Code and simulation data

Zipped folder with code and simulation data

Microscopy data - Part 4

Zipped microscopy data split by Mac OS, 8 parts in total

Microscopy data - Part 2

Zipped microscopy data split by Mac OS, 8 parts in total

Approximate mutant frequencies at mutation–selection balance.

<p>Ploidy is <i>c</i> = 2^<i>n</i> (<i>n</i> ≥ 1) in the polyploid cases, is the per-copy mutation rate, and <i>s</i> is the cost of the mutation in homozygotes (in heterozygotes, the cost is masked in the recessive case but expressed in the dominant case).</p

README_computer_code

This file describes how to use the deposited code and simulation data to reproduce the manuscript figures

정부부문 부패실태에 관한 연구

Zipped microscopy data split by Mac OS, 8 parts in total

Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts

<div><p>Stochasticity in gene regulation has been characterized extensively, but how it affects cellular growth and fitness is less clear. We study the growth of <i>E. coli</i> cells as they shift from glucose to lactose metabolism, which is characterized by an obligatory growth arrest in bulk experiments that is termed the lag phase. Here, we follow the growth dynamics of individual cells at minute-resolution using a single-cell assay in a microfluidic device during this shift, while also monitoring <i>lac</i> expression. Mirroring the bulk results, the majority of cells displays a growth arrest upon glucose exhaustion, and resume when triggered by stochastic <i>lac</i> expression events. However, a significant fraction of cells maintains a high rate of elongation and displays no detectable growth lag during the shift. This ability to suppress the growth lag should provide important selective advantages when nutrients are scarce. Trajectories of individual cells display a highly non-linear relation between <i>lac</i> expression and growth, with only a fraction of fully induced levels being sufficient for achieving near maximal growth. A stochastic molecular model together with measured dependencies between nutrient concentration, <i>lac</i> expression level, and growth accurately reproduces the observed switching distributions. The results show that a growth arrest is not obligatory in the classic diauxic shift, and underscore that regulatory stochasticity ought to be considered in terms of its impact on growth and survival.</p></div

Dynamics at the population level and in single cells.

<p>(A) Growth curve for a typical microcolony, indicating the sum of all cell lengths within the colony. (B) Mean fluorescence intensity (per unit area) within cells, averaged over a microcolony. (C) Single-cell length over time for three different lineages, representing cases with no growth rate decrease (green), a lag phase (blue) and a longer lag phase (red). Arrows indicate cell division events. The curves are vertically shifted for clarity. (D) Elongation rates obtained by exponential fits to the length data at sub-cell cycle resolution. Drawn lines are fitted parameterized functions. ΔTµ₂ is the time difference between the time of shift and the half maximum to growth recovery after shift. (E) Fluorescence levels for the three lineages in (C) and (D). Drawn lines are fitted parameterized functions. ΔT_F is the time difference between the time of shift and the half maximum to induction after shift. Black bar: 120 min before the shift, over which data was averaged to determine the expression level prior to the shift.</p

Switching synchrony of sister cells.

<p>The growth recovery delays ΔTµ₂ are plotted for pairs of sister cells. (A) Data obtained from experiments. N = 75, r² = 0.52, p-value <0.001. (B) Data resulting from simulations. N = 660, r²≈0.13 and p<0.001. Note that in both cases lineages in which one cell switches but its sister or its progeny does not are not plotted (in total: 22 pairs for the experimental data, 146 pairs for the numerical data).</p

Reconciling Luria-Delbrück fluctuation test with phenotypic delay by effective polyploidy.

<p>(A) The original Luria-Delbrück mutation model disregards polyploidy. For instance, a phenotypic delay of two generations results in four mutants appearing at once. (B) The observation of many one-mutant (“singleton”) populations was interpreted as evidence against the existence of a delay [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004644#pbio.2004644.ref001" target="_blank">1</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004644#pbio.2004644.ref003" target="_blank">3</a>]. (C) With polyploidy considered, cells with four genome copies require two divisions to generate a homozygous mutant that expresses a selectable recessive phenotype. Therefore, a delay of two generations can generate just one mutant. (D) Heterozygous cells containing recessive mutations will not survive selection, leading to an underestimation of mutational events.</p