Mineral
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA495753 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8039750_1.fastq.gz | Fastqsanger.gz | |||
| SRR8039750_2.fastq.gz | Fastqsanger.gz | |||
| SRR8039760_1.fastq.gz | Fastqsanger.gz | |||
| SRR8039760_2.fastq.gz | Fastqsanger.gz | |||
| SRR8039780_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 80 |
Similar Datasets
Project description:Decreased mineral density is a risk factor for skeletal pathologies including bone metastasis, the leading cause of mortality in patients with advanced breast cancer, but the underlying mechanisms are poorly understood. While reduced mineral density can drive pathological bone remodeling via direct effects on select cell types, indirect effects due to broad changes of the microenvironment may be similarly important. However, how bone mineral content affects microenvironmental heterogeneity remains to be elucidated. Here, we leverage decellularized bone matrices with varied mineral content in combination with single-cell RNA-sequencing to study how reduced bone mineral content affects microenvironmental complexity and tumor growth. We performed single-cell RNA sequencing on implanted decellularized bovine bone scaffolds in which the mineral was either maintained at physiological levels or removed to simulate scenarios of impaired bone mineralization as, for example, present during aging. Using this approach, we explored the heterogeneous stromal response to varied bone mineral content in both an immunocompromised and immunocompetent, syngeneic mouse model in the presence and absence of cancer cells.
2024-03-04 | GSE256109 | GEO
Project description:Cell lysates of Fusarium sp. DS 682, a saprotrophic fungus, were prepared from fungal biomass grown on PDA agar without M9 and micronutrients. Fungus was exposed to minerals, 100 uL of 50% (w/v) natural kaolinite solution. Three fungal plate collections for each growth condition, with (+ mineral) and without mineral (- mineral), were grown for 14 days on PDA (incubated at 28 C) and harvested after 15 days. Extracted hyphae (500 mg) was prepared using the MPLEx protocol. A nanoACQUITY ultra performance liquid chromatography (LC) with a 2DLC system was used for separation of protein digests. Eluted peptides from the C18 column were analyzed using a Q-Exactive Plus Orbitrap MS for high resolution MS and high-energy collision-induced dissociation tandem MS by electrospray ionization for subsequent quantitative proteomic analysis. Data was searched with MaxQuant. Additional post-processed results and metadata can be accessed at https://doi.org/10.25584/KSOmicsFspDS682/1766303
2021-04-16 | MSV000087221 | MassIVE
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base. The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ferrous iron to ferric and removing sulphur compounds that can accumulate on the mineral surface. Metals are most efficiently released from sulphide ores if the microorganisms form a thin layer, termed a ‘biofilm’, on the mineral surface. A crucial stage in bioleaching is how efficiently the microbes attach to the mineral. This project will test how rapidly a biofilm is formed and copper is released from the mineral by different combinations of microorganisms and the order that they are added. Data on the biological processes the microorganisms carry out will be used in computer modelling to suggest the best combination and order in which to add the different types of microbes. This in turn will increase the efficiency of industrial bioleaching by reducing the time between when a heap is built and when the first metals are collected.
2020-06-29 | PXD011504 | Pride
Project description:Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base. The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ferrous iron to ferric and removing sulphur compounds that can accumulate on the mineral surface. Metals are most efficiently released from sulphide ores if the microorganisms form a thin layer, termed a ‘biofilm’, on the mineral surface. A crucial stage in bioleaching is how efficiently the microbes attach to the mineral. This project will test how rapidly a biofilm is formed and copper is released from the mineral by different combinations of microorganisms and the order that they are added. Data on the biological processes the microorganisms carry out will be used in computer modelling to suggest the best combination and order in which to add the different types of microbes. This in turn will increase the efficiency of industrial bioleaching by reducing the time between when a heap is built and when the first metals are collected.
2020-06-29 | PXD011503 | Pride
Project description:Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base. The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ferrous iron to ferric and removing sulphur compounds that can accumulate on the mineral surface. Metals are most efficiently released from sulphide ores if the microorganisms form a thin layer, termed a ‘biofilm’, on the mineral surface. A crucial stage in bioleaching is how efficiently the microbes attach to the mineral. This project will test how rapidly a biofilm is formed and copper is released from the mineral by different combinations of microorganisms and the order that they are added. Data on the biological processes the microorganisms carry out will be used in computer modelling to suggest the best combination and order in which to add the different types of microbes. This in turn will increase the efficiency of industrial bioleaching by reducing the time between when a heap is built and when the first metals are collected.
2020-06-29 | PXD012780 | Pride
Project description:Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.
2019-06-24 | GSE129320 | GEO
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.
2014-04-01 | GSE54940 | GEO
Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply.
2015-09-24 | GSE64897 | GEO