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In a previous work, we reported that P. aeruginosa has a high mutation frequency to fosfomycin resistance in vitro [24].
We also observed an approximate 100 fold increase in rifampicin resistance mutation frequency in our experiments using the ΔmutS strain, as well as for the ΔmutL strain constructed in our laboratory, and were able to restore the mutation frequency to wild-type levels by complementation of each of these genes (data not shown).
The authors attribute the discrepancy in mutation frequency to the use of massively parallel sequencing.
For example, is the spontaneous mutation frequency to rifampicin resistance the same in the founder vs evolved strains?
An extract that was mutagenic in bacteria did not induce a significant increase in mutation frequency to human lymphoblasts.
Considering that MAPK3/1 is downstream of the RAF pathway, we used BRAF mutation frequency to determine a cutoff for p-MAPK3/1 positivity.
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One representative low-frequency variant for each of the five mutations tested was verified by clonal sequencing which found the mutation frequencies to be between 0.7% 11%.
The overall procedure of using nucleotide mutation frequencies to estimate codon mutation frequencies was first suggested by Deminoff et al. who argued that adequate statistical power could not be realized if only codon-triplet mutations were analyzed.
Previous work by de Lima et al. described five mutational hotspots (R6, R84, R250, R400, and R412) and attributed the high-mutation frequencies to the CpG dinucleotides in these codons.
G-tests were used to compare the observed mutation frequency at variable sites to a null model with a frequency of 0.5.
We expected to find a relatively high mutation frequency due to HCV's high genetic plasticity, but contrary to our expectations, the 0.9% mutation frequency observed in the samples was relatively small in relation to the variability among independent HCV isolates (10 12%), and was in the range of quasispecies variability typically found in a given individual (∼1 4%).
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