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Next generation sequencing technologies have strongly favoured the analyses of small RNA regulatory networks, detecting rare molecules and small RNA variants with unprecedented precision and sensitivity.
RNA-Seq revealed that ∼30% of the differentially expressed genes had two or more differentially expressed RNA variants (data not shown).
Although most cells were killed, a small number of drug-tolerant cells survived, which expressed unique RNA variants influencing cell adhesion, cell surface signaling, and microtubule organization/stabilization [43].
For example, in Roundup-tolerant GM soybeans, it has been found that read-through transcripts into sequences present downstream of the transgene integration site resulted in four different RNA variants, which might code for unknown fusion proteins [17].
In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel.
We further measured affinity of the E. coli RNase P protein to chimeric RNase P RNA variants, consisting of an E. coli specificity domain and an engineered archaeal catalytic domain.
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In addition, a compensatory RNA mutation within a defective RNA variant was found.
These screens identified a glycine to serine mutation of L30e, which specifically restores activity to an RNA variant containing a U that replaces a helix-capping G. Similarly, an asparagine to alanine mutation was found to suppress a substitution at a position where the L30e RNA nucleotide extends out into the protein pocket.
Instead, they resulted in a posttranscriptional processing equilibrium yielding Snord115 as well as the novel L-Snord115 RNA variant.
The CXCR4 small interfering RNA variant (siCXCR4) had no specific effect on the proliferation of wt-SUM44, wt-MCF7 and their LTED derivatives.
Similar to Snord115, the L-Snord115 RNA variant contains the antisense element to the 5HT2c pre-mRNA located in the 5′-portion of snoRNA (fig. 4 B).
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