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The ratio of alternative reads to canonical mature miRNA reads were analyzed for developmental trends.
Kinetin did not modify the ratio of alternative splicing around exon 2 and exon 36, suggesting its specific mechanism of action on exon 20 inclusion (data not shown).
These results strongly suggest that the sterol-induced changes in the ratio of alternative spliced to full-length HMGCS, MVK, LDLR12, and PCSK9 are not due to splice variant specific differences in transcript stability.
This may be indirectly related to temperature (decreased temperature with increased latitude), as habitat structure related thermal conditions influence the ratio of alternative mate-locating strategies (i.e. aggressive perching sit and wait strategy on a sunlit patch versus a searching patrolling strategy [48].
The consolidation strategy perhaps allows for improvements in gene-level differential expression analysis, but it may eliminate any potential for detecting bona fide differential regulation of alternative transcripts, e.g., cases where the treatment under investigation changes the ratio of alternative forms expressed by the same transcriptional unit.
Briefly, this measure is obtained as a log likelihood ratio of alternative to null hypothesis.
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Ratio of alternative-to-constitutive nucleotides is shown in the column on the right.
Thus, the ratio of alternative-to-constitutive nucleotides is reversed in the 5'UTRs compared to the CDS: the average of alternative-to-constitutive nucleotides was ~3:1 in the 5'UTR, and ~1 3 in the CDS.
The ratio of alternative-to-constitutive nucleotides is much higher in 5'UTRs than in coding regions, suggesting the possibility that alternative regions play a major role in regulating translation of the respective genes.
To determine if sterol-induced changes in the ratios of alternative spliced to full-length transcripts were due to transcript-specific differences in mRNA decay rates, HepG2 cells were pre-incubated with either 2.0 µM simvastatin + 10% LPDS or sham buffer + 10% FBS for 24 hours, after which 1 µg/ml actinomycin D was added to the media (n = 12 experiments).
Further studies on alternative splicing have demonstrated that some single nucleotide polymorphisms (SNPs) are responsible for variations in the ratios of alternative spliced transcripts [ 8- 11].
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