Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1004450 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pseudomonas aeruginosa is an opportunistic human pathogen, infecting immuno-compromised patients and causing persistent respiratory infections in people affected from cystic fibrosis. Pseudomonas strain Pseudomonas aeruginosa PA14 shows higher virulence than Pseudomonas aeruginosa PAO1 in a wide range of hosts including insects, nematodes and plants but the precise cause of this difference is not fully understood. Little is known about the host response upon infection with Pseudomonas and whether or not transcription is being affected as a host defense mechanism or altered in the benefit of the pathogen. In this context the social amoeba Dictyostelium discoideum has been described as a suitable host to study virulence of Pseudomonas and other opportunistic pathogens.
2008-07-09 | E-TABM-464 | biostudies-arrayexpress
Project description:Using in vitro directed evolution, we show that mismatch repair-deficient Pseudomonas aeruginosa can engage novel resistance mechanisms to ceftazidime-avibactam.
2021-08-30 | GSE180086 | GEO
Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa. RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.
2016-07-20 | E-GEOD-76513 | biostudies-arrayexpress
Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.
2019-12-20 | GSE137648 | GEO
Project description:Oberhardt2008 - Genome-scale metabolic
network of Pseudomonas aeruginosa (iMO1056)
This model is described in the article:
Genome-scale metabolic
network analysis of the opportunistic pathogen Pseudomonas
aeruginosa PAO1.
Oberhardt MA, Puchałka J, Fryer
KE, Martins dos Santos VA, Papin JA.
J. Bacteriol. 2008 Apr; 190(8):
2790-2803
Abstract:
Pseudomonas aeruginosa is a major life-threatening
opportunistic pathogen that commonly infects immunocompromised
patients. This bacterium owes its success as a pathogen largely
to its metabolic versatility and flexibility. A thorough
understanding of P. aeruginosa's metabolism is thus pivotal for
the design of effective intervention strategies. Here we aim to
provide, through systems analysis, a basis for the
characterization of the genome-scale properties of this
pathogen's versatile metabolic network. To this end, we
reconstructed a genome-scale metabolic network of Pseudomonas
aeruginosa PAO1. This reconstruction accounts for 1,056 genes
(19% of the genome), 1,030 proteins, and 883 reactions. Flux
balance analysis was used to identify key features of P.
aeruginosa metabolism, such as growth yield, under defined
conditions and with defined knowledge gaps within the network.
BIOLOG substrate oxidation data were used in model expansion,
and a genome-scale transposon knockout set was compared against
in silico knockout predictions to validate the model.
Ultimately, this genome-scale model provides a basic modeling
framework with which to explore the metabolism of P. aeruginosa
in the context of its environmental and genetic constraints,
thereby contributing to a more thorough understanding of the
genotype-phenotype relationships in this resourceful and
dangerous pathogen.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180020.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180020 | BioModels
Project description:How opportunistic pathogens undergo adaptation during the complex transition from growth in their natural environment to chronic host colonization is not well understood. Successful bacterial pathogens must satisfy specific metabolic requirements constrained by the host environment to cause infection. Evolution has optimized the structure and regulation of metabolism in primary pathogens to operate within host constraints; a systematic evaluation of this process may identify novel targets for therapeutic intervention. An ideal model system for this investigation is the long-term evolution of Pseudomonas aeruginosa within the lungs of cystic fibrosis patients. Using this model, we experimentally determined activity in central metabolism of patient isolates using growth profiling and isotope-labeling experiments. We developed isolate-specific genome-scale metabolic models through integration of transcriptomic and genomic data; these models contextualize our experimental findings from a systems perspective and elucidate specific metabolic adaptations during chronic infection. We find strong experimental evidence for a shift in metabolism towards fixation of carbon dioxide through reversal of the glycine cleavage system, which may operate as an alternative redox recycling reaction as supported by our computational modeling. This particular metabolic shift may be necessary for the bacteria to survive the oxidative stresses in the human lung environment; we provide support for this hypothesis with computational predictions of isolate-specific essential genes and altered redox pathway activity. Redox-related metabolic adaptation merits greater consideration as an important enabler of pathogen persistence and potential therapeutic target in Pseudomonas and other emergent pathogens.
2016-11-20 | GSE62970 | GEO
Project description:Pseudomonas aeruginosa is a virulent opportunistic pathogen responsible for high morbity in COPD, burns , implanted medical devices and cystic fibrosis. Pseudomonas aeruginosa is a problematic colonizer of the human lung. P. aeruginosa produces a phospholipase C (PlcH) that degrades choline-containing lipids such as phosphatidylcholine and sphingomylein that are found in lung surfactant and in host membranes. In this study, we analyzed gene expression in mutants defective in PlcH production (delta-plcH and delta-gbdR) and the wild type when growing in medium with lung surfactant.
2013-01-01 | GSE41926 | GEO