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+ | {{:Team:Tokyo_Tech/tpl/head|Parameters and Tools}} | ||
+ | {{:Team:Tokyo _Tecj/tpl/fortables}} | ||
+ | |||
+ | |||
+ | <html><article></html> | ||
+ | ==Parameters== | ||
+ | No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below. | ||
+ | |||
+ | {|class="wikitable sortable" | ||
+ | !Parameter!!Value!!Description!!Reference | ||
+ | |- | ||
+ | |g||0.0123||Growth rate of each cells||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |P<sub>max</sub>||3.6641||Carrying capacity||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |E<sub>DiMazF</sub>||0.101715||Effect of MazF dimer on growth rate of each cells||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |k||5 min<sup>-1</sup>||Transcriptional rate of mRNA under P<sub>tet</sub>||Assumed | ||
+ | |- | ||
+ | |leak<sub>P<sub>lux</sub></sub>||0.113 nMmin<sup>-1</sup>||Leakage of P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |leak<sub>P<sub>rhl</sub></sub>||3.5 nMmin<sup>-1</sup>||Leakage of P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |κ<sub>P<sub>lux</sub></sub>||10.3 nM<sup>-1</sup>min<sup>-1</sup>||Maximum transcriptional rate of mRNA under P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |κ<sub>P<sub>rhl</sub></sub>||9.73 nM<sup>-1</sup>min<sup>-1</sup>||Maximum transcriptional rate of mRNA under P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |n<sub>Lux</sub>||2.5||Hill coefficient for P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |n<sub>Rhl</sub>||2.5||Hill coefficient for P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |K<sub>mLux</sub>||78.32 nM||Lumped parameter for the Lux system||Estimated from Literature | ||
+ | |- | ||
+ | |K<sub>mRhl</sub>||1969 nM||Lumped parameter for the Rhl system||Estimated from Literature | ||
+ | |- | ||
+ | |F<sub>DiMazF</sub>||5 nM<sup>-1</sup>min<sup>-1</sup>||Cutting rate at ACA sequences on mRNA by MazF dimer||Assumed | ||
+ | |- | ||
+ | |f||0.409213||The probability of distinction of ACA sequences on mRNA by MazF dimer||Estimated | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>RFP</sub></sub>||10||The number of ACA arrays in mRNA<sub>RFP</sub>||Extraction of data | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>GFP</sub></sub>||23||The number of ACA arrays in mRNA<sub>GFP</sub>||Extraction of data | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>RhlI</sub></sub>||1||The number of ACA arrays in mRNA<sub>RhlI</sub>||Extraction of data | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>LasI</sub></sub>||10||The number of ACA arrays in mRNA<sub>LasI</sub>||Extraction of data | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>MazF</sub></sub>||2||The number of ACA arrays in mRNA<sub>MazF</sub>||Extraction of data | ||
+ | |- | ||
+ | |f<sub>mRNA<sub>MazE</sub></sub>||10||The number of ACA arrays in mRNA<sub>MazE</sub>||Extraction of data | ||
+ | |- | ||
+ | |α||5 min<sup>-1</sup>||Translation rate of protein||Assumed | ||
+ | |- | ||
+ | |k<sub>DiMazF</sub>||5.226124 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of MazF dimer||Literature | ||
+ | |- | ||
+ | |k<sub>-DiMazF</sub>||3.151962 min<sup>-1</sup>||Dissociation rate of MazF dimer||Literature | ||
+ | |- | ||
+ | |k<sub>DiMazE</sub>||6.759816 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of MazE dimer||Literature | ||
+ | |- | ||
+ | |k<sub>-DiMazE</sub>||3.808504 min<sup>-1</sup>||Dissociation rate of MazE dimer||Literature | ||
+ | |- | ||
+ | |k<sub>Hexa</sub>||3.170544 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of Maz hexamer||Literature | ||
+ | |- | ||
+ | |k<sub>-Hexa</sub>||8.344358 min<sup>-1</sup>||Dissociation rate of Maz hexamer||Literature | ||
+ | |- | ||
+ | |p<sub>Las</sub>||1 min<sup>-1</sup>||Production rate of 3OC12AHL by LasI||Assumed | ||
+ | |- | ||
+ | |p<sub>Rhl</sub>||1 min<sup>-1</sup>||Production rate of C4AHL by RhlI||Assumed | ||
+ | |- | ||
+ | |D||1 nM<sup>-1</sup>min<sup>-1</sup>||Decomposition rate of 3OC12AHL by AmiE||[Assumed | ||
+ | |- | ||
+ | |d||0.2773 min<sup>-1</sup>||Degradation rate of mRNA||Literature | ||
+ | |- | ||
+ | |d<sub>RFP</sub>||0.017 min<sup>-1</sup>||Degradation rate of RFP||Literature | ||
+ | |- | ||
+ | |d<sub>GFP</sub>||0.017 min<sup>-1</sup>||Degradation rate of GFP||Literature | ||
+ | |- | ||
+ | |d<sub>RhlI</sub>||0.0167 min<sup>-1</sup>||Degradation rate of RhlI||Literature | ||
+ | |- | ||
+ | |d<sub>LasI</sub>||0.0167 min<sup>-1</sup>||Degradation rate of LasI||Literature | ||
+ | |- | ||
+ | |d<sub>MazF</sub>||0.173286 min<sup>-1</sup>||Degradation rate of RhlI||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |d<sub>DiMazF</sub>||0.700037 min<sup>-1</sup>||Degradation rate of MazF dimer||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |d<sub>MazE</sub>||0.340082 min<sup>-1</sup>||Degradation rate of MazE||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |d<sub>DiMazE</sub>||0.166615 min<sup>-1</sup>||Degradation rate of MazE dimer||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |d<sub>Hexa</sub>||0.155088 min<sup>-1</sup>||Degradation rate of Maz hexamer||[ここにリンク先 Fitted to experimental data] | ||
+ | |- | ||
+ | |d<sub>C4AHL</sub>||0.000222 min<sup>-1</sup>||Degradation rate of C4AHL||Literature | ||
+ | |} | ||
+ | |d<sub>C12AHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of 3OC12AHL||Literature | ||
+ | |} | ||
+ | |d<sub>AmiE</sub>||0.01 min<sup>-1</sup>||Degradation rate of mRNA||Assumed | ||
+ | |} | ||
+ | <html></article></html> | ||
+ | |||
+ | <html><article></html> |
Revision as of 14:24, 12 October 2016
![](https://static.igem.org/mediawiki/2016/f/f6/T--Tokyo_Tech--goTop.png)
Detail Descriptions
Model Development
Parameters
No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.
Parameter | Value | Description | Reference |
---|---|---|---|
g | 0.0123 | Growth rate of each cells | [ここにリンク先 Fitted to experimental data] |
Pmax | 3.6641 | Carrying capacity | [ここにリンク先 Fitted to experimental data] |
EDiMazF | 0.101715 | Effect of MazF dimer on growth rate of each cells | [ここにリンク先 Fitted to experimental data] |
k | 5 min-1 | Transcriptional rate of mRNA under Ptet | Assumed |
leakPlux | 0.113 nMmin-1 | Leakage of Plux | [ここにリンク先 Fitted to experimental data] |
leakPrhl | 3.5 nMmin-1 | Leakage of Prhl | [ここにリンク先 Fitted to experimental data] |
κPlux | 10.3 nM-1min-1 | Maximum transcriptional rate of mRNA under Plux | [ここにリンク先 Fitted to experimental data] |
κPrhl | 9.73 nM-1min-1 | Maximum transcriptional rate of mRNA under Prhl | [ここにリンク先 Fitted to experimental data] |
nLux | 2.5 | Hill coefficient for Plux | [ここにリンク先 Fitted to experimental data] |
nRhl | 2.5 | Hill coefficient for Prhl | [ここにリンク先 Fitted to experimental data] |
KmLux | 78.32 nM | Lumped parameter for the Lux system | Estimated from Literature |
KmRhl | 1969 nM | Lumped parameter for the Rhl system | Estimated from Literature |
FDiMazF | 5 nM-1min-1 | Cutting rate at ACA sequences on mRNA by MazF dimer | Assumed |
f | 0.409213 | The probability of distinction of ACA sequences on mRNA by MazF dimer | Estimated |
fmRNARFP | 10 | The number of ACA arrays in mRNARFP | Extraction of data |
fmRNAGFP | 23 | The number of ACA arrays in mRNAGFP | Extraction of data |
fmRNARhlI | 1 | The number of ACA arrays in mRNARhlI | Extraction of data |
fmRNALasI | 10 | The number of ACA arrays in mRNALasI | Extraction of data |
fmRNAMazF | 2 | The number of ACA arrays in mRNAMazF | Extraction of data |
fmRNAMazE | 10 | The number of ACA arrays in mRNAMazE | Extraction of data |
α | 5 min-1 | Translation rate of protein | Assumed |
kDiMazF | 5.226124 nM-1min-1 | Formation rate of MazF dimer | Literature |
k-DiMazF | 3.151962 min-1 | Dissociation rate of MazF dimer | Literature |
kDiMazE | 6.759816 nM-1min-1 | Formation rate of MazE dimer | Literature |
k-DiMazE | 3.808504 min-1 | Dissociation rate of MazE dimer | Literature |
kHexa | 3.170544 nM-1min-1 | Formation rate of Maz hexamer | Literature |
k-Hexa | 8.344358 min-1 | Dissociation rate of Maz hexamer | Literature |
pLas | 1 min-1 | Production rate of 3OC12AHL by LasI | Assumed |
pRhl | 1 min-1 | Production rate of C4AHL by RhlI | Assumed |
D | 1 nM-1min-1 | Decomposition rate of 3OC12AHL by AmiE | [Assumed |
d | 0.2773 min-1 | Degradation rate of mRNA | Literature |
dRFP | 0.017 min-1 | Degradation rate of RFP | Literature |
dGFP | 0.017 min-1 | Degradation rate of GFP | Literature |
dRhlI | 0.0167 min-1 | Degradation rate of RhlI | Literature |
dLasI | 0.0167 min-1 | Degradation rate of LasI | Literature |
dMazF | 0.173286 min-1 | Degradation rate of RhlI | [ここにリンク先 Fitted to experimental data] |
dDiMazF | 0.700037 min-1 | Degradation rate of MazF dimer | [ここにリンク先 Fitted to experimental data] |
dMazE | 0.340082 min-1 | Degradation rate of MazE | [ここにリンク先 Fitted to experimental data] |
dDiMazE | 0.166615 min-1 | Degradation rate of MazE dimer | [ここにリンク先 Fitted to experimental data] |
dHexa | 0.155088 min-1 | Degradation rate of Maz hexamer | [ここにリンク先 Fitted to experimental data] |
dC4AHL | 0.000222 min-1 | Degradation rate of C4AHL | Literature |
|dC12AHL||0.004 min-1||Degradation rate of 3OC12AHL||Literature |} |dAmiE||0.01 min-1||Degradation rate of mRNA||Assumed |}