Experimental fossilization of photosynthetic microbial mats in coarse-grained siliciclastic sediments
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PROVIDER: PRJEB18038 | ENA |
REPOSITORIES: ENA
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Project description:Simulated experimental samples from sediments Raw sequence reads
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Project description:Several mechanisms are known to cause monomeric protein misfolding. Coarse-grained simulations have predicted an additional mechanism exists involving off-pathway, non-covalent lasso entanglements, which are long-lived kinetic traps and structurally resemble the native state. Here, we examine whether such misfolded states occur in long-timescale, all-atom folding simulations of ubiquitin and λ-repressor. We find these entangled misfolded states are populated in higher-resolution models. However, due to the small size of ubiquitin and λ-repressor, these states are short-lived. In contrast, coarse-grained simulations of a larger protein, IspE, predict it populates long-lived misfolded states. Using an Arrhenius extrapolation applied to all-atom simulations we estimate that indeed these IspE misfolded states have lifetimes similar to the native state, while remaining soluble. We further show these misfolded states are consistent with the structural changes inferred from limited proteolysis and crosslinking mass spectrometry experiments. Our results indicate that misfolded states composed of non-native entanglements can persist for long timescales in both all-atom simulations and experiments.
2025-08-11 | PXD066083 | Pride
Project description:Several mechanisms intrinsic to a protein’s primary structure are known to cause monomeric protein misfolding. Coarse-grained simulations, in which multiple atoms are represented by a single interaction site, have predicted that a novel mechanism of misfolding exists involving off-pathway, non-covalent lasso entanglements, which are distinct from protein knots and slip knots. These misfolded states can act as long-lived kinetic traps and, intriguingly, may resemble the native state structurally according to those simulations. Here, we examine whether such misfolded states occur in long-timescale, physics-based all-atom simulations of protein folding, focusing on ubiquitin and λ-repressor. Our findings confirm the formation of these entangled misfolded states in this higher-resolution model, some of which share structural similarities with the native state. However, due to the small size of ubiquitin and λ-repressor, these misfolded states are short-lived. In contrast, coarse-grained simulations of a larger, typical size protein, ispE, reveal several long-lived misfolded clusters with non-native entanglements. These misfolded clusters are consistent with digestion patterns observed in Limited Proteolysis and Cross-linking Mass Spectrometry experiments. Using an Arrhenius extrapolation from all-atom simulations we estimate these ispE misfolded clusters can persist for extended periods, potentially months, while remaining soluble. Our results suggest that monomeric proteins can exhibit subpopulations of misfolded, self-entangled states that may explain long-timescale changes in protein structure and function in vivo.
2025-08-11 | PXD055795 | 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 amoA-carrying AOA within these sediments.
2013-08-24 | GSE50163 | GEO
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.
2015-01-30 | GSE65430 | GEO
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:Photosynthetic Activated Sludge Bioreactor Metagenome
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Project description:Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated microbial community profiles as well as directly assayed nitrogen cycling genes that encode the enzymes responsible for overall nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms responsible for production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that elevated rates of nitrous oxide production and consumption are the result of changes in community structure, not simply changes in microbial activity.
2018-01-13 | GSE108888 | GEO