Project description:The purpose of this study was to define the TZD effect in Pseudomonas aeruginosa. Transcriptional profiling of Pseudomonas aeruginosa wild-type strain,reference strain PAO1, as control Vs. PAO1 strain exposed to a final 0.02mM of TZD derivative ((z)-5-octylidenethiazolidine-2,4-dione).
Project description:We report a study conducted to investigate the variation on gene expression of the pathogenic fungus Aspergillus fumigatus upon co-cultivation with the pathogenic bacterium Pseudomonas aeruginosa. The study was conducted by investigating the gene expression variation at different time points (45, 90 and 180 minutes after co-incubation). As control, we used data obtained by cultivating the fungus either without bacteria, or with heat-inactivated Pseudomonas. Overall design: Examination of Aspergillus fumigatus co-cultivated with Pseudomonas aeruginosa.
Project description:Persister cells, transiently resist antimicrobial therapy, are implicated in impaired infection clearance. Pseudomonas aeruginosa is known to form persister cells during infection. Here, we report the transcriptome sequence of P. aeruginosa persister, biofilm, planktonic, and stationary cultures and the differential gene expression observed when persisters are compared to untreated cells. Overall design: P. aeruginosa persister, biofilm, planktonic, and stationary cultures
Project description:Genomic DNA from Pseudomonas aeruginosa strains PAO1 and PA14 Overall design: Pseudomonas aeruginosa genomic DNA was isolated, fragmented and hybridized to Affymetrix Pseudomonas GeneChips.
Project description:Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip-flow reactors on a medium composed to mimic the exudate from a chronic wound (CWE). After 72 hours, the biofilms were treated with CWE (control biofilms) or CWE containing ciprofloxacin (treated biofilms) for an additional 24 hours. Planktonic samples were cultivated to early logarithmic phase in CWE. The biofilm specific growth rate was estimated via elemental balances to be approximately 0.37 h-1, or one-third of the planktonic maximum specific growth rate. Global analysis of gene expression indicated decreased anabolic activity in biofilms compared to planktonic cells. A focused transcriptomic analysis revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing. Overall design: Three biological replicates were prepared and analyzed for the following three growth conditions: (1)Pseudomonas aeruginosa was grown planktonically to early log phase. (2) Pseudomonas aeruginosa was grown in drip flow biofilm reactors on hydroxyapetite-coated glass slides for four days. (3) Pseudomonas aeruginosa was grown in drip flow biofilm reactors on hydroxyapetite-coated glass slides for three days and then treated with 1 mg/ml ciprofloxacin for an additional day.
Project description:Analysis of Pseudomonas aeruginosa PAO1 treated with 200 µM sphingomyelin. Results provide insight into the response to sphingomyelin in P. aeruginosa. Overall design: P. aeruginosa PAO1 was cultured in the presence and absence of sphingomyelin. The orginal culture was divided into two parts. One was treated with 200 μM sphingomyelin and the other served as a control. The experiment was performed in tripricates.
Project description:Oberhardt2008 - Genome-scale metabolic
network of Pseudomonas aeruginosa (iMO1056)
This model is described in the article:
network analysis of the opportunistic pathogen Pseudomonas
Oberhardt MA, Puchałka J, Fryer
KE, Martins dos Santos VA, Papin JA.
J. Bacteriol. 2008 Apr; 190(8):
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
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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_P4 infecting PAK strain of P. aeruginosa. Overall design: 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 P4. Three biological replicates for each time point.
Project description:The ParS/ParR two component regulatory system plays important roles for multidrug resistance in Pseudomonas aeruginosa. In this study we report RNA-seq analyses of the transcriptomes of P. aeruginosa PAO1 wild type and par mutants growing in a minimal medium containing 2% casamino acids. This has allowed the quantification of PAO1 transcriptome, and further defines the regulon that is dependent on the ParS/ParR system for expression. Our RNA-seq analysis produced the first estimates of absolute transcript abundance for the 5570 coding genes in P. aeruginosa PAO1. Comparative transcriptomics of P. aeruginosa PAO1 and par mutants identified a total of 464 genes regulated by ParS and ParR. Results also showed that mutations in the parS/parR system abolished the expression of the mexEF-oprN operon by down-regulating the regulatory gene mexS. In addition to affecting drug resistance genes, transcripts of quorum sensing genes (rhlIR and pqsABCDE-phnAB), were significantly up-regulated in both parS and parR mutants. Consistent with these results, a significant portion of the ParS/ParR regulated genes belonged to the MexEF-OprN and quorum sensing regulons. Deletion of par genes also lead to overproduction of phenazines and increased swarming motility, consistent with the up-regulation of quorum sensing genes. Our results established a link among ParS/ParR, MexEF-OprN and quorum sensing in Pseudomonas aeruginosa. Based on these results, we propose a model to illustrate the relationship among these regulatory systems in P. aeruginosa. A total of 9 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas aeruginosa PAO1 wild type strain (3 replicates); Pseudomonas aeruginosa parS mutant (3 replicates); Pseudomonas aeruginosa parR mutant (3 replicates).