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LogRatios were adjusted using a time zero flask transfer comparison to remove affects from flask transfer thus setting the time zero expression ratio at 1.
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We adapted these two phages across serial flask transfers for hundreds of generations to identify the mechanisms and generality of evolution to an optimal lysis time.
Cells were incubated with Dulbecco's PBS without calcium chloride and magnesium chloride (Sigma-Aldrich) at 37°C for five minutes and then removed from the flask, transferred into a Falcon tube, and spun for three minutes at 13,000 rpm.
An isolate of a lab strain of φX174 (GenBank accession AF176034) was pre-adapted to our experimental conditions: serial flask transfers in 20 ml liquid media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, and 2.0 mM CaCl2) with 30-minute growth periods per flask on E. coli CGW317.
This is a rough estimate due to transition/transversion bias, among-site rate variation, and strong bottleneck effects from the flask-to-flask transfer regime.
We found that mutations with relatively large selection coefficients can be out-competed and that there were as many as three competing genotypes in many of the populations where resource was abundant, even though the regular strong bottlenecks inherent to our flask-to-flask transfer protocol strongly decreased our ability to observe most mutations.
The cells were scraped off the flasks, transferred to 5 ml test tubes and collected by centrifugation at 450 g for 10 minutes.
The bottleneck effects from flask-to-flask transfers are so strong during experimental evolution of φX174 that there is an extremely low probability that small-effect or neutral mutations will attain appreciable frequency in the population.
Treated or mock-incubated PWBC were scraped from tissue culture flasks, transferred to a 50 ml centrifuge tube filled with PBS and centrifuged at 3700 × g for 20 min at 20°C to pellet the cells.
Irrespective of shake flask mass transfer implications, the elevated substrate consumption did not generally lead to any enhancement of cellular yield or TE formation.
Subsequently, the flask was transferred into a water bath set at a certain temperature.
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