(A) Schematic representation of the coupling between cell size and cell cycle progression. The transition between G1 (red) and S phases of the cell cycle at the G1/S transition (orange) can evolve …
(A) Typical 2D fitness trajectory for an evolutionary run. Individual networks are dots color coded by their epoch within the evolutionary trajectory. Fitness function of the number of divisions of …
(A) Average period of the oscillator of Model A1 as a function of the control volume at the G1/S transition. Period is normalized by the doubling time of the cell, and volume is rescaled by …
Summary statistics for evolutionary simulations each having 500 epochs. Model A1 shown in Figure 2A-G was used as the initial seed network. 60 simulations were performed using Pareto optimization of …
Snapshots of an evolutionary simulation of 2500 epochs initialized with the Model A1 network topology along with an S. pombe-like cell cycle structure with a timer in G1 followed by a sizer in …
(A) Size-dependent molecular noise arises due to Poissonian fluctuations in molecule number. Consider a protein production-degradation scheme for protein quantity X with production rate and …
X-coordinate is the quantity of the transcriptional regulator . Y-coordinate is the probability of the G1/S transition occurring at the next time step . Parameters and .
(A) Schematic representation of the way we break the feedback in the system and impose a control volume (red arrow) at the G1/S transition in order to record the induced cell cycle period . (B) …
Columns indicate the size scaling assumption of the protein production rates as indicated above the figure. Rows indicate quantity or concentration sensing of inhibitor at the G1/S transition …
We begin with a user-defined initial seed network as starting point of the evolutionary process. The seed network is cloned to give a first population of networks. Individuals are then mutated …
Summary statistics for evolutionary simulations each having 500 epochs. Model A1 was used as the initial seed network. 30 simulations were performed using Pareto optimization of the number of …
Summary statistics for evolutionary simulations each having 500 epochs. Model A1 was used as the initial seed network. Only 30 simulations were performed using Pareto optimization of the number of …
Summary statistics for evolutionary simulations each having 500 epochs. Model A1 was used as the initial seed network. Only 30 simulations were performed using Pareto optimization of the number of …
(A) Network topology of the evolved Model A3. S3 is as a size sensor and titrates in a size-dependent manner. (B) Size distributions at birth (red), G1/S (orange), and division (purple). (C) …
(A) Network topology of the evolved Model A4. S4 is the size sensor and represses the production of in a size-dependent manner. (B) Size distributions at birth (red), G1/S (orange) and division …
(A) Network topology of the evolved Model A5. S3 is the size sensor and represses the production of in a size-dependent manner. (B) Size distributions at birth (red), G1/S (orange) and division …
Models | Data | |||
---|---|---|---|---|
Name | Cell type | Time of size measure | ||
A1 | 0.098 | Haploid budding yeast | Budding | 0.17 |
A2 | 0.095 | Haploid fission yeast | Fission | 0.06 |
B | 0.235 | Mouse epidermal stem cell | Birth | 0.17 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 0.369408 | 0.4574764 | |
1.104619 | 6.783001 | ||
3.215727 | 0.195168 | ||
0.083827 | 4.244007 | ||
p3 | 0.703658 | 0.021174 | |
0.044938 | 1.075146 | ||
3.266732 | 1.1010876 |
Parameter | Value | Parameter | Value |
---|---|---|---|
1.915601 | 2.751652 | ||
0.17872 | 0.441106 | ||
2.09054 | 2.780297 | ||
0.962612 | 0.045051 | ||
2.144666 | 0.839879 | ||
0.019495 | 0.381067 | ||
1.944803 | 0.913992 | ||
0.422939 | 0 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 4.968896 | 3.189190 | |
2.569361 | 0.246561 | ||
0.952178 | p4 | 4.674459 | |
0.131057 | 1.010978 | ||
9.219961 | kf | 3.194116 | |
0.521437 | kb | 4.634009 | |
p3 | 0.113586 | 1.165439 | |
2.183079 | C0 | 1 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 5.606156 | 1.410420 | |
0.066136 | 3.434213 | ||
8.177965 | kf | 1.930909 | |
b2 | 0.911279 | kb | 3.871610 |
0.257920 | 0.013294 | ||
p3 | 5.887584 | 1.803926 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 5.6604334 | 0.001059 | |
0.408208 | kf | 0.843408 | |
1.769233 | kb | 1.680321 | |
0.887392 | 0.825150 | ||
6.437683 | p4 | 4.674459 | |
0.197495 | 0.744119 | ||
3.238633 | 3.451469 | ||
b2 | 0.800255 | 1.929584 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 2.379635 | b4 | 2.624939 |
0.142770 | 1.499653 | ||
0.383384 | 0.006318 | ||
0.714386 | 0.983140 | ||
8.642875 | 0.481592 | ||
1.754776 | 0.226150 | ||
7.783080 | 3.793388 | ||
b2 | 0.195855 | 1.608325 | |
0.576282 | 3.322565 | ||
b3 | 0.582449 | 2.999118 | |
0.318466 | 0.906997 |
Parameter | Value | Parameter | Value |
---|---|---|---|
p2 | 0.369408 | 0.093159 | |
0.748731 | 0.533415 | ||
3.850889 | 3.141514 | ||
p3 | 3.868044 | 0.626507 | |
0.082081 | 3.911233 | ||
3.638939 | 1.885120 | ||
0.599375 | 0.821609 | ||
6.300643 | 1.882484 |