Non-genetic inheritance restraint of cell-to-cell variation
- Department of Physics and Astronomy, The Dietrich School of Arts and Sciences, University of Pittsburgh, United States
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, United States
Figures
Figure 1 with 2 supplements
Scheme of the experimental setup for tracking sister cells.
(A) Long (30 μm) narrow traps (1 μm—1 μm) are connected on one end and open on the other to wide (30 μm—30 μm) perpendicular flow channels through which fresh medium is pumped and washes out cells …
Figure 1—figure supplement 1
The ACFs of individual lineages measured in separate traps.
The ACFs of individual lineages, measured in the same experiment in separate traps in the mother machine, are presented in different colors. Each ACF was calculated from a lineage longer than 150 …
Figure 1—video 1
Creation of sister cells (SCs) in the experimental setup.
Figure 2
Individuality of cellular growth dynamics in different microenvironments.
(A) Depicts the cell length of two pairs of SCs measured in two different V-shaped traps as a function of time. The length of each cell is presented in a ‘stitched’ form, where the length of the …
Figure 3
The effect of the v-shaped channel on the distribution of the different cellular characteristics between SCs during division.
(A) Probability distribution Function (PDF) of the difference in the first cell-cycle time of two sister cells after separation relative to the population’s average cycle time under the same …
Figure 4 with 5 supplements
PCF of cell-cycle time and cell size measured in cell pairs as a function of number of generations.
(A) Three types of pairs used for calculating PCF. (B) PCF of cell-cycle time for SCs (122 pairs from three separate experiments) exhibit memory that extends for almost nine generations (half …
Figure 4—figure supplement 1
Distributions of different cell parameters.
In order to avoid artifacts arising in calculations due to differences between experiments carried out on different days, raw data from these experiments was normalized by subtracting the mean (μ) …
Figure 4—figure supplement 2
Correlation in cell-cycle times for SCs was verified by calculating slopes of best fits to the plots of normalized TimeA vs TimeB.
(A–I) Slopes of the best fit lines for TimeA vs TimeB show that cell-cycle times are strongly correlated for first few generations in SCs (summary of the slopes values is presented in Appendix …
Figure 4—figure supplement 3
The PCF of cell-cycle time (T) for SCs in different growth conditions.
The PCF of SCs cell-cycle time in LB at 37°C (57 pairs from two separate experiments) (A) and in M9CL at 32°C (29 pairs from two separate experiments) (B). Existence of strong correlation between …
Figure 4—figure supplement 4
Raw PCF values of cell size as a function of time for SCs, NCs, and RPs.
The cell size PCF for SCs (A) and for NCs (B) are compared in both graphs with the cell size ACF and PCF for RPs. Sister cells show strong cell size correlation that decays slowly over a long time. …
Figure 4—figure supplement 5
PCF values of cell size and cell-cycle duration as a function of time for NCs with different starting sizes.
PCF of cell-cycle time (A) and cell length (B) for NCs starting from random initial sizes are compared in both graphs with ACF and PCF for RPs. NCs starting with random initial sizes show almost no …
Figure 5 with 4 supplements
Variance () as a function of the time.
(A) of the growth rate difference () between cell pairs for NCs and RPs as a function of time (see Figure 5—figure supplement 3 for the details of the calculation). The variance for both pair …
Figure 5—figure supplement 1
Cell-cycle time variance () as a function of time.
(A–C) Individual traces showing difference in cell-cycle times () for SCs, NCs, and RPs, respectively. The variance () of cell cycles times differences () as a function of time (D) represent …
Figure 5—figure supplement 2
Cell size variance () as a function of time.
Birth size variance was calculated similar to in Figure 5—figure supplement 1. for SCs increases slowly and saturates at a fixed value after ∼7 generations (mean lifetime ∼3.5 generations) …
Figure 5—figure supplement 3
Exponential elongation rate difference () as a function of time.
Individual traces showing the difference between the exponential elongation rates () for SCs (A), NCs (B), and RPs (C). (D) The mean of for all cell pairs remains zero along time as expected. …
Figure 5—figure supplement 4
Mean fluorescence variance () as a function of time.
Individual traces showing the difference in mean fluorescence intensity (δf) of gfp expressed in SCs (A), NCs (B), and RPs (C). (D) The variance ( calculated similarly to in Figure 5—figure …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | MG1655 | Coli Genetic Stock Center (CGSC) | 6300 | F-, , rph-1 |
| Recombinant DNA reagent | pZA3R-GFP | Lutz and Bujard, 1997 | https://academic.oup.com/nar/article/25/6/1203/1197243 | GFP expressed from the λ Pr promoter |
| Recombinant DNA reagent | pZA32wt-GFP | Lutz and Bujard, 1997 | https://academic.oup.com/nar/article/25/6/1203/1197243 | GFP expressed from the LacO promoter |
| Software, algorithm | MATLAB | MathWorks | N/A | |
| Software, algorithm | Oufti | Paintdakhi et al., 2016 | http://oufti.org/ |
Appendix 1—table 1
The calculated values of the PCF for SCs were verified by calculating the slopes of best fits to the plots of TimeA vs TimeB graphs (Figure 4—figure supplement 2).
| Generation | PCF | Slope of best fit line (Figure 4—figure supplement 2) |
|---|---|---|
| 1st | 0.86 ± 0.02 | 0.87 |
| 2nd | 0.65 ± 0.05 | 0.69 |
| 3rd | 0.54 ± 0.06 | 0.44 |
| 4th | 0.36 ± 0.07 | 0.42 |
| 5th | 0.28 ± 0.08 | 0.25 |
| 6th | 0.23 ± 0.08 | 0.25 |
| 7th | 0.12 ± 0.09 | 0.11 |
| 8th | 0.23 ± 0.09 | 0.25 |
| 9th | 0.00 ± 0.09 | 0.00 |
