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To aggregate fluorescence data across experiments and adjust for day-to-day variability, size-adjusted and square-root transformed fluorescence measurements for each mutant and each day were then centered and scaled according to the mean and variance of that day's wild-type nematode size-adjusted and square-root transformed fluorescence measurements.
Three biological replicates were included for both wild-type control and fpgs1 mutant and each replicate had ten pooled plants.
To obtain the standard deviation, we assessed the activity in media from three independent transfections for each mutant, and each medium has been evaluated in duplicate.
Coexposure assays were performed by incubating the bacteria at 37°C for 30 minutes with the mutant and each extract prior to plating on MGA plates.
We used a parameter from the curve fitting to quantify each gene interaction by comparing growth inhibition between the Yor1-ΔF single mutant and each respective double mutant across multiple oligomycin concentrations.
An epistasis coefficient among pairs of mutations i and j, ε ij, was calculated as ε ij = W00 W ij − W i 0 W0 j [ 52], where W00, W ij, W i 0, and W0 j correspond to the relative fitness of the WT, the double mutant and each single mutant, respectively.
Similar(53)
However, in our case, the instantaneous rate of substitution (R ss' ), and thus the structure/sequence score function, have to be computed for each possible nearest neighbor mutant, and for each substitution, along the entire evolutionary tree.
We have analyzed LVS mutants with in-frame deletions in each of the four igl genes and our recently published data showed that there were no significant effects of the expression of the three other proteins in each of the four mutants and each of the phenotypes could be complemented [19], [46].
The vector pTOPO-vilya (above) was used to generate the site-directed mutants, and each was cloned into the yeast expression vector (pGBKT7) using the primers above.
To evaluate the lyase activity of each VenL-ΔC mutant, we incubated the VenA peptide with each mutant and then subjected each to MALDI-ToF MS. Incubation of VenA with wild-type VenL-ΔC at 25 °C for 2 h in the presence of ATP, MgCl2, and TCEP resulted in 4-fold dehydrated VenA.
For each comparison, a linear contrast was set up to obtain the relative fold changes between each mutant and WT control for each tissue at all time points.
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