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We checked whether gene conservation status in distant species correlates with the replication timing on the genome scale and compared the replication time of genes with and without homologs in distant species in two cell cultures, embryonic Kc and somatic Cl8 (Schwaiger et al. 2009).
There is a number of experiments that could be directly infered from our results, e.g. transfer a significantly slower or faster replicating segment to another location in the genome and check whether the replication time is conserved, or mutate the sequence of this segment to investigate the potential changes of the elongation time.
The authors put forth the ribosome as an example of a natural molecular machine; because the ribosome suffers from neither problem, they must not be fundamental, saying: The authors also questioned Smalley's figures for the replication time of nanomachines.
It seems intuitive that the larger the segment of DNA is, the longer the replication time.
This means that, if the replication time is longer than average, the rate would be decelerated and vice versa.
Obviously, we cannot rule out completely that there is a nucleotide composition-specific effect on the replication time.
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Nonetheless, we filtered these two results (non-nucleotide-dependency and length correlation) from the replication times.
On the contrary, we found almost no dependency between the replication times and the base composition of the segments.
At this point, the reason for the observed local deviations in the replication times remain unclear, but this might be changed as more and more experimental data become available.
We compared the three independent experimental measures of replication origin efficiency: calculated from fork-direction gels (Friedman et al., 1997); inferred from the replication time-course experiment; and inferred from the mapping of Okazaki fragments (Smith and Whitehouse, 2012).
Next we measured the replication times of these deletion plasmids, using the same methods as in Figure 4. Flow cytometry showed that the rate of passage through S phase was almost identical for each of the four strains containing deleted plasmids.
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