Team:Aberdeen Scotland/parameters

From 2009.igem.org

(Difference between revisions)
(→Internal Dynamics Parameters)
(→Internal Dynamics Parameters)
Line 18: Line 18:
<td>Degradation of mRNA</td>
<td>Degradation of mRNA</td>
<td>0.003</td>
<td>0.003</td>
 +
<td>1</td>
<td>1</td>
<td>1</td>
</tr>
</tr>
Line 26: Line 27:
<td>0.00000802</td>
<td>0.00000802</td>
<td>2</td>
<td>2</td>
 +
<td>1</td>
</tr>
</tr>
Line 32: Line 34:
<td>Degradation of Y</td>
<td>Degradation of Y</td>
<td>0.00000802</td>
<td>0.00000802</td>
 +
<td>1</td>
<td>4</td>
<td>4</td>
</tr>
</tr>
Line 39: Line 42:
<td>Degradation of lambda CI</td>
<td>Degradation of lambda CI</td>
<td>0.002888</td>
<td>0.002888</td>
 +
<td>1</td>
<td>6</td>
<td>6</td>
</tr>
</tr>
Line 47: Line 51:
<td>Degradation of LacI</td>
<td>Degradation of LacI</td>
<td>0.001155</td>
<td>0.001155</td>
 +
<td>1</td>
<td>8</td>
<td>8</td>
</tr>
</tr>
Line 54: Line 59:
<td>Degradation of TetR</td>
<td>Degradation of TetR</td>
<td>0.00288811</td>
<td>0.00288811</td>
 +
<td>1</td>
<td>10</td>
<td>10</td>
</tr>
</tr>
Line 61: Line 67:
<td>Degradation of Holin</td>
<td>Degradation of Holin</td>
<td>0.0002</td>
<td>0.0002</td>
 +
<td>1</td>
<td>guessed; half-life of an hour</td>
<td>guessed; half-life of an hour</td>
</tr>
</tr>
Line 68: Line 75:
<td>Degradation of Endolysin</td>
<td>Degradation of Endolysin</td>
<td>0.0002</td>
<td>0.0002</td>
 +
<td>1</td>
<td>guessed; half-life of an hour</td>
<td>guessed; half-life of an hour</td>
</tr>
</tr>
Line 75: Line 83:
<td>Degradation of Antiholin</td>
<td>Degradation of Antiholin</td>
<td>0.0002</td>
<td>0.0002</td>
 +
<td>1</td>
<td>guessed; half-life of an hour</td>
<td>guessed; half-life of an hour</td>
</tr>
</tr>
Line 83: Line 92:
<td>Degradation of LuxI</td>
<td>Degradation of LuxI</td>
<td>0.002888</td>
<td>0.002888</td>
 +
<td>1</td>
<td>tagged; half-life of 4 min</td>
<td>tagged; half-life of 4 min</td>
</tr>
</tr>
Line 90: Line 100:
<td>Degradation of LuxR</td>
<td>Degradation of LuxR</td>
<td>0.0002</td>
<td>0.0002</td>
 +
<td>1</td>
<td>0</td>
<td>0</td>
</tr>
</tr>
Line 97: Line 108:
<td>Degradation of HSL</td>
<td>Degradation of HSL</td>
<td>0.00016667</td>
<td>0.00016667</td>
 +
<td>1</td>
<td>0; value for AHL</td>
<td>0; value for AHL</td>
</tr>
</tr>
Line 104: Line 116:
<td>Translation rate of Protein</td>
<td>Translation rate of Protein</td>
<td>0.1</td>
<td>0.1</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 111: Line 124:
<td>Rate of production of HSL from LuxI</td>
<td>Rate of production of HSL from LuxI</td>
<td>0.45</td>
<td>0.45</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 118: Line 132:
<td>Rate of diffusion of HSL in/out of the cell</td>
<td>Rate of diffusion of HSL in/out of the cell</td>
<td>0.4</td>
<td>0.4</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 125: Line 140:
<td>Rate of diffusion of IPTG in/out of the cell</td>
<td>Rate of diffusion of IPTG in/out of the cell</td>
<td>0.014</td>
<td>0.014</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 132: Line 148:
<td>Rate of formation of the HSL-LuxI complex</td>
<td>Rate of formation of the HSL-LuxI complex</td>
<td>0.00010</td>
<td>0.00010</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 139: Line 156:
<td>Rate of dissociation of the HSL-LuxI complex</td>
<td>Rate of dissociation of the HSL-LuxI complex</td>
<td>0.003</td>
<td>0.003</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>
Line 146: Line 164:
<td>Rate of dissociation of the HSL-LuxI complex</td>
<td>Rate of dissociation of the HSL-LuxI complex</td>
<td>0.003</td>
<td>0.003</td>
 +
<td>1</td>
<td>2</td>
<td>2</td>
</tr>
</tr>

Revision as of 13:18, 13 August 2009

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 Unit Reference
mRNA Degradation of mRNA 0.003 1 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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