16 research outputs found
Non-synonymous SNPs and DIPs among <i>P. aeruginosa</i> LES isolates found in regulatory genes.
<p>*indicates that the polymorphism introduces a stop codon or a frame shift in the protein sequence.</p>1<p>Genes selected have a PseudoCAP annotation that includes terms “Transcriptional regulators” and/or “Two-component regulatory systems” (pseudomonas.com).</p>2<p>Virulence factor database annotation is indicated between parentheses when applicable.</p>3<p>LESL: LESlike.</p
Swimming, swarming and biofilm formation.
<p>Swimming and swarming: the isolate was considered non-motile when bacterial growth could be observed only at the site of inoculation. Biofilm: mean and standard deviation from 8 wells in a single 96-well microplate assay. Results shown are from 1 of 3 replicate experiments.</p
Assembled genomes for 7 <i>P. aeruginosa</i> isolates of the Liverpool epidemic strain.
1<p>Shotgun libraries of the first 3 strains (UK) were sequenced individually on a quarter (LES400, LESB65) or a half (LES431) 454 plate. Shotgun libraries of the last 4 strains (Ontario, Canada) were barcoded and sequenced on a full 454 plate.</p>2<p><i>De novo</i> assembly was performed with GS De Novo Assembler (Roche); genome finishing was done with Consed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087611#pone.0087611-Gordon1" target="_blank">[20]</a>.</p
Pyocyanin and pyoverdine production.
<p>A. Measurements of pyocyanin from overnight culture supernatants, error bars: standard deviation from 3 independent experiments. B. Pyoverdine production on Pseudomonas agar F (Difco) visualized under long wavelength UV light, results shown are from 1 of 3 replicates.</p
Pseudomonas Community Annotation Project (PseudoCAP) annotation of polymorphic genes among <i>P. aeruginosa</i> LES isolates.
<p>P-values are from Fisher’s exact tests comparing genes with non-synonymous polymorphisms with LESB58 whole genome composition (* p<0.05, ** p<0.01 & q <0.05).</p
Proteolitic and elastolytic activity in culture supernatants.
<p>Proteolytic activity was measured using BHI agar plates containing 1% skim milk; - no activity,+small halo of proteolysis,++halo diameter multiple times that of the culture supernatant sample. Results were reproducible. Elastolytic activity was determined with the Elastin-Congo Red Assay after 3 hours. Measurement values varied greatly between experiments, hence data was normalized so that OD495 = 0.15 for PAO1 in all experiments, error bars: standard deviation from 3 independent experiments.</p
Conserved polymorphisms among <i>P. aeruginosa</i> LES isolates from the UK and/or Canada.
1<p>“High” for nonsense (*) or frame-shifting (fs) mutations, “Moderate” for amino acid substitutions, “Low” for silent coding and non-coding mutations.</p>2<p>c.: position in the gene sequence.</p>3<p>p.: position in the protein sequence.</p
Non-synonymous SNPs and DIPs among <i>P. aeruginosa</i> LES isolates that are in genes associated with virulence factors, biofilm formation and antibiotic resistance.
1<p>According to the Virulence factor database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087611#pone.0087611-Chen1" target="_blank">[35]</a>, virulence factor associated genes are classified into categories and subcategories.</p>2<p>LESL: LESlike.</p>3<p>TTSS: type III secretion system.</p
Summary of SNPs and DIPs among <i>P. aeruginosa</i> LES isolates and between LES and laboratory strain PAO1.
1<p>Polymorphisms were identified with CLC Genomics Workbench (CLCbio) with the following criteria: default parameters for base quality, minimum coverage = 6, minimum frequency  = 0.8 for each new genome against reference LESB58 and 0.95 for all LES or LESlike against reference PAO1.</p
Circular genome map of <i>P. aeruginosa</i> LESB58 compared to 7 LES isolates and strain PAO1.
<p>Map and underlying analysis were performed with the CGView Comparison Tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087611#pone.0087611-Grant1" target="_blank">[23]</a>. Rings from the outside inward: LESB58 plus-strand, LESB58 minus-strand, 308 unique non-synonymous polymorphisms among LES isolates, LES400, LES431, LESB65, LESlike1, LESlike4, LESlike5, LESlike7, PAO1 and GC content plot. LES prophages (Pro), genomic islands (GI) and LES specific mini island (MI) are indicated on the outside of the map <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087611#pone.0087611-Winstanley1" target="_blank">[10]</a>. Orange colored BLAST hits: 90–98% identity, blue colored BLAST hits: 0–90% identity.</p