Ontology highlight
ABSTRACT:
PROVIDER: PRJNA784321 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sourdough starter samples Raw sequence reads
| PRJNA589612 | ENA
Project description:Effect of chlorination on the toxicity of wastewater effluents treated by activated sludge (AS) and submerged membrane bioreactor (S-MBRB) systems to HepG2 human hepatoblastoma cells was investigated. In addition to cytotoxicity assay, the DNA microarray-based transcriptome analysis was performed to evaluate the change in modes of toxic actions (MOAs) of effluents by chlorination. Effluent organic matters (EfOM) and disinfection by-products (DBPs) were characterized by using Fourier transform mass spectrometry (FT-MS). The cytotoxicity of AS effluent was elevated by chlorination, while the toxicity of S-MBRB effluent was reduced. The averaged O/C ratio of EfOM in S-MBRB effluent was lower than that in AS effluent. The results of the transcriptome and FT-MS analyses suggested that lower O/C molecules influenced on “response to hormone stimulus” and “acute inflammatory response” but those were decreased by chlorination, which consequently reduced cytotoxicity. On the other hand, larger number of DBPs and other molecules were increased in AS effluents by chlorination. Those molecules might influence on “cellular metabolic process”, which consequently elevated cytotoxicity. Therefore, the combination of the toxicity assays and chemical analysis demonstrated the changes in severity of cytotoxicity and MOAs by chlorination, and the difference of chemical characteristics which relate to those toxicity changes.
2013-06-21 | GSE48157 | GEO
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:Effect of chlorination on the toxicity of wastewater effluents treated by activated sludge (AS) and submerged membrane bioreactor (S-MBRB) systems to HepG2 human hepatoblastoma cells was investigated. In addition to cytotoxicity assay, the DNA microarray-based transcriptome analysis was performed to evaluate the change in modes of toxic actions (MOAs) of effluents by chlorination. Effluent organic matters (EfOM) and disinfection by-products (DBPs) were characterized by using Fourier transform mass spectrometry (FT-MS). The cytotoxicity of AS effluent was elevated by chlorination, while the toxicity of S-MBRB effluent was reduced. The averaged O/C ratio of EfOM in S-MBRB effluent was lower than that in AS effluent. The results of the transcriptome and FT-MS analyses suggested that lower O/C molecules influenced on M-bM-^@M-^\response to hormone stimulusM-bM-^@M-^] and M-bM-^@M-^\acute inflammatory responseM-bM-^@M-^] but those were decreased by chlorination, which consequently reduced cytotoxicity. On the other hand, larger number of DBPs and other molecules were increased in AS effluents by chlorination. Those molecules might influence on M-bM-^@M-^\cellular metabolic processM-bM-^@M-^], which consequently elevated cytotoxicity. Therefore, the combination of the toxicity assays and chemical analysis demonstrated the changes in severity of cytotoxicity and MOAs by chlorination, and the difference of chemical characteristics which relate to those toxicity changes. We examined the gene expression alteration in human hepatoma cell line, HepG2 exposed to the chlorinated wastewater effluents from membrane bioreactor and the activated sludge process. Human Genome Focus Array, which represents 8,795 verified human sequences, was used. All effluent samples were concentrated by using solid phase extraction (SPE). SPE fraction from MQ water was used as controll. For duplicate, two dishes were prepared for each sample and individually treated in parallel.
2013-06-21 | E-GEOD-48157 | biostudies-arrayexpress
Project description:In this study, we investigated the transcriptional response of the human isolate L. reuteri ATCC 55730 during sourdough fermentation by using whole-genome microarrays. Significant changes of mRNA levels were found for 101 genes involved in diverse cellular processes, e.g., carbohydrate and energy metabolism, cell envelope biosynthesis, exopolysaccharide production, stress responses, signal transduction and cobalamin biosynthesis. Our results evidence extensive changes of the organism’s gene expression to the growth in sourdough as compared to the growth in chemically defined medium, and thus allowed us to uncover pathways involved in the adaptation of L. reuteri to the ecological niche of sourdough. An impact of several genes of L. reuteri for effective growth in sourdough was shown by implementation of mutant strains in sourdough fermentation. This study contributes to the understanding of the molecular fundamentals of L. reuteri’s ecological competitiveness, and provides a basis for further exploration of genetic traits involved in adaptation to the food and/or intestinal environment. Keywords: environment-specific gene expression, sourdough fermentation, chemically defined medium, dye swap
2008-02-13 | GSE10495 | GEO
Project description:Investigation of the effect of chow diet integration with standard baker's yeast leavened carasau bread (SB) or with functional sourdough-leavened carasau bread (FB) on the gut microbiota of young rats.
2019-08-19 | PXD011441 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE15686: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15691: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15692: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) GSE15693: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) Refer to individual Series
2010-07-07 | E-GEOD-15803 | biostudies-arrayexpress
Project description:Undefined milk starter cultures Targeted loci environmental
| PRJNA281573 | ENA
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. The labeled aRNA samples were hybridized using a loop design, i.e. two consecutive samples (e.g., pH 3.5 and pH 4.0, pH 4.0 and pH 4.5, etc.) were hybridized on the same microarray slide, each labeled with another fluorescent dye (Cy3 or Cy5), and the loop was closed by hybridizing sample pH 5.5 together with sample pH 3.5.
2011-07-31 | E-GEOD-23945 | biostudies-arrayexpress