Sonal Shewaramani

University of Ottawa · Department of Biology

Pseudomonas aeruginosa , a ubiquitous opportunistic pathogen, is a leading cause of chronic infection of airways in cystic fibrosis ( CF ) patients. Chronic infections typically arise from colonization by environmental strains, followed by adaptation of P. aeruginosa to the conditions within the CF airway. It has been suggested that oxygen availabi...

Pseudomonas aeruginosa is among the most problematic opportunistic pathogens for adults with cystic fibrosis (CF), causing repeated and resilient infections in the lung and surrounding airways. Evidence suggests that long-term infections are associated with diversification into specialized types but the underlying cause of that diversification and...

Background Many bacteria are facultative anaerobes, and can proliferate in both anoxic and oxic environments. Under anaerobic conditions, fermentation is the primary means of energy generation in contrast to respiration. Furthermore, the rates and spectra of spontaneous mutations that arise during anaerobic growth differ to those under aerobic grow...

Supplementary Tables

Author Summary When organisms are exposed to different environments, the rates and types of mutations that spontaneously arise in each environment can vary due to differing mutagenic pressures imposed by each environment, and these can potentially influence the evolution of the organism. Little is known about the types of mutations that arise when...

E. coli mutation rates calculated from fluctuation assays. (DOCX)

Spectra of BPSs amongst the aerobic and anaerobic lineages. (DOCX)

REL4536 IS element features and mutation rates. (DOCX)

Relative distribution of mutations within the macrodomains of E. coli. (DOCX)

Mutations detected amongst the aerobic and anaerobic lineages. (XLSX)

Expression values of E. coli REL4536 genes involved in DNA repair, replication and transposition. (DOCX)

Relative abundance of IS gene transcripts in aerobic and anaerobically grown cells. (DOCX)

Expression of genes involved in arginine biosynthesis. (DOCX)

Primers used to verify SV break points. (DOCX)

Significantly up-regulated genes, as a proportion of genes in the pathway, known to be involved in DNA repair and replication (classified by pathway). To identify significant expression, Benjamini-Hochberg adjusted p < 0.05 were used. Asterisk denotes a significant enrichment of the gene list under anaerobic conditions by Fisher’s exact test (*, p...

Genome re-sequencing reference-based mapping and de novo assembly statistics for MA clones. (XLSX)

Clockwise and counter-clockwise replichores of E. coli REL4536. (DOCX)

Cumulative distribution of mutations in the genomes of aerobic and anaerobic MA lineages. Shown are the relationships between cumulative mutations and chromosomal position for A) expected random distribution of mutations around the genome, B) BPSs, C) SVs, and D) indels. (TIF)

Comparison of mutation rates expressed per generation and per unit time. Shown are: Mean mutation rates of mutational classes expressed A) per nucleotide per generation, B) per nucleotide per day of growth, C) Conditional BPS rates expressed per nucleotide per generation and D) Conditional BPS rates expressed per nucleotide per day of growth. Error...

IS150 genome location. (DOCX)

Comparison of SV mutation rates. Shown are: A) and C) Mutation rates of different SV classes expressed per nucleotide per generation, and B) and D) Mutation rates of different SV classes expressed per nucleotide per day of growth. Error bars represent standard errors of the mean. * denotes p < 0.05 by Mann-Whitney U-test. (TIF)