Team:Paris/Modeling/f3bis

From 2008.igem.org

(Difference between revisions)
Line 22: Line 22:
|unit
|unit
|value
|value
 +
|comments
|-
|-
|[expr(pFlhDC)]
|[expr(pFlhDC)]
|expression rate of <br> pFlhDC '''with RBS E0032'''
|expression rate of <br> pFlhDC '''with RBS E0032'''
-
|nM.s<sup>-1</sup>
+
|nM.min<sup>-1</sup>
-
|see [[Team:Paris/Modeling/Programs|"findparam"]] <br> need for 20 + 20 measures <br> and 5x5 measures for the ''SUM''?
+
|
 +
|need for 20 mesures with well choosen values of [aTc]<sub>i</sub> <br> and for 20 mesures with well choosen values of [arab]<sub>i</sub> <br> and 5x5 measures for the relation below?
|-
|-
|γ<sub>GFP</sub>
|γ<sub>GFP</sub>
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|min<sup>-1</sup>
|min<sup>-1</sup>
|0.0198
|0.0198
 +
|
|-
|-
|[GFP]
|[GFP]
|GFP concentration at steady-state
|GFP concentration at steady-state
|nM
|nM
-
|need for 20 + 20 measures <br> and 5x5 measures for the ''SUM''?
+
|
 +
|need for 20 + 20 measures <br> and 5x5 measures for the relation below?
|-
|-
|(''fluorescence'')
|(''fluorescence'')
|value of the observed fluorescence
|value of the observed fluorescence
|au
|au
-
|need for 20 + 20 measures <br> and 5x5 measures for the ''SUM''?
+
|
 +
|need for 20 + 20 measures <br> and 5x5 measures for the relation below?
|-
|-
|''conversion''
|''conversion''
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|nM.au<sup>-1</sup>
|nM.au<sup>-1</sup>
|(1/79.429)
|(1/79.429)
 +
|
|}
|}
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|unit
|unit
|value
|value
 +
|comments
|-
|-
-
|β<sub>12bis</sub>
+
|β<sub>13</sub>
-
|production rate of FliA-pFlhDC '''with RBS E0032''' <br> replace β<sub>12</sub> (not written)
+
|production rate of FliA-pFlhDC '''with RBS E0032''' <br> β<sub>13</sub>
|nM.min<sup>-1</sup>
|nM.min<sup>-1</sup>
 +
|
|
|
|-
|-
-
|(K<sub>11bis</sub>/{coef<sub>fliA</sub>})
+
|(K<sub>12</sub>/{coef<sub>fliA</sub>})
-
|activation constant of FliA-pFlhDC <br> K<sub>11bis</sub>
+
|activation constant of FliA-pFlhDC <br> K<sub>12</sub>
|nM
|nM
 +
|
|
|
|-
|-
-
|n<sub>11bis</sub>
+
|n<sub>12</sub>
-
|complexation order of FliA-pFlhDC <br> replace n<sub>11</sub> (not written)
+
|complexation order of FliA-pFlhDC <br> n<sub>12</sub>
|no dimension
|no dimension
 +
|
|
|
|-
|-
-
|-
+
|β<sub>2</sub>
-
|β<sub>2bis</sub>
+
|production rate of OmpR-pFlhDC '''with RBS E0032''' <br> β<sub>2</sub>
-
|production rate of EnvZ-pFlhDC '''with RBS E0032''' <br> β<sub>2bis</sub>
+
|nM.min<sup>-1</sup>
|nM.min<sup>-1</sup>
 +
|
|
|
|-
|-
-
|(K<sub>19bis</sub>/{coef<sub>envZ</sub>})
+
|(K<sub>22</sub>/{coef<sub>omp</sub>})
-
|activation constant of EnvZ-pFlhDC <br> replace K<sub>19</sub> (not written)
+
|activation constant of OmpR-pFlhDC <br> K<sub>22</sub>
|nM
|nM
 +
|
|
|
|-
|-
-
|n<sub>19bis</sub>
+
|n<sub>22</sub>
-
|complexation order of EnvZ-pFlhDC <br> n<sub>19bis</sub>
+
|complexation order of OmpR-pFlhDC <br> n<sub>22</sub>
|no dimension
|no dimension
 +
|
|
|
|}
|}
-
 
-
<br><br>
 
-
 
-
Then, if we have time, we want to verify the expected relation
 
-
 
-
[[Image:SumpFlhDC2.jpg|center]]
 

Revision as of 09:19, 16 October 2008

F3env.png
(see the considerations on the use of EnvZ)

We have [EnvZ]produced = {coefenv}expr(pTet) = {coefenv} ƒ1([aTc]i)

and [EnvZ]total = [EnvZ]b + [EnvZ]produced

and [FliA] = {coefFliA}expr(pBad) = {coefFliA} ƒ2([arab]i)

So, if we denote phosphorylated OmpR by OmpR*, we have

F3ompfromenv.jpg

that we can then introduce in the previous expression (ƒ 3) :

F3ompfinal.jpg



param signification unit value comments
[expr(pFlhDC)] expression rate of
pFlhDC with RBS E0032 		nM.min-1 need for 20 mesures with well choosen values of [aTc]i
and for 20 mesures with well choosen values of [arab]i
and 5x5 measures for the relation below?
γGFP dilution-degradation rate
of GFP(mut3b) 		min-1 0.0198
[GFP] GFP concentration at steady-state nM need for 20 + 20 measures
and 5x5 measures for the relation below?
(fluorescence) value of the observed fluorescence au need for 20 + 20 measures
and 5x5 measures for the relation below?
conversion conversion ratio between
fluorescence and concentration 		nM.au-1 (1/79.429)



param signification
corresponding parameters in the equations 		unit value comments
β13 production rate of FliA-pFlhDC with RBS E0032
β13 		nM.min-1
(K12/{coeffliA}) activation constant of FliA-pFlhDC
K12 		nM
n12 complexation order of FliA-pFlhDC
n12 		no dimension
β2 production rate of OmpR-pFlhDC with RBS E0032
β2 		nM.min-1
(K22/{coefomp}) activation constant of OmpR-pFlhDC
K22 		nM
n22 complexation order of OmpR-pFlhDC
n22 		no dimension
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