight zone.

INSTRUMENT(S):

ORGANISM(S): Alteromonadales

SUBMITTER: He Yanbin

LAB HEAD: Siqi Liu

PROVIDER: PXD014630 | Pride | 2021-03-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	P10_1_1.raw	Raw
	P10_1_10.raw	Raw
	P10_1_2.raw	Raw
	P10_1_3.raw	Raw
	P10_1_4.raw	Raw

Items per page:

1 - 5 of 482

Similar Datasets

Remineralization of particulate organic carbon in an ocean oxygen minimum zone.

Project description:Biological oceanic processes, principally the surface production, sinking and interior remineralization of organic particles, keep atmospheric CO2 lower than if the ocean was abiotic. The remineralization length scale (RLS, the vertical distance over which organic particle flux declines by 63%, affected by particle respiration, fragmentation and sinking rates) controls the size of this effect and is anomalously high in oxygen minimum zones (OMZ). Here we show in the Eastern Tropical North Pacific OMZ 70% of POC remineralization is due to microbial respiration, indicating that the high RLS is the result of lower particle fragmentation by zooplankton, likely due to the almost complete absence of zooplankton particle interactions in OMZ waters. Hence, the sensitivity of zooplankton to ocean oxygen concentrations can have direct implications for atmospheric carbon sequestration. Future expansion of OMZs is likely to increase biological ocean carbon storage and act as a negative feedback on climate change.

| S-EPMC5364423 | biostudies-literature

Complete list of canonical post-transcriptional modifications in Bacillus subtilis ribosome.

Project description:Using bottom-up oligonucleotide LC-MS/MS in combination with stable isotope labeling, chemical derivatization, and bioinformatics variable modification search, a total of 25 modifications were mapped to the sequences of 16S and 23S RNA in B. subtilis. 10 modification sites, previously identified by others using alternative methods were independently confirmed using targeted MS/MS data analysis. Modification types, namely base/ribose methylation, pseudouridines and dihydrouridine, and modification positions are fully consistent with prior experimental evidence and agree well with modifications that were annotated in E. coli and other bacteria species.

2024-08-06 | PXD050367 | Pride

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Project description:While insulin replacement therapy restores the health and prevents the onset of diabetic complications (DC) for many decades, some T1D patients have elevated hemoglobin A1c values suggesting poor glycemic control, a risk factor of DC. We surveyed the stool microbiome and urinary proteome of a cohort of 220 adolescents and children, half of which had lived with T1D for an average of 7 years and half of which were healthy siblings. Phylogenetic analysis of the 16S rRNA gene did not reveal significant differences in gut microbial alpha-diversity comparing the two cohorts. The urinary proteome of T1D patients revealed increased abundances of several lysosomal proteins that correlated with elevated HbA1c values. In silico protein network analysis linked such proteins to extracellular matrix components and the glycoprotein LRG1. LRG1 is a prominent inflammation and neovascularization biomarker. We hypothesize that these changes implicate aberrant glycation of macromolecules that alter lysosomal function and metabolism in renal tubular epithelial cells, cells that line part of the upper urinary tract.

2019-03-28 | PXD012413 | Pride

Uncertainties of particulate organic carbon concentrations in the mesopelagic zone of the Atlantic ocean.

Project description:Measurements of particulate organic carbon (POC) in the open ocean provide grounds for estimating oceanic carbon budgets and for modelling carbon cycling. The majority of the published POC measurements have been collected at the sea surface. Thus, POC stocks in the upper layer of the water column are relatively well constrained. However, our understanding of the POC distribution and its dynamics in deeper areas is still modest due to insufficient POC measurements. Moreover, the uncertainty of published POC estimates is not always quantified, and neither is it fully understood. In this study, we determined the POC concentrations of samples collected in the upper 500 m during an Atlantic Meridional Transect and described a method for quantifying its experimental uncertainties using duplicate measurements. The analysis revealed that the medians of the total experimental uncertainties associated with our POC concentrations in the productive and mesopelagic zones were 2(±2) mg/m 3 and 3(±1) mg/m 3, respectively. In relative terms, these uncertainties corresponded to ∼12% and ∼35% of POC concentrations, respectively. We modelled the POC uncertainty in order to identify its main causes. This model however could explain only ∼19% of the experimental POC uncertainty. Potential sources of the unexplained uncertainty are discussed.

| S-EPMC10446083 | biostudies-literature

In serach of the pH limit of growth in halo-alkaliphilic cyanobacteria

Project description:We cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP-dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.

2024-10-17 | PXD052563 | Pride

Oxygen minimum zone of the Mexican Pacific

Project description:Oxygen minimum zone of the Mexican Pacific Raw sequence reads

| PRJNA780024 | ENA

Gene expression in germinal center light zone and dark zone B cells

Project description:This SuperSeries is composed of the following subset Series: GSE38696: Gene expression in mouse germinal center light zone and dark zone B cells GSE38697: Gene expression in human germinal center light zone and dark zone B cells Keywords: Expression profiling by array Refer to individual Series

2012-06-13 | E-GEOD-38712 | biostudies-arrayexpress

Krill faecal pellets drive hidden pulses of particulate organic carbon in the marginal ice zone.

Project description:The biological carbon pump drives a flux of particulate organic carbon (POC) through the ocean and affects atmospheric levels of carbon dioxide. Short term, episodic flux events are hard to capture with current observational techniques and may thus be underrepresented in POC flux estimates. We model the potential hidden flux of POC originating from Antarctic krill, whose swarming behaviour could result in a major conduit of carbon to depth through their rapid exploitation of phytoplankton blooms and bulk egestion of rapidly sinking faecal pellets (FPs). Our model results suggest a seasonal krill FP export flux of 0.039 GT C across the Southern Ocean marginal ice zone, corresponding to 17-61% (mean 35%) of current satellite-derived export estimates for this zone. The magnitude of our conservatively estimated flux highlights the important role of large, swarming macrozooplankton in POC export and, the need to incorporate such processes more mechanistically to improve model projections.

| S-EPMC6385259 | biostudies-literature

Gene expression in human germinal center light zone and dark zone B cells

Project description:Microarrays of gene expression in human germinal center light zone and dark zone B cells sorted according to the expression of cell surface molecules CD83 and CXCR4 We used microarray data to identify genes differentially expressed by B cells in the light and dark zones of germinal centers from human tonsil specimens. Germinal center B cells (CD19+CD38+IgD-) were sorted from pediatric tonsil discard specimens into light zone (CXCR4hi/CD83lo) and dark zone (CXCR4lo/CD83hi) populations, from which RNA was extracted

2012-06-13 | E-GEOD-38697 | biostudies-arrayexpress

In-vitro evaluation of Pseudomonas fluorescens antibacterial activity against Listeria spp. isolated from New Zealand horticultural environments

Project description:Beneficial bacteria with antibacterial properties are an attractive alternative to chemical-based antibacterial or bactericidal agents. The aim of our study was to source such bacteria from horticultural produce and environments and to explore the mechanisms of their antimicrobial properties. Four strains of Pseudomonas fluorescens were isolated that possessed antibacterial activity against the pathogen Listeria monocytogenes.

2023-03-10 | PXD019965 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data