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Phenotypic screens of target-gene mutants have identified several with rhythm-specific circadian defects, indicative of effects on clock output pathways.
Loss of DNA methylation at frq has only minor effects on clock function and manifests as a small phase advance (Belden et al. 2011).
Since light is an easily applicable stimulus that provokes strong effects on clock phase, the paper focuses on the application of different lighting conditions.
While the hepatic core clock was surprisingly resilient to miRNA loss, whole transcriptome sequencing uncovered widespread effects on clock output gene expression.
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These examples illustrate the ability of alcohol to have profound and long-lasting effects on clock-gene expression in multiple organs and tissues.
In our previous work [3], we considered a conservative approach to software bypassing and investigated its effect on clock cycle performance and reduction in register files reads and writes depending on the heuristic parameter guiding bypassing decisions.
Moreover, not only has light a differential effect on clock gene expression in different organs, the changes in clock gene expression, too, do not correlate in a consistent manner with the changes in the expression of the output genes studied.
However, when REV-ERBα expression was decreased by ∼57% using siRNA, the expression of CLOCK was increased 3.2-fold, as shown in Figure 2c, indicating that endogenous REV-ERBα exerts a repressive effect on CLOCK expression.
Related MADS-box genes had less effect on clock function.
DOI: http://dx.doi.org/10.7554/eLife.00473.010 Loss of RVE8 function has neither a strong effect on clock function nor on expression levels of evening-phased genes (Farinas and Mas, 2011; Rawat et al., 2011; Hsu and Harmer, 2012).
This work identifies ELF3 as repressing gene expression of clock components, resulting in widespread effects on the clock gene network.
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