An easy-to-use simulation program demonstrates variations in bacterial cell cycle parameters depending on medium and temperature.

PloS One
Caroline StokkeKirsten Skarstad

Abstract

Many studies are performed on chromosome replication and segregation in Escherichia coli and other bacteria capable of complex replication with C phases spanning several generations. For such investigations an understanding of the replication patterns, including copy numbers of origins and replication forks, is crucial for correct interpretation of the results.Flow cytometry is an important tool for generation of experimental DNA distributions of cell populations. Here, a Visual Basic based simulation program was written for the computation of theoretical DNA distributions for different choices of cell cycle parameters (C and D phase durations, doubling time etc). These cell cycle parameters can be iterated until the best fit between the experimental and theoretical DNA histograms is obtained. The Excel file containing the simulation software is attached as supporting information.Cultures of Escherichia coli were grown at twelve different media and temperature conditions, with following measurements by flow cytometry and simulation of the DNA distributions. A good fit was found for each growth condition by use of our simulation program. The resulting cell cycle parameters displayed clear inter-media differences in replication p...Continue Reading

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Citations

Jun 28, 2014·Journal of Bioinformatics and Computational Biology·Vitaly A Likhoshvai, Tamara M Khlebodarova
Mar 13, 2014·Microbiology·Ingvild Odsbu, Kirsten Skarstad
Jun 28, 2015·Journal of Theoretical Biology·Alfonso Jiménez-Sánchez
Oct 22, 2016·ACS Synthetic Biology·Sarah MilbredtTorsten Waldminghaus
Oct 14, 2016·PloS One·Getachew Tesfaye BeyeneTone Tønjum
Dec 23, 2016·Critical Reviews in Biochemistry and Molecular Biology·Ding Jun JinYan Ning Zhou
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Mar 10, 2018·PLoS Genetics·Anurag Kumar SinhaBénédicte Michel
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Sep 30, 2020·FEMS Microbiology Reviews·Alix MeunierManuel Campos

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Methods Mentioned

BETA
flow cytometry
PCR

Software Mentioned

FlowJo
Excel Worksheet
Excel
Visual Basic

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