Due to the fact that each of the RNA data sets has a differing number of mutants, the bootstrapping is done by sampling 20 mutants from each of the other data sets besides FTL, in order to correct for any bias that might come up due to one program/metric favoring one data set over another.
Since synonymous mutations are less likely to be eliminated by purifying selection, this latter number provides a lower bound on the fraction of codon mutations that were sampled by the mutant viruses.
Note that these numbers are only a lower bound on the fraction of codon mutations sampled by the mutant viruses even synonymous mutations to influenza are sometimes strongly deleterious (Marsh et al., 2008), and so some of the missing synonymous codon mutations may have been introduced into mutant viruses but then purged by purifying selection.
RbcL was rapidly degraded by subtilisin in samples of the mutant, while the RbcL degradation was clearly delayed in wild-type extracts with bound microcystin (Fig. 6B and C).
We sampled the solution space of the wild-type E. coli, ldhA mutant, pflB mutant, and NZN111 using ACHR method to characterize their respective network properties.
As shown in Figure 4, we estimated that 85% of possible codon mutations were sampled at least five times by the mutant viruses.
Virus generation by reverse genetics does introduce a bottleneck but fortunately, this bottleneck is sufficiently mild that at least half of all possible codon mutations are still sampled at least five times by the mutant viruses in each individual replicate.
Four mutants βF24G, βF24A, βF24S, and βF24P were recovered by screening the mutant bank.
Phylogenetic analysis and data gathered by pyrosequencing and cloning directly on clinical samples suggest that the mutant emerged de novo.
Ferrets that had already been exposed to flu viruses were not affected by the mutant strain.
