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Carotenoid production of the transformants was compared with that of E. coli transformant carrying plasmid pACCAR25Δ crtE and pBAA encoding mouse GGPP synthase (positive control) [ 16], and with transformant carrying plasmid pACCAR25Δ crtE and a pBluescript II KS- (pBS) vector (negative control).
To determine the statistical significance of LOH for a specific transforming DNA and strain after growth of transformants on 5-FOA-containing medium, the number of transformants that lost Hyg or Nat resistance (LO Htransformants) was compared to those with no LOH.
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The double mutant was transformed with pHT01ribMopt or the empty plasmid and both transformants were compared in growth assays on LB plates.
When the rpoB sequences of Rif resistant transformants were compared with those of corresponding donor and recipient, we found that for ∼10% of the recombinant clones, the stretch of integrated DNA from the Rif resistant donor was interrupted by one or multiple short fragments where the sequence was identical to that of the recipient.
For the ade2 assay, the numbers of Ade+ Ura+ transformants were compared to Ade− Ura+ transformants, while for the leu2 assay Leu+ Ura+ transformants were compared to the number of Leu− Ura+ transformants.
The phenotypes of M184 and the three transformants were compared to confirm that the upregulation of patAB observed in the transformants conferred a phenotype similar to that of M184.
When the phenotype of the Δ gvpC (pARK-C) transformants were compared to the parental Δ gvpC and ∆ ura3 strains, increasing opacity resulting from increasing gas vesicle content was observed in the following order: Δ gvpC < Δ gvpC (pARK-C1) < Δ gvp (pARK-C2) < Δ gvpC (pARK-C3) ≈ Δ gvpC (pARK-C4) ≈ ∆ ura3.
The transformant was compared with the untransformed control strain regarding respiration (SOUR) at both high oxygen concentration (starting at 100% saturation) as well as low oxygen concentration (starting at 25% saturation) (Fig. 4).
In individual experiments, the mean level of adhesion and standard deviation from triplicate wells of each transformant were compared to wild-type cells by ANOVA with the Dunnett post test.
The telomere length of two independent transformants of each mutant was compared to four controls: wild type, RIF2, rif2 Δ, and the original NAAIRS mutant haploid strain.
To determine statistical significance of template switching vs. chromosomal recombination, the number of template switching transformants (W/R on 5-FOA) was compared to the number of BIR-associated chromosomal recombinants (W/W on 5-FOA; Figure 3A, Figure 4B, Figure 6B, and Figure S3).
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