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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)