Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1305373 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A heterotrophic ammonia-oxidizing bacterium Alcaligenes sp. HO-1 was isolated from the activated sludge of a bioreactor treating ammonia-rich piggery wastewater. The goal and objectives of this experiment are to analyze the transcriptome profiles of nitrogen-metabolism-related genes of Alcaligenes sp. HO-1 in response to ammonium stimulation over time and to find out potential genes involved in ammonia oxidation process. So the RNA-seq anaylsis was performed by setting up each time points (0, 3.5, 10, 22 hours) when strain HO-1 were exposed to ammonia. HO-1 was cultured with 83 mM succinate and 14 mM ammonium sulfate until ammonia was completely consumed and then another 14 mM of ammonium sulfate was added to the culture. Cells were harvested at 0 h, 3.5 h, 10 h and 22 h after the addition of ammonium sulfate. The sequencing data of RNAs obtained from strain HO-1 cells at each time was analyzed.
2022-05-20 | GSE174685 | GEO
Project description:Detecting chemical signals is important for identifying food sources and avoiding harmful agents. Like many animals, C. elegans use olfaction to chemotax towards their main food source, bacteria. However, little is known about the bacterial compounds governing C. elegans attraction to bacteria and the physiological importance of these compounds to bacteria. Here, we address these questions by investigating the function of a small RNA, P11, in the pathogen, Pseudomonas aeruginosa, that was previously shown to mediate learned pathogen avoidance. We discovered that this RNA also affects the attraction of untrained C. elegans to P. aeruginosa and does so by controlling production of ammonia, a volatile odorant produced during nitrogen assimilation. We describe the complex regulation of P. aeruginosa nitrogen assimilation, which is mediated by a partner-switching mechanism involving environmental nitrates, sensor proteins, and P11. In addition to mediating C. elegans attraction, we demonstrate that nitrogen assimilation mutants perturb bacterial fitness and pathogenesis during C. elegans infection by P. aeruginosa. These studies define ammonia as a major mediator of trans-kingdom signaling, implicate nitrogen assimilation as important for both bacteria and host organisms, and highlight how a bacterial metabolic pathway can either benefit or harm a host in different contexts.
2024-08-06 | GSE273751 | GEO
Project description:Magnetic field therapy holds promise for tumor treatment, yet its underlying mechanisms remain controversial. The traditional ROS theory fails to fully explain the observed magnetic field-induced inhibition. Building on prior findings, we identified the key target of magnetic field-mediated tumor suppression and established a magnetic inhibition model. Integrative multi-omics analysis (transcriptome + proteome) of 293T and A549 cells exposed to (5 mT, 20 Hz) magnetic fields pinpointed RSRP1 as a critical molecular target. We experimentally validated RSRP1's essential role using CRISPR-Cas9-mediated gene disruption and TET-on inducible expression systems. Proteomic analysis revealed that magnetic field exposure (5 mT, 20 Hz) induced >200-fold upregulation of RSRP1 protein in both non-tumorigenic 293T and tumorigenic A549 cells. CRISPR-Cas9-mediated RSRP1 knockout completely abolished A549 cells' responsiveness to magnetic fields. Notably, restoring RSRP1 expression via a doxycycline-inducible system reinstated magnetic field-induced secretion of inhibitory factors, with conditioned media from exposed cells significantly inhibiting naive tumor cell proliferation (p<0.05). Magnetic field (5 mT, 20 Hz) exposure transcriptionally upregulated RSRP1 endogenously, as confirmed by transcriptomic and qPCR analyses, while exogenously overexpressed RSRP1 via a doxycycline-inducible system remained unresponsive, indicating that magnetic regulation requires endogenous transcriptional control. This study establishes a "magnetic field→RSRP1→secretory factor→target response" cascade, providing a transformative framework for non-invasive tumor therapy.
2026-05-12 | GSE297517 | GEO
Project description:Magnetic field therapy holds promise for tumor treatment, yet its underlying mechanisms remain controversial. The traditional ROS theory fails to fully explain the observed magnetic field-induced inhibition. Building on prior findings, we identified the key target of magnetic field-mediated tumor suppression and established a magnetic inhibition model. Integrative multi-omics analysis (transcriptome + proteome) of 293T and A549 cells exposed to (5 mT, 20 Hz) magnetic fields pinpointed RSRP1 as a critical molecular target. We experimentally validated RSRP1's essential role using CRISPR-Cas9-mediated gene disruption and TET-on inducible expression systems. Proteomic analysis revealed that magnetic field exposure (5 mT, 20 Hz) induced >200-fold upregulation of RSRP1 protein in both non-tumorigenic 293T and tumorigenic A549 cells. CRISPR-Cas9-mediated RSRP1 knockout completely abolished A549 cells' responsiveness to magnetic fields. Notably, restoring RSRP1 expression via a doxycycline-inducible system reinstated magnetic field-induced secretion of inhibitory factors, with conditioned media from exposed cells significantly inhibiting naive tumor cell proliferation (p<0.05). Magnetic field (5 mT, 20 Hz) exposure transcriptionally upregulated RSRP1 endogenously, as confirmed by transcriptomic and qPCR analyses, while exogenously overexpressed RSRP1 via a doxycycline-inducible system remained unresponsive, indicating that magnetic regulation requires endogenous transcriptional control. This study establishes a "magnetic field→RSRP1→secretory factor→target response" cascade, providing a transformative framework for non-invasive tumor therapy.
2026-05-12 | GSE297180 | GEO
Project description:The widespread use of electricity raises the question of whether or not 50 Hz (power line frequency in Europe) magnetic fields (MFs) affect organisms. We investigated the transcription of Escherichia coli K-12 MG1655 in response to extremely low-frequency (ELF) MFs. Fields generated by three signal types (sinusoidal continuous, sinusoidal intermittent, and power line intermittent; all at 50 Hz, 1 mT), were applied and gene expression was monitored at the transcript level using an Affymetrix whole-genome microarray. Bacterial cells were grown continuously in a chemostat (dilution rate D = 0.4 h-1) fed with glucose-limited minimal medium and exposed to 50 Hz MFs with a homogenous flux density of 1 mT. For all three types of MFs investigated, neither bacterial growth (determined using optical density) nor culturable counts were affected. Likewise, no statistically significant change (fold-change > 2, P ≤ 0.01) in the expression of 4,358 genes and 714 intergenic regions represented on the gene chip was detected after MF exposure for 2.5 h (1.4 generations) or 15 h (8.7 generations). Moreover, short-term exposure (8 min) to the sinusoidal continuous and power line intermittent signal neither affected bacterial growth nor showed evidence for reliable changes in transcription. In conclusion, our experiments did not indicate that the different tested MFs (50 Hz, 1 mT) affected the transcription of E. coli. A total of 60 chips are included in this study. Each comparison (treated vs. sham-treated cultures; untreated negative control cultures) consists of three replicates. The three magnetic field test conditions include sinusoidal continous, sinusoidal intermittent (2 min on, 4 min off) and power line intermittent (2 min on, 4 min off). Exposure periods were 8 min, 2.5 h, or 15 h. The response control consists of E. coli cells treated for 10 min with 1 mM H2O2 or the equivalent water volume. The negative control comprises samples taken from cultures grown with the exposure chambers swiched off.
2012-01-28 | E-GEOD-35371 | biostudies-arrayexpress