|
|
| Line 188: |
Line 188: |
| | <td>NA</td> | | <td>NA</td> |
| | <td>Notation convention</td> | | <td>Notation convention</td> |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/5/5e/LacI_inact_concentration.png' style='height:22px;'></td>
| |
| - | <td>Inactived LacI concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/e/e3/LacI_tot_concentration.png' style='height:22px;'></td>
| |
| - | <td>Total LacI concentration</td>
| |
| - | <td>TBD</td>
| |
| - | <td>Steady state for equation</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/c/cd/T7%27_concentration.png' style='height:22px;'></td>
| |
| - | <td>T7 RNA polymerase (emitter, T7') concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/8/89/MRNA_T7%27_concentration.png' style='height:22px;'></td>
| |
| - | <td>mRNA associated with T7' concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/3/35/T7%27%27_concentration.png' style='height:22px;'></td>
| |
| - | <td>T7 RNA polymerase (auto-amplification, T7'') concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/3/37/MRNA_T7%27%27_concentration.png' style='height:22px;'></td>
| |
| - | <td>mRNA associated with T7'' concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/f/f5/GFP_concentration.png' style='height:22px;'></td>
| |
| - | <td>GFP concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/5/5f/MRNA_GFP_concentration.png' style='height:22px;'></td>
| |
| - | <td>mRNA associated with GFP concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/4/47/RFP_concentration.png' style='height:22px;'></td>
| |
| - | <td>RFP concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/1/17/MRNA_RFP_concentration.png' style='height:22px;'></td>
| |
| - | <td>mRNA associated with RFP concentration</td>
| |
| - | <td>NA</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>Notation convention</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/6/63/Beta_const.png' style='height:22px;' /></td>
| |
| - | <td>Maximal production rate of pVeg promoter (constitutive)</td>
| |
| - | <td>0.02</td>
| |
| - | <td>molecules.s<sup>-1</sup> <br>or pops</td>
| |
| - | <td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/d/d9/BetapLac.png' style='height:22px;' /></td>
| |
| - | <td>Maximal production rate of pLac promoter</td>
| |
| - | <td>0.02</td>
| |
| - | <td>molecules.s<sup>-1</sup> <br>or pops</td>
| |
| - | <td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/5/5d/BetapT7.png' style='height:22px;' /></td>
| |
| - | <td>Maximal production rate of pT7 promoter</td>
| |
| - | <td>0.02</td>
| |
| - | <td>molecules.s<sup>-1</sup> <br>or pops</td>
| |
| - | <td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Promoter_strengths">justification</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/7/72/KIPTGLacI.png' style='height:22px;' /></td>
| |
| - | <td>Dissociation constant for IPTG to LacI</td>
| |
| - | <td>1200</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/0/0c/KLacI.png' style='height:22px;' /></td>
| |
| - | <td>Dissociation constant for LacI to LacO (pLac)</td>
| |
| - | <td>700</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td><a href='https://2009.igem.org/Team:Aberdeen_Scotland/parameters/invest_1'>Aberdeen 2009 wiki</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/5/5d/KT7.png' style='height:22px;' /></td>
| |
| - | <td>Dissociation constant for T7 RNA polymerase to pT7</td>
| |
| - | <td>10</td>
| |
| - | <td>molecules <br>per cell</td>
| |
| - | <td>We used the classic assumption 1nM=1 molecule per cell and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion#references">[1]</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/a/a3/Gamma_protein.png' style='height:22px;' /></td>
| |
| - | <td>Translation rate of proteins</td>
| |
| - | <td>0.9</td>
| |
| - | <td>s<sup>-1</sup></td>
| |
| - | <td>Estimated, see the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Protein_translation_rate_justification">justification</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/0/05/Delta_dil.png' style='height:22px;' /></td>
| |
| - | <td>Dilution rate in exponential phase</td>
| |
| - | <td>2.88x10<sup>-4</sup></td>
| |
| - | <td>s<sup>-1</sup></td>
| |
| - | <td>Calculated with a 40 min generation time. See explanation</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/7/7d/Delta_mrna.png' style='height:22px;' /></td>
| |
| - | <td>Degradation rate of mRNA</td>
| |
| - | <td>2.88x10<sup>-3</sup></td>
| |
| - | <td>s<sup>-1</sup></td>
| |
| - | <td>Uri Alon (To Be Confirmed)</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/9/95/Delta_GFP.png' style='height:22px;' /></td>
| |
| - | <td>Degradation rate of GFP</td>
| |
| - | <td>10<sup>-4</sup></td>
| |
| - | <td>s<sup>-1</sup></td>
| |
| - | <td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=105188&ver=2&hlid=56398">BioNumbers</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/1/1c/Delta_RFP.png' style='height:22px;' /></td>
| |
| - | <td>Degradation rate of RFP</td>
| |
| - | <td>10<sup>-4</sup></td>
| |
| - | <td>s<sup>-1</sup></td>
| |
| - | <td>Estimated equal to GFP degradation rate</td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/a/a8/TT7.png' style='height:22px;'/></td>
| |
| - | <td>Delay due to T7 RNA polymerase production and maturation</td>
| |
| - | <td>300</td>
| |
| - | <td>s</td>
| |
| - | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion#references">[2]</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/f/f0/TGFP.png' style='height:22px;'/></td>
| |
| - | <td>Delay due to GFP production and maturation</td>
| |
| - | <td>360</td>
| |
| - | <td>s</td>
| |
| - | <td><a href="http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=102972&ver=8">BioNumbers</a></td>
| |
| - | </tr>
| |
| - | <tr>
| |
| - | <td><img src='https://static.igem.org/mediawiki/2011/b/bc/TRFP.png' style='height:22px;'/></td>
| |
| - | <td>Delay due to RFP production and maturation</td>
| |
| - | <td>360</td>
| |
| - | <td>s</td>
| |
| - | <td>Estimated equal to GFP delay (similar molecules)</td>
| |
| | </tr> | | </tr> |
| | <tr> | | <tr> |
Modeling Overview
1. Description of the whole system
To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added.
We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended
project description and the 3 modelling pages:
freeze,
antifreeze and
cell death.
2. Full Model
There are in total 5 different kinetic equations we used in the model
Transcription equation
For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity.
Translation equation
RNA degradation
Protein degration
Assimiliation
3. Simulation tests
In the table below the parameters for our full model are displayed. However it was hard to find accurate parameters, because databases for kinetic parameters are limiting.
The parameters used in this model are:
| Parameter |
Description |
Value |
Reference |
 |
Active LacI concentration (LacI which is not inactivated by IPTG) |
NA |
Notation convention |
 |
IPTG concentration |
NA |
Notation convention |
 |
Delay due to mRNA production |
30 |
s |
BioNumbers with an approximation: all our contructs are around 1-2kb |
References
- Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes,
X Gao and L Huang, accessible here
- Molecular Biology for Masters by Dr. G. R. Kantharaj, accessible here
"
