ASEDMAR
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR149036.fastq.gz | Fastqsanger.gz | |||
| ERR149037.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Crude oil is the one of the most important natural assets of humankind, yet it is a major environmental pollutant, in particular, in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, where the metabolic potential of indigenous populations towards the chronic pollution at a large scale is yet to be defined, particularly in anaerobic and micro-anaerobic marine sites. Here, we provided a novel insight into the active microbial metabolism in sediments from three environments along the coastline of Italy. Microbial proteomes exhibited prevalence in anaerobic metabolism, not related to the biodegradation directly, suggesting the strong limitation by oxygen induced by the carbon overload. They also point at previously unrecognized metabolic coupling between methane and methanol utilizers as well as sulfur reducers in marine petroleum polluted sediments.
2015-07-24 | PXD001490 | Pride
Project description:Protein expression in Staphylococcus sp. NIOSBK35 isolated from marine environment (mangrove sediments) to different concentrations of arsenic (III)
2019-12-02 | PXD013569 | Pride
Project description:Talemi2014 - Arsenic toxicity and
detoxification mechanisms in yeast
The model implements arsenite (AsIII)
transport regulation, its distribution within main cellular AsIII
pools and detoxification. The intracellular As pools considered are
free AsIII (AsIIIin), protein-bound AsIII (AsIIIprot), glutathione
conjugated AsIII (AsGS3) and vacuolar sequestered AsIII (vAsGS3).
This model is described in the article:
Mathematical modelling of
arsenic transport, distribution and detoxification processes in
yeast.
Talemi SR, Jacobson T, Garla V,
Navarrete C, Wagner A, Tamás MJ, Schaber J.
Mol. Microbiol. 2014 Jun; 92(6):
1343-1356
Abstract:
Arsenic has a dual role as causative and curative agent of
human disease. Therefore, there is considerable interest in
elucidating arsenic toxicity and detoxification mechanisms. By
an ensemble modelling approach, we identified a best
parsimonious mathematical model which recapitulates and
predicts intracellular arsenic dynamics for different
conditions and mutants, thereby providing novel insights into
arsenic toxicity and detoxification mechanisms in yeast, which
could partly be confirmed experimentally by dedicated
experiments. Specifically, our analyses suggest that: (i)
arsenic is mainly protein-bound during short-term (acute)
exposure, whereas glutathione-conjugated arsenic dominates
during long-term (chronic) exposure, (ii) arsenic is not stably
retained, but can leave the vacuole via an export mechanism,
and (iii) Fps1 is controlled by Hog1-dependent and
Hog1-independent mechanisms during arsenite stress. Our results
challenge glutathione depletion as a key mechanism for arsenic
toxicity and instead suggest that (iv) increased glutathione
biosynthesis protects the proteome against the damaging effects
of arsenic and that (v) widespread protein inactivation
contributes to the toxicity of this metalloid. Our work in
yeast may prove useful to elucidate similar mechanisms in
higher eukaryotes and have implications for the use of arsenic
in medical therapy.
This model is hosted on
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and identified by:
BIOMD0000000547.
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2024-09-02 | BIOMD0000000547 | BioModels
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
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Project description:Arsenic (As) is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification, and adaptation mechanisms in bacteria that are associated with host in arsenic-rich conditions can provide novel insights into dynamics of host-microbe-microenvironment interactions. In the present study, we have investigated an arsenic resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. oryzae (Xoo), which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12kb ars cassette in Xoo IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. This cassette has spread in lineage with highly virulent strains owing to a particular lineage’s evolutionary success. Further, we performed the transcriptomic analysis of Xoo strain IXO1088 under arsenate/arsenite exposure using RNA sequencing. The transcriptomic analysis revealed that arsenic detoxification and efflux, oxidative stress response, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. The study provides useful insights into the acquisition, detoxification, and adaptation mechanisms among Xoo populations to adapt under arsenic-rich environmental conditions.
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Project description:Marine viral concentrates (VCs) contains a substantial amount of non-cellular biological particles, e.g. viruses, gene transfer agents (GTAs) and membrane vesicles that are ecological significant. Metagenomic sequencing of VCs has been extensively applied to study the diversity and function potential of natural virions whereas information of nonn-viral components are often excluded for investigation. Here we apply a shotgun proteomic approach to characterize the origin and function of proteins in the VCs collected from the deep chlorophyll maximum (DCM) of the South China Sea. Using a custom database, we identified 636 non-redundant proteins represented by a total of 7220 spectra from the two VC samples. Cyanophages, pelagiphages, Phycodnaviridae and a group of uncultured viruses (previouly collected from DCM of Mediterranean Sea) contributed the most in the viral proteome. Seldom proteins related to RNA viruses and known GTAs were found despites of the presence of their sequences in the protein-searching database, suggested that these particles might be low abundant in the samples. Over 60% of identified spectra could not be assigned to viruses. The non-viral spectra were dominated by microbial groups of SAR324, SAR11, Actinobacteria and picoeukaryotic algae such as prasinophytes.Interestingly, we found that periplasmic proteins such as diverse ABC and TRAP transporters, and 56 kDa selenium-binding proteins, were enriched in this fraction.Together with other detected non-viral proteins,we could identify significant microbial functions, such as the utilization of glycine betaine, 3-dimethylsulphoniopropionate,and taurine by SAR11,and urea by prochlorococcus, nitrous oxide production by ammonia-oxidizing archaea and peroxide detoxification by unkonwn gammaproteobacteria. Our study of marine VCs demonstrates the potential application of metaproteomics to link the nano-size materials to the diversity of virions and interesting microbial functions in the ocean.
2018-05-02 | PXD007174 | Pride
Project description:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches. 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.
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