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ABSTRACT:
PROVIDER: PRJEB33463 | ENA |
REPOSITORIES: ENA
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Project description:Acidophilic autotrophic biocathode Raw sequence reads
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Project description:In-depth organic mass cytometry reveals differential contents of 3-hydroxybutanoic acid on single cell level. Single-cell transcriptome indicates the expression difference of BHB downstream anti-oxidative stress proteins such as MT2A while Fluorescence Activated Cell Sorting (FACS) assay validates positive relationship between BHB and target proteins, which suggests that contents heterogeneity of BHB may endow cancer cells with variant ability to resist surrounding oxidative stress. Our ID-organic cytoMS paves the way for deep single-cell metabolome profiling and the investigation of cancer physiological and pathological processes. Comprehensive single-cell metabolic profiling is critical for revealing phenotypic heterogeneity and elucidating molecular mechanisms of biological processes. However, single-cell metabolomics remains challenging because of the limited metabolites coverage and disability of isomer discrimination. Herein, we establish a novel single-cell metabolomics platform of in-depth organic mass cytometry (ID-organic cytoMS). Extended single-cell analysis time guarantees sufficient MS/MS acquisition for metabolites identification and the isomers discrimination with online high-throughput analysis, achieving the largest number of about 600 metabolites identified in single cells. Fine sub-typing of MCF-7 cells are first demonstrated by differential contents of 3-hydroxybutanoic acid (BHB) among clusters. Single-cell transcriptome indicates the expression difference of BHB downstream anti-oxidative stress proteins such as MT2A while Fluorescence Activated Cell Sorting (FACS) assay validates positive relationship between BHB and target proteins, which suggests that contents heterogeneity of BHB may endow cancer cells with variant ability to resist surrounding oxidative stress. Our ID-organic cytoMS paves the way for deep single-cell metabolome profiling and the investigation of cancer physiological and pathological processes.
2024-03-31 | GSE262591 | GEO
Project description:Comparative phenotype and transcriptome analyses were performed with Bacillus cereus ATCC 14579 exposed to acid down-shock to pH 5.5 set with different acidulants. When acidified with hydrochloric acid (HCl), growth was diminished, whereas 2 mM undissociated lactic acid (HL) or acetic acid (HAc) stopped growth without inactivation (bacteriostatic condition), and 15 mM undissociated HAc caused growth arrest and, finally, cell death, as reflected by a 3 to 4 log inactivation (bactericidal condition). Within the first 60 min after pH down-shock, the intracellular ATP levels of cultures shocked with HCl were increased. The bacteriostatic pH shocks did not result in increased nor decreased intracellular ATP levels, indicating that the high energy status within the stressed aerobically grown B. cereus cells could be maintained. In contrast, exposure to 15 mM undissociated HAc resulted in significant lower ATP levels, which was in accordance with the observed inactivation. The transcriptomic responses pH down-shocked cultures were studied in the same time frame. The analyses revealed general and specific responses coupled to the different phenotypes and the acidulant used. The general acid stress response, shown in all different pH shocks, involves modulation of pyruvate metabolism and an oxidative stress response. The shifts in pyruvate metabolism include induction dehydrogenases of a butanediol fermentation pathway under non-lethal acid stress conditions and of lactate, formate, and ethanol fermentation pathways under 15 mM HAc stress. Other 15 mM HAc-specific responses were induction of the alternative electron-transport systems, including cydAB, and fatty acid biosynthesis genes. Differences in gene expression for the bacteriostatic organic acid stress conditions compared to the growth-retarded inorganic stress condition indicated a more stringent oxidative stress response, including induction of an additional catalase gene and a gene encoding a Dps-like protein. Moreover, modulations in amino acid and oligopeptide transport were also found for the 2 mM HAc and HL shocks. HL-specific and HAc-specific responses both involve amino acid metabolism. Our study on the genome-wide responses of aerobically grown B. cereus pH 5.5 shocks provides a unique overview of the different responses induced by three acidulants relevant for food preservation. Per acid down-shock three exposure times (i.e., 10, 30 and 60 min) were each compared with non-exposed cells (i.e., t0). In total 4 different pH 5.5 acid down-shocks were applied. pH 5.5 was reached by adding different acidulants i.e., hydrochloric acid (HCl), lactic acid (HL) resulting in 2 mM undissociated HL, acetic acid (HAc) resulting in 15 mM undissociated HAc, and a combination of acetic acid and hydrochloric acid (HAc/HCl) resulting in 2 mM undissociated HAc. The experiments were performed in duplicate and the duplicate samples were hybridised with a dye-swap.
2010-06-25 | E-GEOD-15140 | biostudies-arrayexpress