Team:Aberdeen Scotland/parameters

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University of Aberdeen iGEM 2009

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 Death”iGEM wiki. 13th August 2009. <https://2008.igem.org/Team:KULeuven/Model/CellDeath>