Team:ETH Zurich/test

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==Switch Circuit==
 
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Using a novel pulsing mechanism consisting of two signals – a start signal that initiates the synthesis of restriction enzymes, and a terminating signal, which switches gene expression off – we are able to delete genome fragments in vivo. To simulate this system we developed, a switch circuit which works (see Switching Curcuit) as follows: Restriction enzyme gene expression is under the control of LacI and can be induced by the addition of IPTG. In order to stop gene expression, the IPTG-sensitive LacI is replaced by IPTG-insensitive LacIS, which shuts restriction enzyme gene expression off again. The synthesis of LacIS is started by the addition of Tetracyclin to the system, which binds to the tet repressor TetR and thus de-represses the expression of the lacIS gene. This circuit is modeled by ca. 40 reactions and is simulated using ODE solver and stochastic simulations.
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<html><table border=1> <colgroup>
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    <col width="250">
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[[Image:Circuit model.JPG|center|600px]]
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    <col width="*">
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  </colgroup>
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== Implementation and Simulation ==
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<tr width="950px"><td></html>[[Image:Circuit_TetR_PLacIIs.JPG|thumb|250px]]<html></td><td></html>
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== Implementation ==
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For the implementation, different steps having no significant effects on the aspired results have been neglected for the sake of simplicity. In the transcriptions the additional step involving the RNA-Polymerase and in the translations the step involving the ribosomes have not been taken into account. Furthermore, the effects of the dimerization of TetR as well as the impacts of dimerization and tetramerization of LacI and LacIIs have not been considered in the final implementation. <br>
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This simplified model still comprises more than 20 different species and over 30 kinetic reactions and has been implemented by using the Simbiology Toolbox in MATLAB.<br>
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[[Image:model.PNG|thumb|center|600px|diagram view of the model]]
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To get any useful results form the model, we performed deterministic and stochastic simulations based on the Mass-Action-Kinetics. The stochastic simulations turned out to be computationally very exhaustive but generated no further significant information compared to the deterministic simulations.<br>
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=== Simulation Results ===
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=== Sensitivity Analysis ===
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We define the sensitivity as the change of the production of the desired fluorescence protein - which is the output of our system - depending on the change of the paramters.
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[[Image:sensitivities.JPG|thumb|right|500px|Sensitivity analysis]]
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The sensitivity analysis shows, that the concentration of the fluorescent protein strongly depends on its decay rate (paramter 13) the decay rate of its mRNA (paramter 10) and of course the transcription and translation rates of the protein (paramters 29 and 27), which is no surprise.
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We can also see that the decay rate of LacIIs (paramter 9) and the transcription rate of LacIIs (paramter 31) have an influence on the expression of the fluorescent protein.
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<br clear="all" >
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== Results and Discussion ==
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The simulations show that our system actually should create a nice pulse-shaped expression of the fluorescent protein (FP). This expression can be started by inducing with IPTG and stopped by subsequent addition of tet into the medium. By tagging the protein it will be degraded much faster by the Clp protease, so that the overall concentration is bounded and, after activating the stop-signal, the remaining proteins disappear quickly.<br>
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Another fact, our simulations show, is that in order to get one single pulse, the tet-concentration inside the medium must not reach zero before all the IPTG has degraded too. Otherwise, there would still be IPTG in the system inhibiting the binding of LacI to the FP-promotor and leading to an unwanted expression of our protein of interest as the LacIIs degrades.<br>
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One way to overcome this problem is simply by inducing a much higher quantity of tet than IPTG, so that it takes longer for it to completely degrade or being washed away. Another way would be to wait a bit longer after the induction with IPTG, so that it has already partly vanished until stopping the FP-expression with tet.
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== Detailed Model ==
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=== diffusion of IPTG ===
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In order to switch on the circuit, we induce with IPTG. When IPTG is added into the medium it diffuses reversibly between the medium and the cells, where it is slowly degraded. In a chemostat extracellular IPTG is washed away.<br>
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<html><img src="https://static.igem.org/mediawiki/2008/6/62/Circuit_iptg_diff.JPG" alt="Grafik" width="30%"></img></html>
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[[Image:Diffusion_iptg.JPG|left width=30%]]
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<br clear="all" />
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=== diffusion of tet ===
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The second inducer which is used in our system is tet. This one also diffuses into the cell when it is added into the medium and degrades slowly.<br>
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<html><img src="https://static.igem.org/mediawiki/2008/9/97/Circuit_tet_diff.JPG" alt="Grafik" width="30%"></img></html>
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[[Image:diffusion_tet.JPG|left width=30%]]
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<br clear="all" />
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=== binding of TetR to LacIIs-promotor ===
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TetR is constitutively expressed and binds to the LacIIs promotor, inhibiting its expression.<br>
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<html><img src="https://static.igem.org/mediawiki/2008/0/0b/Circuit_LacI_LacIIs_Pgfp.JPG" alt="Grafik" width="30%"></img></html>
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[[Image:binding_tetR_to_LacIIs.JPG|left width=30%]]<br clear="all" >
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=== binding of LacI and LacIIs to GFP-promotor ===
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LacI which is constitutively expressed and LacIIs which is under the control of a tet repressor both can bind to the GFP promotor.<br>
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<html><table border=1><tr><td><img src="https://static.igem.org/mediawiki/2008/7/73/Circuit_TetR_PLacIIs.JPG" alt="Grafik" width="30%"></td><td></img></html>
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[[Image:binding_LacIIs_to_Pgfp.JPG|left]]
[[Image:binding_LacIIs_to_Pgfp.JPG|left]]
[[Image:binding_LacI_to_Pgfp.JPG|left]]
[[Image:binding_LacI_to_Pgfp.JPG|left]]
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<html></td></tr></html>
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<html></td></tr></table></html>
<br clear="all" >
<br clear="all" >
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=== binding of tet to TetR ===
 
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<html><img src="https://static.igem.org/mediawiki/2008/0/03/Circuit_tet_tetR.JPG" alt="Grafik" width="30%"></img></html>
 
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[[Image:binding_tet_to_tetR.JPG|left width=30%]]<br clear="all" >
 
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=== binding of IPTG to LacI ===
 
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<html><img src="https://static.igem.org/mediawiki/2008/0/02/Circuit_IPTG_LacI.JPG" alt="Grafik" width="30%"></img></html>
 
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[[Image:binding_IPTG_to_LacI.JPG|left width=30%]]<br clear="all" >
 
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=== transcription and translation of LacI ===
 
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<img src="https://static.igem.org/mediawiki/2008/4/4b/Circuit_LacI_expression.JPG" alt="Grafik" width="30%"></img>
 
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<html><table><tr><td></html>[[Image:Circuit_LacI_expression.JPG|left]]<html></td><td></html>
 
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[[Image:transcription_of_LacI.JPG|left]]
 
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[[Image:translation_of_LacI.JPG|left]]
 
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<html></td></tr></table></html>
 
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=== transcription and translation of LacIIs ===
 
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<html><img src="https://static.igem.org/mediawiki/2008/9/94/Circuit_LacIIs_expression.JPG" alt="Grafik" width="30%"></img></html>
 
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[[Image:transcription_of_LacIIs.JPG|left width=30%]]
 
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[[Image:translation_of_LacIIs.JPG|left]]<br clear="all" >
 
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=== transcription and translation of tetR ===
 
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<html><img src="https://static.igem.org/mediawiki/2008/7/70/Circuit_tetR_expression.JPG" alt="Grafik" width="30%"></img></html>
 
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[[Image:transcription_of_tetR.JPG|left width=30%]]
 
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[[Image:translation_of_tetR.JPG|left]]<br clear="all" >
 
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=== transcription and translation of GFP ===
 
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<html><img src="https://static.igem.org/mediawiki/2008/b/b3/Circuit_gfp_expression.JPG" alt="Grafik" width="30%"></img></html>
 
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[[Image:transcription_of_gfp.JPG|left width=30%]]
 
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[[Image:translation_of_gfp.JPG|left]]<br clear="all" >
 
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=== dimerization of tetR ===
 
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[[Image:dimerization_of_tetR.JPG|left]]<br clear="all" >
 
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=== dimerization and tetramerization of LacI and LacIIs ===
 
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[[Image:dimerization_of_LacI.JPG|left]]<br clear="all" >
 
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[[Image:dimerization_of_LacIIs.JPG|left]]<br clear="all" >
 
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[[Image:tetramerization_of_LacI.JPG|left]]<br clear="all" >
 
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[[Image:tetramerization_of_LacIIs.JPG|left]]<br clear="all" >
 
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== Parameters ==
 
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In this section you can find all the parameters used in the simulation.
 
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{| border="1"
 
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! # !! Parameter name !! Value !! Units !! Reference/Comment
 
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! 1
 
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| k_assoc(IPTG_LacI) || 5.0 || 1/(mole*second) || X
 
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! 2
 
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| k_assoc(LacI) || 5.0 || 1/(mole*second) || X
 
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! 3
 
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| k_assoc(LacIs) || 5.0 || 1/(mole*second) || X
 
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! 4
 
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| k_assoc(tet) || 5.0 || 1/(mole*second) || X
 
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! 5
 
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| k_assoc(tetR) || 5.0 || 1/(mole*second) || X
 
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! 6
 
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| k_dec(IPTG) || 0.0002 || 1/second || X
 
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! 7
 
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| k_dec(IPTG_ext) || 0.001 || 1/second || X
 
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! 8
 
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| k_dec(LacI) || 0.05 || 1/second || X
 
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! 9
 
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| k_dec(LacIs) || 0.05 || 1/second || X
 
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! 10
 
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| k_dec(gfp) || 0.25 || 1/second || X
 
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! 11
 
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| k_dec(mRNA_LacI) || 0.05 || 1/second || X
 
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! 12
 
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| k_dec(mRNA_LacIs) || 0.05 || 1/second || X
 
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! 13
 
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| k_dec(mRNA_gfp) || 0.1 || 1/second || X
 
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! 14
 
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| k_dec(mRNA_tetR) || 0.05 || 1/second || X
 
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! 15
 
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| k_dec(tetR) || 0.05 || 1/second || X
 
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! 16
 
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| k_dec(tet) || 0.0002 || 1/second || X
 
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! 17
 
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| k_dec(tet_ext) || 0.001 || 1/second || X
 
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! 18
 
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| k_diff(IPTG) || 0.1 || 1/second || X
 
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! 19
 
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| k_diff(tet) || 0.1 || 1/second || X
 
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! 20
 
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| k_dissoc(IPTG_LacI) || 1.0 || 1/second || X
 
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! 21
 
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| k_dissoc(LacI) || 1.0 || 1/second || X
 
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! 22
 
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| k_dissoc(LacIs) || 1.0 || 1/second || X
 
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! 23
 
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| k_dissoc(tet) || 1.0 || 1/second || X
 
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! 24
 
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| k_dissoc(tetR) || 1.0 || 1/second || X
 
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! 25
 
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| k_tl(LacI) || 5.0 || 1/second || X
 
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! 26
 
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| k_tl(LacIs) || 5.0 || 1/second || X
 
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! 27
 
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| k_tl(gfp) || 5.0 || 1/second || X
 
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! 28
 
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| k_tl(tetR) || 5.0 || 1/second || X
 
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! 29
 
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| k_tr(gfp) || 1.0 || 1/second || X
 
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! 30
 
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| k_tr(LacI) || 0.1 || 1/second || X
 
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! 31
 
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| k_tr(LacIs) || 0.1 || 1/second || X
 
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! 32
 
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| k_tr(tetR) || 1.0 || 1/second || X
 
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|}
 
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== References ==
 
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(1) ''"Spatiotemporal control of gene expression with pulse-generating networks"'', Basu et al., ''PNAS'', 2004
 
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(2) ''"Genetic circuit building blocks for cellular computation, communications, and signal processing"'', Weiss et al.,  ''Natural Computing'', 2003
 
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(3) ''"Predicting stochastic gene expression dynamics in single cells"'', Mettetal et al., ''PNAS'', 2006
 
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(4) ''"Engineered gene circuits"'', Hasty et al., ''Nature'', 2002
 
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Latest revision as of 15:41, 29 October 2008


Circuit TetR PLacIIs.JPG
Binding LacIIs to Pgfp.JPG
Binding LacI to Pgfp.JPG


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