Code and simulation data

Zipped folder with code and simulation data

Phenotypic delay in <i>E</i>. <i>coli</i>.

<p>(A) Phenotypic penetrance (mean ± SE; <i>n</i> = 6) over time for three antibiotic resistance mutations. Gray dashed lines: time at 50% phenotypic penetrance. (B) Frequency of homozygous mutants among all mutants (orange) for the three resistance mutations assessed by <i>lacZ</i> reporter constructs (<i>rpoB-lacZ</i>, <i>gyrA-lacZ</i>, <i>rpsL-lacZ</i>), overlaid with their respective phenotypic penetrance. (C) Genotypic mutant frequency for the resistance mutations. (D) Phenotypic penetrance of the lactose prototrophy (<i>rpsL-lacZ</i>) mutation. (E) Colonies founded by homozygous (blue) and heterozygous (sectored) lac⁺ mutants. The numerical data for panels A to D can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004644#pbio.2004644.s005" target="_blank">S1 Data</a>. MIC, minimum inhibitory concentration.</p

Microscopy data - Part 4

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

README_computer_code

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

Microscopy data - Part 2

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

정부부문 부패실태에 관한 연구

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

Schematic of the model used to evaluate SGV and rescue, illustrated for ploidy <i>c</i> = 4.

<p>(A) Flow diagram of all events. A cell is represented by a grey oval, containing four chromosomes (complete or partial, so long as they contain the gene of interest). These chromosomes are colored blue if wild-type at the gene of interest or red if mutant. A cell either divides to produce two daughter cells with type-specific probability <i>p</i>_<i>j</i> or otherwise dies. These probabilities <i>p</i>_<i>j</i> differ between the old environment (to model SGV) and the new environment (to model rescue). Upon type 0 division, mutation (producing type 1) occurs with probability in each daughter cell; otherwise, the daughter is also type 0. In the remaining types, chromosome segregation determines the types of the daughter cells. (B) A mechanistic view of chromosome replication and segregation, illustrated for the production of one type 2 and one type 0 daughter cell from a type 1 mother cell. On each chromosome, the black dash indicates the origin of replication. SGV, standing genetic variation.</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

Single-cell analysis of fluorescent mutants.

<p>(A) Overlay of phase-contrast and fluorescence images showing a microcolony containing fluorescent mutants (see also <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004644#pbio.2004644.s016" target="_blank">S1 Movie</a>). Yellow arrow: the first cell showing significantly higher fluorescence than background in the given frame. Accounting for the time required for YFP protein folding and maturation, the ssDNA integration is estimated to have happened before the first division of the labeled cell. (B) Genealogy of the aforementioned microcolony. The yellow arrow indicates the cell in A, while the remaining arrows indicate three lineages in which fluorescence was quantified. (C) YFP expression history of three lineages in B showing fully, transiently, and non-fluorescent phenotypes (green, blue, and red, respectively). Yellow dashed line: onset of fluorescence. Black and grey dashed lines correspond to the black and grey arrows in B. Black: emergence of the first homozygous mutant; grey: its first division. (D) Distribution of time to form 34 homozygous mutant lineages from 25 microcolonies. The data are obtained by directly analyzing genealogies as in B and compiled from two separate experiments. The dashed grey line indicates the estimated generations to form half of the homozygous mutant lineages. (E) Photo of a microcolony with one filamentous fluorescent cell. (F) The distribution of number of generations to form homozygous mutant lineages sorted by the presence/absence of filamentation. The numerical data for panels C, D, and F can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004644#pbio.2004644.s005" target="_blank">S1 Data</a>. ssDNA, single-stranded DNA; YFP, yellow fluorescent protein.</p