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Pairwise comparisons between strains were conducted using Tukey's Honestly Significant Difference (HSD), based on ANOVAs with vial as a nesting factor, with the sample sizes shown in Table 1 unless noted otherwise.
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Determination of differential gene expression between strains was conducted by the creation of an R script by use of the linear fitting and empirical Bayes methods of limma (Smyth 2004, 2005).
In addition, two predefined adjusted survival time comparisons between MAC and other NTM strains were conducted, including ATS 2007 positivity (positive vs. negative) and underlying diseases according to the McCabe classification (3 4 vs. 1 2) as additional dichotomous covariates.
Comparative bioassays between the LiTOX and the susceptible Bora-Bora strains were conducted after 30 generations of laboratory selection.
Three passages of these strains were conducted.
Pulsed field gel electrophoresis of the environmental K. pneumoniae strains was conducted to determine the clonal relationship between these strains and a variety of clinical strains.
A retrospective study on collection of the AFSSA strains was conducted because of a suspected misidentification between the closely related M. canis and M. bovirhinis species.
Routine culture of E. coli strains was conducted in 2× yeast extract-tryptone (2xYT) medium.
To allow us to make direct comparisons between isogenic strains, experiments were conducted using a phage-free lab strain of P. aeruginosa, PAO-1, as the bacterial host.
Comparisons between the isolate contigs to the ancestral strain's sequence were conducted using the ClustalW application within BioEdit [ 39].
The DFA was conducted on partial warp scores, to determine whether differences observed between strains were powerful enough to reclassify according to strain.
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