Team:Aberdeen Scotland/parameters

Internal Dynamics Parameters

When modeling any process, it is essential to use parameters which reflect reality, otherwise the model will not give accurate predictions. Thus we spend a considerable time researching, analysing and estimating parameters so that our model will reflect real life behaviour as accuratly as possible.

Parameter	Description	Value	Reference
mRNA	Degradation of mRNA	0.003	1
X	Degradation of X	0.00000802	2
Y	Degradation of Y	0.00000802	4
λ-CI	Degradation of lambda CI	0.002888	6
LacI	Degradation of LacI	0.001155	8
TetR	Degradation of TetR	0.00288811	10
Holin	Degradation of Holin	0.0002	guessed; half-life of an hour
Endolysin	Degradation of Endolysin	0.0002	guessed; half-life of an hour
Antiholin	Degradation of Antiholin	0.0002	guessed; half-life of an hour
LuxI	Degradation of LuxI	0.002888	tagged; half-life of 4 min
LuxR	Degradation of LuxR	0.0002	0
HSL	Degradation of HSL	0.00016667	0; value for AHL
Protein	Translation rate of Protein	0.1	2
	Rate of production of HSL from LuxI	0.45	2
HSL	Rate of diffusion of HSL in/out of the cell	0.4	2
IPTG	Rate of diffusion of IPTG in/out of the cell	0.014	2
P	Rate of formation of the HSL-LuxI complex	0.00010	2
-P	Rate of dissociation of the HSL-LuxI complex	0.003	2
-P	Rate of dissociation of the HSL-LuxI complex	0.003	2

References

[1] Goryachev, A.B., D.J. Toh and T. Lee. “System analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constant.” BioSystems 2006: 83, 178-187.

[2] Alon, Uri. “An Introduction to Systems Biology Design Principles of Biological Circiuts.” London: Chapman & Hall/CRC, 2007.

[3] Kepes, A., 1960, “Etudes cinetiques sur la galactoside-permease D'Escherichia coli. Biochim.” Biophys. Acta 40, 70-84.

[4] Canton, B. and Anna Labno. “Part: BBa_F2620.” BioBrick Registry. 13th August 2009. <http://partsregistry.org/Part:BBa_F2620>

[5] Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S. “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria.” Appl Environ Microbiol. 1998 Jun; 64(6):2240-6.

[6] Elowitz MB, Leibler S.; “A synthetic oscillatory network of transcriptional regulators.” Nature 2000 Jan; 403(6767):335-8.;

[7] BCCS-Bristol 2008. “Modelling Parameters” iGEM wiki. 13th August 2009. <https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters>

[8] Subhayu Basu; “A synthetic multicellular system for programmed pattern formation.” Nature April 2005: 434, 1130-1134

[9] KULeuven 2008. “Cell Beath”iGEM wiki. 13th August 2009. <https://2008.igem.org/Team:KULeuven/Model/CellDeath>