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Anti-mutator mutants, with lower than normal mutation rates, have been observed in bacteria [32], in the phage T4 [33], and in RNA viruses evolving in the presence of mutagens [34].
Influenza represents a particularly problematic therapeutic challenge since high viral mutation rates have often confounded many conventional antivirals.
In addition, RNA virus mutation rates have primarily been estimated from phylogenetic comparisons of viral lineages, and were thus likely affected by purifying selection and possibly by population bottlenecks.
Somewhat higher mutation rates have been reported for Mycoplasma gallisepticum (0.8 1.2 × 10−5) isolated from house finches and poultry23, and for the human pathogens Neisseria gonorrhoeae24 (4.6 × 10−5) and Campylobacter jejuni25 (3.2 × 10−5), but those were based on polymorphisms that have predominantly arisen by recombination between isolates rather than by mutation.
Although SNPs in DNA repair/replication genes have been suggested as a source of hypermutation in M. tuberculosis31,32, only small increases in mutation rates have been observed due to these polymorphic genes (for example, polymorphisms in PHP exonuclease domain of the DNA-polymerase DnaE1 (ref. 30)).
Until recently, good estimates of mutation rates have been hard to come by.
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In turn, research using RNA viruses as replicons with short generation times and high mutation rates has been an invaluable tool to test models of quasispecies theory.
The study of the evolution of mutation rates has been addressed theoretically [13], [18] [21], and using digital organisms [17].
However, current positional mutation rates are under suspicion because the methods employed to compute them could be flawed [28], [29], and only recently a new proposal of site-specific mutation rates has been published aimed at overcoming the problems of past approaches [29].
Nevertheless, we believe that other lines of evidence indicate that convergence between intra- and interspecific mutation rates has not occurred.
Oxidative deamination leading to high C→U/T transitional mutation rates has been reported in ssDNA phage M13 (Kreutzer and Essigmann 1998).
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