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Reflectance profiles for every isolated cone and rod were generated by plotting reflectance as a function of time, where reflectance at a given time point is defined as the average intensity of all the pixels within the photoreceptor mask.
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Antimicrobial drug susceptibility testing, at least to erythromycin and ciprofloxacin, is recommended for every isolate (10 ).
Two methods were used for every isolate examined: the boiling method (14) and alkaline lysis (15).
Occasionally, cultures became contaminated, or a technical mishap occurred; therefore, not every laboratory submitted an image for every isolate.
For every isolate, a total of 6 to 10 samples were harvested at regular intervals of 2 to 8 hours throughout the IDC.
TaqMan™ Minor Groove Binding (MGB) allelic discrimination assays were used to determine the precise canSNP grouping for every isolate used in this study [ 19, 47].
Within 15 days, 4-5 passages were used for each isolates which produce a total cell number of approximately 3-5 × 106 cells/mL for every isolates which start from approximately 1 × 105 cells/mL.
For every isolate, aligned reads were resampled to a total of approximately 50,000 reads to accommodate for the difference in the total number of mapped reads amongst isolates using SAMTools [ 29].
DNA sequencing was performed in Ion Torrent for single-end using 100 bp chemistry libraries (Life Technologies, Carlsbad, CA) and in 454 FLX+ for mate paired-end libraries with a 3,000 bp span (Roche), for every isolate except PMA37.5.
A 10-locus expanded panel derived from loci recently described for Irish zoonotic M. bovis strains (8 ) improved strain discrimination by producing different profiles for every isolate (Table 1).
Cells were incubated at 28 °C for 2 3 days for isolated colonies.
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