Team:ETH Zurich/Modeling/Switch Circuit

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Switch Circuit

Detailed Model

diffusion of IPTG

The circuit is induced by IPTG which is added into the medium and diffuses into the cell and from the cell the IPTG can diffuse back into the medium. Moreover IPTG also degrades slowly inside the cell and also outside where it is additionally washed away in case if we run the whole system inside a chemostat.
Grafik

diffusion of tet

Grafik

binding of tetR to LacI-promotor and LacIIs-promotor

binding of LacI and LacIIs to GFP-promotor

binding of tet to tetR

binding of IPTG to LacI

transcription and translation of LacI

transcription and translation of LacIIs

transcription and translation of tetR

transcription and translation of GFP

dimerization of tetR

dimerization and tetramerization of LacI and LacIIs

Implementation

The model of the switch circuit has been implemented using the Simbiology Toolbox in MATLAB.

For the sake of simplicity, the effects of dimerization and dimerization/tetramerization of tetR and LacI/LacIIs have been neglected. So we did with the additional steps involving the RNApolymerase in the transcription of proteins and the ribosomes in the translation of proteins.

diagram view of the model

Simulation

In order to get some useful results out of this model, we ran deterministic and stochastic simulations.

Results and Discussion

Parameters

In this section you can find all the parameters used in the simulation.

#	Parameter name	Value	Reference
1	k_assoc(IPTG_LacI)	5.0	X
2	k_assoc(LacI)	5.0	X
3	k_assoc(LacIs)	5.0	X
4	k_assoc(tet)	5.0	X
5	k_assoc(tetR)	5.0	X
6	k_dec(IPTG)	0.002	X
7	k_dec(IPTG_ext)	0.005	X
8	k_dec(LacI)	5.0	X
9	k_dec(LacIs)	5.0	X
10	k_dec(gfp)	1.0	X
11	k_dec(mRNA_LacI)	0.1	X
12	k_dec(mRNA_LacIs)	0.1	X
13	k_dec(mRNA_gfp)	0.2	X
14	k_dec(mRNA_tetR)	0.05	X
15	k_dec(tetR)	0.05	X
16	k_dec(tet)	0.002	X
17	k_dec(tet_ext)	0.005	X
18	k_diff(IPTG)	0.1	X
19	k_diff(tet)	0.1	X
20	k_dissoc(IPTG_LacI)	1.0	X
21	k_dissoc(LacI)	1.0	X
22	k_dissoc(LacIs)	1.0	X
23	k_dissoc(tet)	1.0	X
24	k_dissoc(tetR)	1.0	X
25	k_tl(LacI)	10.0	X
26	k_tl(LacIs)	10.0	X
27	k_tl(gfp)	10.0	X
28	k_tl(tetR)	10.0	X
29	k_tr(LacI)	2.0	X
30	k_tr(LacIs)	2.0	X
31	k_tr(gfp)	2.0	X
32	k_tr(tetR)	2.0	X

References

(1) "Spatiotemporal control of gene expression with pulse-generating networks", Basu et al., PNAS, 2004

(2) "Genetic circuit building blocks for cellular computation, communications, and signal processing", Weiss et al., Natural Computing, 2003

(3) "Predicting stochastic gene expression dynamics in single cells", Mettetal et al., PNAS, 2006

(4) "Engineered gene circuits", Hasty et al., Nature, 2002