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Table 1 Optimization results derived using simulations of cell cycling

From: Control of Caenorhabditis elegans germ-line stem-cell cycling speed meets requirements of design to minimize mutation accumulation

  

Objective function

Free parameters

Optimization setup

Optimization result

  

P.D. first 3000 cells

P.D. gametes

Aggregate fitness

MZ length

MZ width

L2 cell cycle

L4, L4 + 1, L4 + 3 cell cycle

Single cell cycle length

Prod. constraints

Exp. geometry

Pre-meiotic arrest

Max. MZ cell number

Max. MZ length/width

Notes

Objective function optimum

Optimal MZ length

Optimal MZ width

α L4

α L4 + 1

Optimization

1

  

    

2000

2000

 

11.74

359

1

709

198

2

  

  

   

359

2000

 

13.94

1

359

3

  

  

   

2000

2000

 

12.05

1523

1

4

  

  

   

200

2000

 

17.20

1

200

5

 

 

    

2000

500

 

9.62

112

1

48

91

6

 

 

    

2000

30

 

9.65

18

12

3.50

1.36

7

 

 

  

   

2000

2000

 

9.91

1

216

8

  

  

  

1

1.01

1.00

1.02

9

  

  

  

1

1.00

1.00

1.01

10

 

 

 

 

  

500

30

 

9.72

19

12

2.14

1.94

11

 

    

 

 

9.85

2.30

1.43

12

 

    

 

2

8.88

2.34

2.79

13

 

    

 

3

8.85

0.63

0.71

  1. Notes on optimizations:
  2. 1: Optimization 8 was run with deleterious mutation rate U = 0.03, and optimization 9 with U = 0.48
  3. 2: Optimization 12 assumes a mutation rate dependent on cell cycle speed
  4. 3: Optimization 13 assumes that distal cells preserve an immortal DNA strand
  5. Each row shows results for one kind of problem, defined by the objective function to optimize (PD or pedigree depth; see main text and “Methods” for details), the parameters that are free to evolve within bounds during the optimization procedure (which can include MZ dimensions and distal cell cycle lengths at various stages), and other characteristics grouped under “Optimization setup.” Results shown are derived using a grid search (see “Methods”) α is the ratio of cell cycle lengths between the distal end of the DMMZ and the proximal end of the MMZ (slower distal cell cycle for α > 1). See Additional file 1: Table S1 for an extended version of this table, including credible intervals derived from Markov chain Monte Carlo (MCMC)