Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839877 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptomic study of A. ferrooxidans was explored either during aerobic growth with sulfur as an electron source and oxygen as final electron acceptor or in anaerobic conditions with ferric iron as the final electron receptor. Differential RNA levels were related to changes in cellular functions that were used to develop a preliminary model for A. ferrooxidans electron transport during dissimilatory ferric iron reduction.
2012-05-01 | E-MEXP-3361 | biostudies-arrayexpress
Project description:Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation
2024-05-24 | PXD039266 | Pride
Project description:We investigated transcriptional response of CaCo-2 cells to iron treatments, we studied hemin effect by adding hemin to DMEM-FBS medium and iron deficiency effects in using an iron free medium compared to the same supplemented with FAC (ferric ammonium citrate). Keywords: various iron treatment, differential gene expression, hemin treatment, iron-free
2006-07-14 | GSE3573 | GEO
Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site. 2 samples examined from the different electron-acceptors (sulphate or ferric iron) incubates at the time point of maximal toluene degradation.
2011-03-18 | E-GEOD-25449 | biostudies-arrayexpress
Project description:Purpose: In previous work, we found that iron supplementation to cells rescues impairment of cell viability and proliferation upon lysosomal dysfunction due to inhibition of the vATPase complex. The goal of this study is to characterize the transcriptomic changes (RNA-seq) upon Bafilomycin mediated lysosomal dysfunction with and without iron (Ferric Ammonium Citrate) supplementation. Methods: mRNA profiles of wild type HEK293T cells treated +/- ferric ammonium citrate (0.1mg/ml) and +/- BafilomycinA1 (10nM) were generated by deep sequencing, in triplicate, using Illumina NextSeq500. Results: We mapped about 30-40 million sequence reads per sample to the human genome (build GRCh38). Conclusions: Our study characterizes the transcriptomic changes upon lysosomal dysfunction upon small molecule (Bafilomycin A1) inhibition of vATPase complex. We conclude that there are several notable trasncriptomic changes upon lysosomal dysfunction some of which are reversed by iron supplementation.
2019-12-06 | GSE141507 | GEO
Project description:Anaerobic ammonium oxidation bioreactor metagenome
| PRJNA16685 | ENA
Project description:Hydrogen can be an important source of energy for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface. Nevertheless, the current knowledge of microbial hydrogen utilization in acidic environments is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing aerobically and anaerobically (with ferric iron) on hydrogen as an electron donor, and a respiratory model proposed from the results obtained. In this model, both [NiFe] hydrogenases, cytoplasmic uptake and membrane-bound respiratory, oxidize molecular hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated [FeS]-binding proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa3 oxidase via cytochrome bc1 complex and cytochrome c4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux together with the reduction of molecular oxygen to water. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferric iron reductase) via cytochrome bc1 complex and a cascade of electron transporters (cytochrome c4, cytochrome c552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux together with the reduction of ferric iron to ferrous iron. The proton gradient generated by molecular hydrogen oxidation maintains the membrane potential and allows the generation of ATP via ATP synthase and NADH via NADH-ubiquinone oxidoreductase. To a lesser extent, NADH can also be generated by another bidirectional cytoplasmic hydrogenase. ATP and NADH are further utilized in the Calvin–Benson–Bassham cycle for inorganic carbon uptake and assimilation. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition and features of the deep terrestrial subsurface from the distant past to the present.
2020-11-24 | PXD020361 | Pride
Project description:We investigated transcriptional response of CaCo-2 cells to iron treatments, we studied hemin effect by adding hemin to DMEM-FBS medium and iron deficiency effects in using an iron free medium compared to the same supplemented with FAC (ferric ammonium citrate). Experiment Overall Design: Biological replicates were used (3 samples) of each iron treatments (SF-FAC, SF-0, DMEM-FBS, DMEM-Hemin). Each sample was labelled with cy5 and a pool of each sample was constituted and labelled with cy3.
2008-01-19 | E-GEOD-3573 | biostudies-arrayexpress