Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33945372_1.fastq.gz | Fastqsanger.gz | |||
| SRR33945372_2.fastq.gz | Fastqsanger.gz | |||
| SRR33945373_1.fastq.gz | Fastqsanger.gz | |||
| SRR33945373_2.fastq.gz | Fastqsanger.gz | |||
| SRR33945374_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distri- bution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales (Candidatus order) and the acidophile Nitrosotalea devanaterra revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and Nitrosopelagicus brevis proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
2017-05-03 | PXD005297 | Pride
Project description:Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.
2024-06-30 | GSE249031 | GEO
Project description:There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates.
2012-09-30 | GSE34188 | GEO
Project description:The aim of the study was to identify genes which are differentially expressed in the peripheral blood nuclear cells of two breeds of cattle (Holstein-Friesian and Polish Red) and cervine in different points in their physiological states (dry-off period, peak of lactation) RNA from peripheral blood nuclear cells taken from cattle and cervine in peak lactation and dry period were hybridized to Agilent two color microarrays with a common reference. There were four Holstein-Friesian cattle, four Polish Red cattle and four deer investigated. The whole blood was drawn in two time point from each animal – during dry period and peak lactation. This means that there were six research groups (Holstein-Friesian cattle in dry period and Holstein-Friesian cattle in peak lactation; Polish Red cattle in dry period and Polish Red cattle in peak lactation; Deer in dry period and Deer in peak lactation). Using Gene Spring Software (one-way ANOVA and Tukey's HSD Post-hoc test) three lists of differentially expressed transcripts were obtained: a list of 576 transcripts which differ deer in dry period and in peak lactation, a list of 437 transcripts which differ Holstein-Friesian cattle in dry period and in peak lactation and a list of 158 transcripts which differ Polish Red cattle in dry period and in peak lactation.
2014-02-11 | E-GEOD-54790 | biostudies-arrayexpress
Project description:Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition.
2013-06-20 | GSE46851 | GEO