Project description:The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied. To determine the up- or down-regulated expression profile in the presence of dimethyl sulfoxide (DMSO) and ethanol (EtOH), UPEC UTI89 were grown in YESCA broth with 4% dimethyl sulfoxide (DMSO) or 2% ethanol (EtOH) or no comound at 26°C with 200 rpm shaking for 24 hours were used for RNA extraction and hybridization on Affymetrix microarrays.
Project description:The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied.
Project description:Transcriptional analysis of UTI89 - uropathogenic E.coli (UPEC) strain grown in urine/Luria bertani medium culture in vitro as well as during three distinct phases of UPEC bladder infection: intracellular growth, filament formation and filament reversal. UTI89 was used to infect a bladder epithelial cell line cultured within a dynamic flow chamber system and harvested at particular stages of its pathogenecity cascade. Total RNA was processed and cy3 labeled for microarray analysis using Agilent custom Escherichia coli UTI89 arrays designed using E-Array.
Project description:We previously determined that loss of respiratory quinol oxidase cytochrome bd disrupts biofilm formation in uropathogenic Escherichia coli (UPEC). In this study, we extracted and interrogated the outer membrane and extracellular matrix of colony biofilms formed by UPEC isolate UTI89 and an isogenic mutant lacking cytochrome bd (∆cydAB).
Project description:Antibiotic resistance is a growing global health threat. Most research has focused on understanding how mobile genetic elements are acquired by pathogenic bacteria. However, bacteria have intrinsic chromosomally encoded systems to protect themselves against antimicrobial assault. Our lab has uncovered such a system in uropathogenic E. coli. PmrAB and QseBC are connected two component systems that confer resistance to polymyxins, a last resort antibiotic. The histidine kinase PmrB responds to ferric iron and activates its cognate response regulator PmrA, as well as the non-cognate response regulator QseB. QseC, the other histidine kinase plays an important role in resetting the system. To better understand how PmrAB and QseBC mediate polymyxin resistance, this project aimed to elucidate the regulon of the two response regulators QseB and PmrA in the uropathogenic E. coli strain UTI89. In this strain, isogenic mutants were made lacking qseB and pmrA singly and together. These strains and wild-type UTI89 were stimulated with ferric iron and samples for RNA sequencing were taken prior to stimulation and at 15 and 60 minutes post stimulation. Samples were then sent for sequencing on the Illumina platform and analyzed using Rockhopper software.
Project description:The method DFI-seq was developed to enable identification of differentially expressed genes in uropathogenic E. coli strain UTI89 during growth in human urine and in bladder epithelial cells. By utilising this new method, the aim was to identify novel virulence genes in UTI89. DFI-seq is a combination of differential fluorescence induction (DFI) with next-generation sequencing. DFI-seq was compared to DFI by analysing gene expression of UPEC in human urine and thereby confirming that DFI-seq gives a better overview of gene expression. DFI-seq was hereafter used to look at gene expression in UTI89 while infecting bladder epithelial cells. We demonstrate the usefulness of DFI-seq for identification of genes required for optimal growth of UPEC in human urine, as well as potential virulence genes upregulated during infection of bladder epithelial cells. DFI-seq holds potential for the study of bacterial gene expression in live-animal infection systems.
