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Team:Aberdeen Scotland/parameters
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<td>Degradation of mRNA</td> | <td>Degradation of mRNA</td> | ||
<td>0.003</td> | <td>0.003</td> | ||
| - | <td>1</td> | + | <td>1/s</td> |
<td>1</td> | <td>1</td> | ||
</tr> | </tr> | ||
Revision as of 13:20, 13 August 2009
University of Aberdeen - Pico Plumber
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 | Unit | Reference |
 mRNA |
Degradation of mRNA | 0.003 | 1/s | 1 |
| X |
Degradation of X | 0.00000802 | 2 | 1 |
| Y |
Degradation of Y | 0.00000802 | 1 | 4 |
| λ-CI |
Degradation of lambda CI | 0.002888 | 1 | 6 |
| LacI |
Degradation of LacI | 0.001155 | 1 | 8 |
| TetR |
Degradation of TetR | 0.00288811 | 1 | 10 |
| Holin |
Degradation of Holin | 0.0002 | 1 | guessed; half-life of an hour |
| Endolysin |
Degradation of Endolysin | 0.0002 | 1 | guessed; half-life of an hour |
| Antiholin |
Degradation of Antiholin | 0.0002 | 1 | guessed; half-life of an hour |
| LuxI |
Degradation of LuxI | 0.002888 | 1 | tagged; half-life of 4 min |
| LuxR |
Degradation of LuxR | 0.0002 | 1 | 0 |
| HSL |
Degradation of HSL | 0.00016667 | 1 | 0; value for AHL |
 Protein |
Translation rate of Protein | 0.1 | 1 | 2 |
 |
Rate of production of HSL from LuxI | 0.45 | 1 | 2 |
 HSL |
Rate of diffusion of HSL in/out of the cell | 0.4 | 1 | 2 |
| IPTG |
Rate of diffusion of IPTG in/out of the cell | 0.014 | 1 | 2 |
 P |
Rate of formation of the HSL-LuxI complex | 0.00010 | 1 | 2 |
| -P |
Rate of dissociation of the HSL-LuxI complex | 0.003 | 1 | 2 |
 -P |
Rate of dissociation of the HSL-LuxI complex | 0.003 | 1 | 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>
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