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Single-worm PCR was additionally performed to confirm the accuracy of both the oaCGH and qPCR methods in estimating the frequency of existing deletions and duplications.
To determine whether the increases in deletion frequency at these sites were due to expansion of existing deletions or acquisition and accumulation of new deletions, we sought to measure the ratio of unique to total deletions as a function of age.
As such, we concede the probability of relative undercounting in older-aged samples and the likelihood that, in addition to clonal expansion of existing deletions, de novo deletions contribute to the observed increase with age, although not to the degree that the commenters assert.
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We first compare and evaluate the performance of existing deletion callers from the synthetically generated NGS read data with various ranges of deletion size and depth of coverage.
We focused on evaluating the performance of existing deletion calling algorithms for various spanning ranges from low- to high-coverage simulation data.
Next, we took advantage of an existing deletion mutant snr1 6c hdac3 6c, which removes the entire snr1 coding region and the C-terminal region of hdac3.
We first examined the phenotype of an existing deletion in cdc-25.3 to determine whether its function is important for oocyte or embryo development.
We reasoned that the existing deletion mutations of rnt-1 provide a sensitized genetic background so that one could identify interacting genes by looking for synthetic phenotypes.
Larger deletions have not been isolated despite extensive random mutagenesis followed by PCR-based screening (J. H. Ahnn, personal communication), and the phenotype caused by rnt-1 RNAi includes embryonic lethality, which is obviously more severe than that of existing deletion mutations.
In conclusion, re-analysis of the data (Taylor et al., 2014) challenges the authors' inference that diversity of unique deletions remains constant with age and that expansion of pre-existing deletions is the primary factor contributing to age-related accumulation of mtDNA deletions.
The major mechanism leading to the increase in detectable mutations is therefore likely to be the segregation and clonal expansion of pre-existing deletions and point mutations, rather than an increase in the mutation rate per se, given that low-level mitochondrial DNA heteroplasmy seems to be a common finding in healthy individuals (Payne et al., 2013).
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