Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15622261.fastq.gz | Fastqsanger.gz | |||
| SRR15622262.fastq.gz | Fastqsanger.gz | |||
| SRR15622263.fastq.gz | Fastqsanger.gz | |||
| SRR15622264.fastq.gz | Fastqsanger.gz | |||
| SRR15622265.fastq.gz | Fastqsanger.gz |
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Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system.
2013-06-29 | GSE48416 | GEO
Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system. We monitored the gene expression of Synechocystis PCC6083 at standard conditions and after 2 days of iron limitation (0Fe), manganese limitation (0Mn) and combined iron and manganese limitation (0Fe0Mn). Each timepoint and condition was sampled in triplicates. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.
2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress
Project description:The proteins are a pair of closely related superoxide dismutase (SOD) enzymes from the Gram positive bacterium, Staphylococcus aureus. SodA is a Mn-specific SOD (MnSOD), which is inactive when loaded with Fe, whereas SodM is a 'cambialistic' SOD (camSOD), which is catalytically active with either Mn or Fe as a cofactor. Their sequences are 75% identical across their 199 amino acid sequences: the crystal structures of each enzyme in each metal-loaded form: Mn-loaded MnSOD SodA: PDB ID 5N56 Fe-loaded MnSOD SodA: PDB ID 6EX3 Mn-loaded camSOD SodM: PDB ID 5N57 Fe-loaded camSOD SodM: PDB ID 6EX4 The resulting structures (all to approximately 2A resolution) showed no significant differences that indicated molecular reasons for the differences in activity. Because of the differences in activity, therefore, the project aimed to compare three forms of these enzymes to determine whether there are any differences in the dynamics of regions of their structure, most notably those within the active site and the putative substrate access route(s).
2025-05-07 | PXD057066 | Pride
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.
2010-07-22 | GSE12874 | GEO
Project description:We recently established that gene expression in PAXgene stabilized blood RNA distinguishes benign (BN) from malignant (MN) pulmonary nodules in high risk candidates with an AUC of 0.84. We now expand our studies to include incidental nodules identified in routine clinical settings using data from 603 patients analyzed on Illumina microarrays. We identify 300 gene probes achieving an AUC of 0.84 for Indeterminate Pulmonary Nodules (IPN) from 6-25 mm and 0.824 for IPN from 8-20 mm, outperforming 3 prominent clinical models that achieve AUCs of 0.60-0.689. We address the basis for these differences by in silico flow cytometry using CIBERSORT and identify significant differences between MN and BN patients including proportions of T-cells, M0 macrophages, NK cells, B cells and exhausted CD8 T-cells. We identify major increases in expression of genes promoting cell death and strong decreases in functions promoting transcription, lymphogenesis and cell viability. A preferential use of oxidative phosphorylation and a signature of mitochondrial dysfunction are also associated with the presence of a MN.
2020-08-02 | GSE135304 | GEO