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PROVIDER: PRJNA852349 | ENA |
REPOSITORIES: ENA
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Project description:Iron is limiting in the environment, bacteria respond to this deprivation by activating genes required for bacterial iron homeostasis. Transcriptional regulation in response to iron in Gram-negative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe comparative global gene expression analysis using DNA microarray based on the whole genome sequence of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 was conducted between wild type strain and a non-magnetic NMA61 mutant strain, generated by mini-Tn5 transposon mutagenesis which is incapable of assimilating iron to cytoplasm. No induction of the fur genes in NMA61 mutant strain was considered to be due to low intracellular iron concentration. In the iron-replete condition, among 4492 genes, 434 genes were down-regulated and 527 genes were up-regulated in the wild type strain. Among 434 genes down-regulated, 299 genes were not down-regulated in NMA61 mutant strain, indicating these genes are candidates of Fur-regulated. A non-magnetic mutant of Magnetospirillum magneticum AMB-1 (NMA61) generated transposon mutagenesis was grown under various iron conditions. Global gene expression analysis of iron-inducible genes was conducted by using DNA microarray.
2010-07-01 | E-GEOD-5832 | biostudies-arrayexpress
Project description:Purpose:Next Generation Sequencing applying for compare the CD8+ T cells with 0.3T static magnetic field (SMF) or not transcriptome, included pathway-enrichment analysis and genes expression of interests Methods:CD8+ T cells were isolated from splenocytes in 8 week old wild type mice through STEMCELL Technologies negative selection kit. FACS sort CD8+ T cells after 3 days with CD3/CD28 costimulation at 0.3T static magnetic field or not. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer. Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse Conclusions:Our study represents the detailed analysis of CD8+ T cells with 0.3T static magnetic field or not transcriptomes
2020-09-08 | GSE113858 | GEO
Project description:Neural proliferation and differentiation fates of pluripotent stem cells are influenced by external natural forces. Despite the presence of biogenic magnetite nanoparticles in the central nervous system and constant exposure to Earth’s magnetic fields and other sources, there has been scant knowledge regarding the role of electromagnetic stimuli in neurogenesis. Moreover, the emerging application of electrical and magnetic stimulation to treat neurological disorders emphasizes the relevance of understanding the impact and mechanisms behind these stimuli. Here, the effects of magnetic nanoparticles (MNPs) contained in polymeric coatings and the static external magnetic field (EMF, 0.4 Tesla) were investigated on neural induction of murine embryonic stem cells (mESCs) and human induced pluripotent stem cells (hiPSCs) into induced dopaminergic neurons (iDA).
2021-12-17 | GSE190686 | GEO
Project description:Identification of Iron-Inducible Genes in Magnetospirillum magneticum AMB-1 Non-Magnetic Mutant
| PRJNA97227 | ENA
Project description:Investigation of whole genome expression changes in Magnetospririllum magneticum mutants, probing the role of the CtrA regulatory pathway. The mutants are further described in a manuscript submitted for publication at J. Bacteriology. Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and post-translational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probe the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium, Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we show that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagella biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles point to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1 specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from Alphaproteobacteria in which the role of CtrA has been experimentally examined reveals an ancestral role of CtrA in the regulation of motility and suggests that its essential functions in other Alphaproteobacteria were acquired subsequently. Total RNA was recovered from each of the wild-type and mutant strains, reverse transcribed to cDNA, fluorescently labeled, and hybridized to whole genome microarrays. The arrays contain 7 probes/gene, with the entire genome duplicated twice. In addition, the arrays contain 7 probes for 22 unannotated ORFs and tiling of a genomic region from coordinates 977403-1097027.
2012-02-17 | E-GEOD-35625 | biostudies-arrayexpress
Project description:Embryonic stem cells (ESCs) have the ability to differentiate into cells of the three germ layers, and leukemia inhibitory factor (LIF) maintains the pluripotency and promotes the proliferation of ESCs. In the absence of LIF, ESCs spontaneously differentiate and form three-dimensional aggregates known as embryoid bodies (EBs). The differentiation of EBs mimics the process of embryonic development, that is, the differentiation of cells into the three embryonic germ layers (endoderm, mesoderm, and ectoderm), some of which differentiate into beating cardiomyocytes. Static magnetic fields have diverse effects on organisms, studies on the regulation of the differentiation of ESCs to cardiomyocytes by static magnetic fields are not sufficient. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of EBs cultured in two different conditions: conventional incubator, static magnetic field incubator.
2024-01-01 | GSE206413 | GEO
Project description:Investigation of whole genome expression changes in Magnetospririllum magneticum mutants, probing the role of the CtrA regulatory pathway. The mutants are further described in a manuscript submitted for publication at J. Bacteriology. Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and post-translational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probe the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium, Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we show that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagella biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles point to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1 specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from Alphaproteobacteria in which the role of CtrA has been experimentally examined reveals an ancestral role of CtrA in the regulation of motility and suggests that its essential functions in other Alphaproteobacteria were acquired subsequently.
2012-02-17 | GSE35625 | GEO
Project description:This study provides a framework describing how magnetic exposure is transduced from the most-plausible molecular-level âbiosensorâ (lipid membranes) to cell-level responses that include differentiation toward neural lineages. In addition, SMF provided a stimulus that uncovered new relationships â that exist even in the absence of magnetic fields â between gangliosides, the time dependent regulation of IL-6 signaling by these glycolipids, and the fate of embryonic cells. Experiment Overall Design: Subconfluent (70%-80%) undifferentiated LVECs (passage 11) were resuspended at 500k cells in 10 ml culture medium (day 0) and cultured in the presence or absence of static magnetic field. Four conditions were investigated: A) Control (without exposure); B) One day exposure (Exposed on day 6 without recovery); C) Continuous exposure (day 2 to day 5) followed by one day recovery; D) Continuous exposure (day 2 to day 6) without recovery. Cells are harvested on day 7. mRNA was isolated from the cells and microarray analysis was done using the Affymetric Human Genome U133 2.0 Plus Chip.
2010-01-23 | E-GEOD-14474 | biostudies-arrayexpress