Team:KULeuven/Model/Inverter

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Invertimer

Position in the system

The invertimer subsystem receives its input from the filter, T7. The invertimer's function is to produce HSL when no input is present, so a low T7 input gives rise to a high HSL output and vice versa. The production of HSL means that the cell will start a timer that eventually will be used in the celldeath-subsystem to produce ccdB. In this way the cell will die off if no desease remains present.

Describing the system

ODE's

Parameters

*Parameter values (Inverter)*
Name	Value	Comments	Reference
Degradation Rates
d_LuxI	d_LVA = 2.814E-4 s^-1	LVA-tag reduces lifetime to 40 minutes	[http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
d_{RNA_LuxI}	0.0025 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{LuxI_antimRNA}	0.0045303737 s^-1	estimate: because this RNA isn't translated, it degrades faster
d_LacI	d_LVA = 2.814E-4 s^-1	LVA-tag reduces lifetime to 40 minutes	[http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
d_{closed mRNA LacI}	0.0046209812 s^-1	estimate: because this mRNA isn't translated, it degrades faster
d_{open mRNA LacI}	0.0023104906 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{open mRNA LacI complex}	0.0023104906 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_HSL	1.02E-6 s^-1	very stable in the medium, lifetime around 185h	[http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
T7 Transcription
K_T7	421	dissociation constant, recalculated to remove units	[http://www.jbc.org/cgi/content/full/279/5/3239 link]
k_max	0.044 s^-1	maximal T7 transcription rate	[http://www.jbc.org/cgi/content/full/279/5/3239 link]
Key-Lock constants
K_{eq 1}	0,015 [M]	between closed and open T7 mRNA, experimental	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
K_{eq 2}	0.0212 [M]	between closed T7 mRNA and key unlocked mRNA complex, experimental	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
k_dis2	100 s^-1	derived from experimental values	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
k_complex2	57 s^-1	derived from experimental values	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
k_closed	100 s^-1	derived from experimental values	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
k_open	1.5 s^-1	derived from experimental values	[http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
k_translation	0.167 s^-1	lock defined translation rate for LacI	[http://partsregistry.org/Part:BBa_B0032 link]
LacI repression
K_LacI	1.0E-10 M^-1	Dissociation constant
n_LacI	2.0	Hill coefficient for LacI	[http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
k_trans_LacI	0.0050 s^-1	Estimated maximal transcription rate from R0011	[http://partsregistry.org/Part:BBa_R0011 link]
Antisense LuxI
k_complex3	2.12 s^-1	rate constant for formation of asRNA - LuxI mRNA duplex (CHANGE? ALSO KEY THEN)
K_{mRNA_LuxI:antisense_mRNA}	4.22E14	Complex of LuxI mRNA with antisense mRNA
antisense leakiness	0.9 fwd vs 0.1 rev	factor to reflect antisense competition with ribosomes
Translation Rates
k_{transl LuxI}	0.167 s^-1	translation rate for B0032 RBS (0.3 relative efficiency)	[http://partsregistry.org/Part:BBa_B0032 link]
k_{transl LacI}	0.167 s^-1	lock defined translation rate for LacI