Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746800 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15147199_1.fastq.gz | Fastqsanger.gz | |||
| SRR15147199_2.fastq.gz | Fastqsanger.gz |
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Project description:Objective to explore the effect of changing initial pH on the survival rate of freeze-drying strains
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Project description:Lactobacillus plantarum WCFS1 was differentially fermented in 29 different fermentations according to a factorial, combinatorial scheme that included variations in growth temperature (28 or 37C), NaCl concentration (0 or 0.3M), pH (5.2, 5.8, 6.4), as well as oxygen (N2 or air) and amino acid availability (1.1 or 2x concentration).
2011-10-01 | GSE31076 | GEO
Project description:Purpose: The goal of this study was to determine the microRNA (miRNA) content of extracellular vesicles (EVs) derived from murine mesenchymal stem cells (mMSC), and evaluate reproducibility among distinct EV productions. We also aimed at assessing the effect of freeze-drying on EV miRNA content, by performing sequencing on freeze-dried EVs and calculating statistical difference between unmodified and freeze-dried EVs. Methods: mMSC-derived EVs were obtained from mMSC in culture in reduced serum medium Opti-MEM by differential centrifugation, with a final step at 100,000 g for 110 min at 4°C. EV pellets (freeze-dried (n=3) or not (n=2)) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit. cDNA libraries for sequencing were prepared using the TruSeq Small RNA Sample Preparation Kit. Amplified cDNA constructs were purified on 6 % PAGE gel and DNA molecules corresponding to 15–50 nucleotide transcripts were excised, eluted from gel, and concentrated. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out. Differentially expressed miRNA were identified using three Bioconductor packages: edgeR, DESeq and DESeq2. Results: Considering miRNAs detected with at least 5 counts (in terms of normalised counts), 339 miRNAs were identified and miRNA content was highly conserved among the two batches tested, with 237 miRNAs out of the 339 present in both batches (70%). Statistical analysis did not evidence statistical difference between unmodified EVs (n=2) and freeze-dried EVs (n=3) (DESeq2, p<0.05). No statistical difference was found using other Bioconductor packages DESeq and edgeR. These results indicated conservation of miRNA content following freeze-drying. Conclusion: mMSC-EV miRNA content was comparable between the two EV productions analysed, indicating reproducibility. Some of the miRNAs identified were consistent with previously published results on MSC-derived EVs. Freeze-drying conserved miRNA content.
2019-12-09 | GSE140479 | GEO
Project description:In this manuscript, we present a more extensive analysis of inflammatory suppression mediated by L. plantarum at the respiratory tract. Via full genome microarray of whole lung tissue, we have generated an extensive list of soluble proinflammatory mediators that are expressed in response to PVM infection and we identify those mediators that are suppressed and also those that are not suppressed in response to L. plantarum priming. We focused further study on three specific virus-induced soluble mediators that are differentially expressed and that serve as specific biomarkers for Lactobacillus-mediated survival in response to acute respiratory virus infection. Among several novel directions, we use these biomarker cytokines to explore Lactobacillus-mediated actions at the respiratory tract that are unique and distinct from those taking place at gastrointestinal mucosa. innoculation of mouse using combinations of PBS/BSA, Lactobacillus plantarum and pneumonia virus
2015-11-02 | E-GEOD-66721 | biostudies-arrayexpress
Project description:Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts comes to dominate this ecosystem. Although rich in carbohydrates, thus providing an ideal environment to grow, the low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential growth phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was observed as well as of genes involved in plantaricin production and lipoteichoic acid synthesis. The results highlight cellular mechanisms that allow L. plantarum to function at a low environmental pH.
2011-08-01 | GSE23945 | GEO
Project description:In this study, we examined Caco-2 cell gene expression after infection with E. coli (Ec), Lactobacillus plantarum (Lp) and the combination of the two (mix) Keywords: Lactobacillus plantarum and E. coli influences on Caco2 cells gene expression
2007-09-13 | GSE5874 | GEO
Project description:Mannose-specific interactions of Lactobacillus plantarum 299v with jejunal epithelium were investigated using an in situ pig small intestinal segment perfusion (SISP) model. L. plantarum 299v wildtype strain was compared to two isogenic mutant strains either lacking the gene encoding for the mannose-specific adhesin (msa) or sortase (srtA; responsible for anchoring of cell surface proteins like Msa to the cell wall). Salmonella typhimurium served as a positive control for gene expression analysis. Scrapings from jejunal segments were collected after perfusion with bacterial suspensions or PBS (control) for 4 or 8 hours, and host gene expression was assessed using a home-made cDNA porcine microarray. Keywords: host-microbe interaction, Lactobacillus plantarum, mannose-specific adhesion A Small Intestinal Segment Perfusion (SISP) test was performed using 4 pigs. 10 segments were prepared in the jejunum of each pig and perfused with Lactobacillus plantarum 299v wildtype, Lactobacillus plantarum 299v msa mutant strain, Lactobacillus plantarum 299v srtA mutant strain, Salmonella typhimurium or PBS (control) for 4 or 8 hours. Pooled samples from each treatment at each timepoint were used for microarray analysis. 8 comparisons were done: L. plantarum wildtype vs control (4 hours), L. plantarum wildtype vs control (8 hours), L. plantarum msa mutant vs control (4 hours), L. plantarum msa mutant vs control (8 hours), L. plantarum srt mutant vs control (4 hours), L. plantarum srt mutant vs control (8 hours), S. typhimurium vs control (8 hours), samples taken at the beginning of the experiment vs control (8 hours). Dye-swaps were performed for each comparison.
2010-05-25 | E-GEOD-9209 | biostudies-arrayexpress
Project description:In this experiment we analyzed the impact of the disruption of trxB1in Lactobacillus plantarum at the transcriptome level. Furthermore we studied the effect of 3.5 mM peroxide effect on both Lactobacillus plantarum wild type (strain WCFS1) and a trxB1 mutant (strain NZ7608). Keywords: mutant analysis of trxB1, hydrogen peroxide stress
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Project description:In order to understand LBG derived galacto-manno-oligosaccharides utilization by a probiotic bacterium, Lactobacillus plantarum WCFS1, we have grown Lactobacillus plantarum WCFS1 (in duplicates) till mid log phase (OD600nm ~0.5, 10 h) in carbon free MRS (de Man, Rogosa Sharpe ) media containing either galacto-manno-oligosaccharides, mannose, glucose or galactose (1% w/v) as the sole carbon source.
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