Ontology highlight
ABSTRACT:
PROVIDER: PRJNA977404 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24805743_1.fastq.gz | Fastqsanger.gz | |||
| SRR24805743_2.fastq.gz | Fastqsanger.gz | |||
| SRR24805744_1.fastq.gz | Fastqsanger.gz | |||
| SRR24805744_2.fastq.gz | Fastqsanger.gz | |||
| SRR24805745_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Staphylococcus aureus is an important food poisoning bacterium. In food preservation, acidification is a well-known method. Permeant weak organic acids, like lactic and acetic acids, are known to be more effective against bacteria than inorganic strong acids (e.g., HCl). Growth experiments and metabolic and transcriptional analyses were used to determine the responses of a food pathogenic S. aureus strain exposed to lactic acid, acetic acid, and HCl at pH 4.5. Lactic and acetic acid stress induced a slower transcriptional response and large variations in growth patterns compared with the responses induced by HCl. In cultures acidified with lactic acid, the pH of the medium gradually increased to 7.5 during growth, while no such increase was observed for bacteria exposed to acetic acid or HCl. Staphylococcus aureus increased the pH in the medium mainly through accumulation of ammonium and the removal of acid groups, resulting in increased production of diacetyl (2,3-butanedione) and pyrazines. The results showed flexible and versatile responses of S. aureus to different types of acid stress. As measured by growth inhibition, permeant organic acid stress introduced severe stress compared with the stress caused by HCl. Cells exposed to lactic acid showed specific mechanisms of action in addition to sharing many of the mechanisms induced by HCl stress. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-87
2011-04-15 | E-BUGS-87 | biostudies-arrayexpress
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K).
2011-01-17 | GSE24361 | GEO
Project description:Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.
2011-04-14 | GSE28538 | GEO
Project description:Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed. In this work, the whole-genome array was employed to conduct the time-course transcriptome analysis of A. ferrooxidans ATCC 23270 in response to 1% (v/v) Lix984n for 5, 20, 40, and 80 min.
2011-04-14 | E-GEOD-28538 | biostudies-arrayexpress
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K). Acetobacter aceti NBRC14818 was cultivated in the medium containing ethanol, acetate, glucose, or mix of ethanol and glucose as carbon sources in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3-0.4. The experiment was performed in duplicate independent cultures.
2011-01-17 | E-GEOD-24361 | biostudies-arrayexpress
Project description:Reactive nitrogen species (RNS) derived from dietary and salivary inorganic nitrates (NO3-) foment innate host defenses associated with the acidity of the stomach. The mechanisms by which these reactive species exert antibiotic activity in the gastric lumen are, however, poorly understood. To identify targets of RNS, the genetically tractable acid tolerance response (ATR) that enables enteropathogens to survive the harsh acidity of the stomach was screened for signaling pathways responsive to RNS. The nitric oxide (NO) donor spermine NONOate derepressed the Fur regulon that controls secondary lines of resistance against organic acids. Despite inducing a Fur-mediated adaptive response, acidified RNS largely boosted gastric host defenses as demonstrated by the fact that Salmonella bacteria exposed to spermine NONOate during mildly acidic conditions were not only shed in low amounts in feces, but also exhibited ameliorated oral virulence. NO prevented Salmonella from mounting a de novo ATR, but was unable to suppress an already functional protective response, indicating that RNS target regulatory cascades but not the effectors that defend against the rigors of gastric acidity. Transcriptional and translational analyses revealed that the PhoPQ signaling cascade is a critical ATR target of NO in rapidly growing Salmonella. Inhibition of PhoPQ signaling appears to contribute to most of the NO-mediated abrogation of the ATR in log phase bacteria, because the augmented acid sensitivity of phoQ-deficient Salmonella was not further enhanced after RNS treatment. Since PhoPQ-regulated acid resistance is widespread in enteric pathogens, the RNS-mediated inhibition of the Salmonella ATR described herein may represent a common component of the innate host defenses of the gastric lumen. Keywords: acid tolerance response, nitric oxide
2008-03-01 | GSE9398 | GEO
Project description:Coniferous trees use the oleoresin, a mixture of non-volatile non-volatile diterpene acids and a large (20-50%) volatile fraction of mono- and sesquiterpenes, as a defence tool against damaging herbivores and pathogens. Volatilization of monoterpenes increases viscosity of oleoresin and finally leading to polymerization of resin and a formation of protective solid plug. Resin storing conifers form an important source of volatile organic compounds (VOCs) mainly dominated by volatile monoterpenes. In the atmosphere, conifer VOCs react with ozone and OH and nitrous oxide radicals forming secondary organic compounds. This project seeks a better understanding of the genetic control of conifer defences and the role of monoterpenoid compounds under biotic stresses.
2015-04-01 | GSE60383 | GEO
Project description:Reactive nitrogen species (RNS) derived from dietary and salivary inorganic nitrates (NO3-) foment innate host defenses associated with the acidity of the stomach. The mechanisms by which these reactive species exert antibiotic activity in the gastric lumen are, however, poorly understood. To identify targets of RNS, the genetically tractable acid tolerance response (ATR) that enables enteropathogens to survive the harsh acidity of the stomach was screened for signaling pathways responsive to RNS. The nitric oxide (NO) donor spermine NONOate derepressed the Fur regulon that controls secondary lines of resistance against organic acids. Despite inducing a Fur-mediated adaptive response, acidified RNS largely boosted gastric host defenses as demonstrated by the fact that Salmonella bacteria exposed to spermine NONOate during mildly acidic conditions were not only shed in low amounts in feces, but also exhibited ameliorated oral virulence. NO prevented Salmonella from mounting a de novo ATR, but was unable to suppress an already functional protective response, indicating that RNS target regulatory cascades but not the effectors that defend against the rigors of gastric acidity. Transcriptional and translational analyses revealed that the PhoPQ signaling cascade is a critical ATR target of NO in rapidly growing Salmonella. Inhibition of PhoPQ signaling appears to contribute to most of the NO-mediated abrogation of the ATR in log phase bacteria, because the augmented acid sensitivity of phoQ-deficient Salmonella was not further enhanced after RNS treatment. Since PhoPQ-regulated acid resistance is widespread in enteric pathogens, the RNS-mediated inhibition of the Salmonella ATR described herein may represent a common component of the innate host defenses of the gastric lumen. Keywords: acid tolerance response, nitric oxide Microarray analyses were conducted comparing transcript levels of log-phase Salmonella cultured in minimal E salts + 0.4% glucose, pH 4.4 in the presence or absence of 250 µM spermine NONOate for 1 hour. Microarrays were performed in triplicate under identical conditions (3 biological replicates).
2010-05-26 | E-GEOD-9398 | biostudies-arrayexpress
Project description:Genome sequencing project of Lactic acid bacteria
| PRJDB8022 | ENA