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When determining the true IBD, we ignored variants with ≤10 copies in the 2000 individuals, as very recent mutations disrupt sequence identity.
This assumption, however, is being challenged since the discovery that significant structural variations are possible that disrupt sequence collinearity [ 31, 32].
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The first plasmid carried either the wild-type P tar template or a mutant P tar template with base-pair substitutions that disrupt sequence-specific recognition of the transcribed-region −10-like element by σ.
Furthermore, the ∼35-nt pause RNA was barely detected with or without excess σ using a control template carrying base-pair substitutions that disrupt sequence-specific recognition of the transcribed-region −10-like element by σ region 2 (Deighan et al., 2011).
This isoleucine-to-asparagine mutation (I304N) lies within the hydrophobic platform of the RNA-binding pocket of all KH domains studied to date (6, 7) and is predicted to disrupt sequence-specific RNA binding by this domain (8), suggesting that the RNA-binding properties of FMRP are central to its cellular function and role in disease pathogenesis.
When necessary, confirmation of the disrupted sequence was achieved by PCR.
Besides the single mutation, the fragment encoded an otherwise wildtype sequence and was intended to replace the disrupted sequence at the native locus.
Genomic DNA from mice was amplified by PCR using the primers: 5-GTCATTTCCTGACCTCTGACC-3 and 5-AACCGCATTATTCCATGGGGC-3 to detect WT DNA and primers 5-AACCGCATTATTCCATGGGGC-3 and 5-GCCTGCTCTTTACTGAAGGCTC-3 to detect the disrupted sequence.
Using a custom SNP microarray we validated 150 SPGs in a cohort of 468 individuals, with every individual genome averaging 36 disrupted sequence variations, 15 in homozygote form.
Some TvBspA genes are potential pseudogenes with 98 entries currently being annotated as such as they possess ORF disrupting sequence features.
As for the detection for progenies of GD individuals, which might contain homologous disrupted sequence, a heteroduplex formation procedure after mixing with WT PCR product is necessary to avoid omission.
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