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Towards a whole-cell modeling approach for synthetic biology
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10.1063/1.4811182
/content/aip/journal/chaos/23/2/10.1063/1.4811182
http://aip.metastore.ingenta.com/content/aip/journal/chaos/23/2/10.1063/1.4811182

Figures

Image of FIG. 1.
FIG. 1.

. (a) The relationship between the number of additional expressed (solid line) and non-expressed (dashed line) genes and the cell cycle length is shown. Cell cycle length (hours) is plotted against the number of added genes, for 1, 5, 10, 20, 50, and 100 genes added. (b) The mean (per time point, averaged over the length of the cell cycle) number of mRNAs produced from the native genome is plotted against the number of added expressed genes for 1, 5, 10, 20, 50, and 100 genes added. 25 cell simulations were performed for each circuit size. Bars indicate the standard error of the mean.

Image of FIG. 2.
FIG. 2.

Black full lines indicate the optimized gene; red dotted lines indicate the unoptimized gene. (a) , (b). , (c) , (d) . Thick lines indicate the average; thin lines represent the standard error of the mean. Results are truncated at the length of the shortest cell cycle length. In all cases, complexes denote tetramers to ease comparisons between experiments. Results are an average of 25 simulations.

Image of FIG. 3.
FIG. 3.

The mean cell cycle length is plotted for with the unoptimized gene (solid line), and the codon-optimized gene (dashed line), for 1, 5, 10, 20, 50, and 100 genes added. (a) , (b) , (c) (d) . 25 cell simulations were performed for each circuit size. Bars indicate the standard error of the mean.

Image of FIG. 4.
FIG. 4.

. (a) LacI forms a tetramer. (b) The Goodwin oscillator is formed by LacI repressing transcription from its own promoter. Adapted from Ref. .

Image of FIG. 5.
FIG. 5.

. (a) LacI tetramer copy number dynamics in two cells, truncated to the length of the shortest cell cycle. (b) Simulations from (a) with a low-pass filter applied (frequencies greater than 0.001 Hz were removed). (c) Experimental data of the Goodwin oscillator, modified from Stricker [Reproduced with permission from J. Stricker , “A fast, robust and tunable synthetic gene oscillator,” Nature , 516–U39 (2008). Copyright 2008 Nature Publishing Group] Each line depicts oscillatory data from a separate cell.

Tables

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Table I.

Summary of t-test p-values.

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/content/aip/journal/chaos/23/2/10.1063/1.4811182
2013-06-13
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Towards a whole-cell modeling approach for synthetic biology
http://aip.metastore.ingenta.com/content/aip/journal/chaos/23/2/10.1063/1.4811182
10.1063/1.4811182
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