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Here we continue our characterization of these M. leprae strains and present two new 1000 year old mycobacterial genomes, which in combination with previous samples, allow us to describe, in detail, the historical epidemiology of leprosy at this location across the centuries.
Although we have only completely sequenced a limited number of M1 lineages, the combination of HVSI haplotypes and RFLP status carried out for the rest of our M1 samples allow us to be confident that we have not missed any new basic M1 lineage.
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PFGE analysis of digested samples allowed us to use the unique restriction banding patterns of the strains as a genetic screen to visually determine whether the plasmids were transferred to the recipient strains.
The quality selection of the samples allowed us to use the best-fit parameters from each sample as a point estimate for the primary parameters.
The fact that PIRLS uses representative random samples allows us to generalize the findings to the population of fourth graders in the respective countries.
The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species.
Prior to DNA extraction, an appropriate amount of an artificial sequence was spiked into the test samples, allowing us to assess the extraction efficiency used for normalisation.
Because miRNAs are involved in many cell processes [ 3], the use of these patient-matched samples allowed us to remove interpatient variability.
Analyses done with GC MS on whole samples allowed us to specifically list the organic compounds that were used in grounds and possible size layers without pointing to the specific layers from which these compounds originate.
This random variation between samples allowed us to develop and validate the statistical methods (i.e., STOCSY) used in this study.
These samples allowed us to ascertain when only chemical or isotopic changes are occurring, or when both chemical and isotopic changes are occurring.
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