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: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:Pseudomonas chlororaphis strain 30-84 is an effective biological control agent against take-all disease of wheat. In this study, we conducted an RNA-seq analysis by comparing the wild type strain, PCA and O star with a phenazine deficient mutant. RNA-seq analysis identified over 800 genes differentially regulated by phenazines. Overall design: A total of 8 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (2 replicates); Pseudomonas chlororaphis ZN mutant (2 replicates); Pseudomonas chlororaphis PCA strain (2 replicates); Pseudomonas chlororaphis O star (2 replicates).
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.