Ontology highlight
ABSTRACT:
PROVIDER: PRJNA492367 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7888540_1.fastq.gz | Fastqsanger.gz | |||
| SRR7888540_2.fastq.gz | Fastqsanger.gz | |||
| SRR7888550_1.fastq.gz | Fastqsanger.gz | |||
| SRR7888550_2.fastq.gz | Fastqsanger.gz | |||
| SRR7888560_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Fungi actively weather silicate minerals to extract nutrients, using different mechanisms. However, it is not clear whether the same mechanism(s) is used for all minerals. The question addressed here is whether distinct minerals can stimulate different weathering mechanisms and lead to a shift in fungal genes expression. Methods: Microcosm experiments were set up with one fungus and three minerals containing the same targeted metal nutrient (K), but with a variable degree of resistance to dissolution. The experiment used transcriptomics to compare the active gene expression of the ectomycorrhizal basidiomycetes Paxillus involutus fungus in response to developing on each of the three minerals as sole K sources. The selected minerals, with a decreasing resistance to K extraction, were: muscovite, phlogopite, and K-exchanged vermiculite. Results: Gene expression analysis after the experiments indicated that the level of K-deprivation stress was muscovite > phlogopite >> K-vermiculite. Genes and functions overexpressed in the experiments indicated meaningful metabolic activities including K extraction and transport. Conclusions: The fungus Paxillus involutus activated different metabolic pathways and, accordingly, switched on or off different genes depending on the minerals from which it was forced to obtain potassium, a fundamental nutrient for its growth. The differential expression of the fungal genes generated alternative chemical attacks on the minerals, resulting in a tailored kind of dissolution and selective uptake of chemical elements. When exposed to K-vermiculite, the fungus overexpressed gene sets related to the organisation of the cytoskeleton and also to vesicle-mediated transport. If phlogopite was supplied, the fungus overexpressed gene sets involved with organic acid and oxoacid metabolic processes. When the only source of potassium was muscovite, the fungus overexpressed monooxygenase activity and oxidoreductase activity. These changing strategies, which resulted in a different impact on the fungal uptake of the elements, always granted some potassium to the fungus.
2025-10-03 | GSE158973 | GEO
Project description:Asbestos is the general term for a family of naturally occurring fibrous silicate minerals having commercial importance. They have been used widely for construction and for a number of industrial applications until early 70’s. It is now well known that workers exposed to asbestos are at high risk of developing many lung diseases including asbestosis, malignant mesothelioma, bronchial adenocarcinoma; squamous cell carcinoma of the respiratory epithelium and large/ small cell lung carcinoma. However, the disease causing potential and related processes associated with various asbestos/asbestiform fiber exposures are still largely unknown. In this study, we exposed C57BL6 female mice to asbestos (crocidolite, tremolite), asbestiform fibers (erionite) and a low pathogenicity mineral fiber (wollastonite) to assess pulmonary toxicity responses along with gene expression profiles in the lungs following 7 days post pharyngeal aspiration.
2018-03-01 | GSE100900 | GEO
Project description:The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.
2009-12-31 | GSE12133 | GEO
Project description:Phylotypic diversity of bacteria associated with speleothems of a silicate cave
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Project description:The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity. Cultures of Cupriavidus metallidurans CH34 were grown in Tris buffered medium MM284 media (with iron), MM284 without iron and MM284 without iron with sterilized basalt at 25 rpm, 30°C until mid-log phase. RNA was extracted from the cells. Three biological replicates of both samples were differentially labeled (resp. Cy3 and Cy5) and hybridized to three CH34 60-mer oligonucleotide glass-spotted microarray carrying three technical repeats.
2009-12-30 | E-GEOD-12133 | biostudies-arrayexpress
Project description:In this study, we investigated the gene expression induced by locally delivered gold and silicate nanoaprticles with the diameter of 20 and 100 nm in the retina. We injected nanoparticles into the vitreous cavity of 5-week-old male C57BL/6 mice. Au20 indicates gold nanoparticles of which diameters were 20 nm, Au100 gold nanoparticles of which diameters were 100 nm, Si20 silicate nanoparticles of which diameters were 20 nm, and Si100 silicate nanoparticles of which diameters were 100 nm.
2013-07-31 | GSE49371 | GEO
Project description:Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.
2020-08-07 | GSE155316 | GEO