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To assess if the high mutation rate observed at the microsatellite loci [34] might impair this test, we performed a simulation study.
Important implications of our findings are that the mutation rate observed in spermatozoa reflects the exposure load acquired during the entire life span of an individual, whereas the DNA damage levels in spermatozoa are temporary and reflect recent exposures.
No homologs of the conserved mismatch repair genes, mutS and mutL, have been found in the genome of S. acidocaldarius despite its low genomic mutation rate, leading to the puzzling question of what is responsible for the maintenance of the low genomic mutation rate observed in this organism and in the Archaea as a whole [4], [5], [46].
The functional mutS allele of Z2491 was then introduced into Z5463 as described in the experimental procedure section, which reverse this hypermutator phenotype (Fig. 3B), demonstrating that the high mutation rate observed with Z5463 was indeed due to the defective mutS allele.
Further studies, in particular to elucidate if there is any MMR activity in the protein complement of H. salinarum NRC-1, are necessary to differentiate if the low mutation rate observed in this organism is the result of intrinsic properties of its DNA polymerase or if DNA repair activities are recruited to the replication site to remove mismatches.
This confirms that potential recurrent mutations, due to a higher indel mutation rate observed in repeat-rich regions, do not qualitatively alter the results of the analysis.
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Significantly, basal mutation rates were recovered when the nucS deletion was chromosomally complemented with the wild-type gene MSMEG_4923 (nucSSm) (Fig. 2a, Supplementary Table 1), confirming that inactivation of this gene was responsible for the high mutation rates observed.
Based on the low mutation rates observed in large, long-lived individuals, A. gallica appears to have an especially stable genome.
Taken together, these findings suggest that DNA lesions in addition to mismatched base pairs might contribute to the elevated mutation rates observed for MMR-deficient strains.
This finding leads to the puzzling question of what mechanism is responsible for maintenance of the low genomic mutation rates observed in the Archaea, which for the most part do not have MutS and MutL homologs.
This high level of identity is consistent with the stable genome and low mutation rates observed in herpesviruses [ 17, 18].
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