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The bona fide pipo slip site was excluded from the shuffling and motif counting.
To confirm that transcriptional slippage was not specific to TuMV, we analysed RNA from plants infected with two other potyviruses, Bean common mosaic virus (BCMV; aug_GAA_AAA_Auc slip site) and Bean common mosaic necrosis virus (BCMNV; ucg_GAA_AAA_Auu slip site).
Among potyvirid species, all three reading frames (GAA_AAA_A, G_AAA_AAA and GA_AAA_AA) are represented at the pipo slip site.
To further test whether transcriptional slippage might explain P3N-PIPO production, we performed high-throughput sequencing of the slip site region in the context of virus infection.
While investigating translational frameshifting as a potential P3N-PIPO expression mechanism, we had previously performed in vitro translations of reporter constructs containing the pipo slip site and flanking sequences.
To test whether insertions were specific to the pipo slip site, total RNA from systemically infected leaves and virion-derived RNA were subjected to high-throughput sequencing (ENA databank accession PRJEB9490).
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SLiP site-directed mutagenesis is a simple and efficient method that removes any possibility of mutation in the vector region.
Thus, this new SLiCE-mediated PCR-based site-directed mutagenesis (SLiP site-directed mutagenesis) technique simplifies the original overlap extension method by removing several steps.
SLiP site-directed mutagenesis simplifies the steps of PCR-based site-directed mutagenesis, as it exploits the capability of the SLiCE method to insert multiple fragments.
Furthermore, SLiCE was applied to the polymerase chain reaction (PCR -based site-directed mutagenesis method, in a PCR -basedrmed "site-directedd PCR-based site-directed mutagenesis (SLiP site-directed methodnesin)".
The combination of SLiCE using E. coli laboratory strains and SLiP site-directed mutagenesis will facilitate the generation of recombinant plasmids and mutants, and shorten the time for DNA manipulation in the laboratory.
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