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TranscriptomicsGenome-wide prediction and validation of M-OM-^C70 promoters in Lactobacillus plantarum WCFS1
Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor M-OM-^C70 is commonly involved in...
ORGANISM(S): Lactobacillus plantarum WCFS1 
2012-03-28 | E-GEOD-36898 | biostudies-arrayexpress
TranscriptomicsComparative analysis of bacterial transcriptome using DNA microarray and next generation sequencing technologies
Validation of Lactobacillus plantarum WCFS1 transcriptome profile using RNA sequencing (direct cDNA sequencing and 3'-UTR sequencing) in comparison with DNA microarray as a reference platform. Transcriptome analysis was performed on total RNA and enriched mRNA of L. plantarum WCFS1 grown in CDM or M...
ORGANISM(S): Lactobacillus plantarum 
2012-07-09 | E-GEOD-35754 | biostudies-arrayexpress
TranscriptomicsPeroxide stress in Sigma54 mutant and Wt
Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. T...
ORGANISM(S): Lactobacillus plantarum 
2008-05-08 | E-GEOD-11351 | biostudies-arrayexpress
TranscriptomicsWT vs KO of lp_2991 comparison
A mutant of L. plantarumWCFS1 (deletion of lp_2991) was compared with the wildtype grown in standard MRS broth. Cells were sampled at OD1 for mRNA extraction. Knockout vs wildtype. Technical replicates (same mRNA isolation) used for a dye swap.
ORGANISM(S): Lactobacillus plantarum WCFS1 
2010-04-01 | E-GEOD-20515 | biostudies-arrayexpress
TranscriptomicsImprovement of Lactobacillus plantarum Aerobic Growth by Comprehensive Transcriptome Analysis
An aerobic Lactobacillus plantarum culture displayed growth stagnation during early growth. Transcriptome analysis revealed that regain of growth after stagnation correlated with activation of CO2-producing pathways suggesting that limiting CO2-concentration induced stagnation. Analogously providing...
ORGANISM(S): Lactobacillus plantarum WCFS1 
2010-05-26 | E-GEOD-10194 | biostudies-arrayexpress
TranscriptomicsIdentification of the core gene-regulatory network that governs the dynamic adaptation of intestinal homeostasis during conventionalization in mice
Molecular adaptation of the intestinal mucosa occurs during microbial conventionalization to maintain a balanced immune response. However, the genetic regulation of such adaptation is obscure. Here, combined analysis of germ free and conventionalized mice revealed that the major molecular adaptation...
ORGANISM(S): Mus musculus 
2012-07-10 | E-GEOD-32513 | biostudies-arrayexpress
ModelsHoefnagel2002_PyruvateBranches
This a model from the article: Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Hoefnagel MH, Starrenburg MJ, Martens DE, Hugenholtz J, Kleerebezem M, Van Swam II, Bongers R, Westerh...
2024-09-02 | BIOMD0000000017 | BioModels
TranscriptomicsMicrobiota facilitates dietary heme-induced epithelial hyperproliferation and hyperplasia by breaking the mucus barrier
Colorectal cancer risk is associated with diets high in red meat. Heme, the pigment of red meat, induces cytotoxicity of colonic contents and elicits epithelial damage and compensatory hyperproliferation, leading to hyperplasia. Here we explore the possible causal role of the gut microbiota in heme-...
ORGANISM(S): Mus musculus 
2015-08-03 | E-GEOD-40670 | biostudies-arrayexpress
TranscriptomicsMucosal responses of healthy humans to three different probiotic Lactobacillus bacteria
Probiotic bacteria, specific representatives of bacterial species that are a common part of the human microbiota, are proposed to deliver health benefits to the consumer by modulation of intestinal function via largely unknown molecular mechanisms. To explore in vivo mucosal responses of healthy adu...
ORGANISM(S): Homo sapiens 
2010-09-08 | E-GEOD-18741 | biostudies-arrayexpress
TranscriptomicsMolecular and physiological adaptations of Lactococcus lactis at near-zero growth rates
This paper describes the molecular and physiological adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state using carbon-limited retentostat cultivation. Metabolic and transcriptomic analyses revealed that metabolic patterns shifted between homolactic and ...
ORGANISM(S): Lactococcus lactis 
2014-01-01 | E-GEOD-51494 | biostudies-arrayexpress
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