Minnesota/9 June 2009

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|'''[[Minnesota/8 June 2009|Go to Previous Day (June 8)]]'''|| width=158|'''[[Minnesota/10 June 2009|Go to Next Day (June 10)]]'''
|'''[[Minnesota/8 June 2009|Go to Previous Day (June 8)]]'''|| width=158|'''[[Minnesota/10 June 2009|Go to Next Day (June 10)]]'''
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The basic model has some issues we would like to address, and so some changes are being made. First, due to the way that the experiments are conducted, the aTc concentration in the cell is essentially constant during the entire experiment. This is not the case in the model shown on the previous day. There is a reaction that creates aTc from nothing, which is not the case in the experiments. <br>
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Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.<br>
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The first change that we made to the model is to eliminate this reaction and include the aTc concentration into all of the reactions that it is involved with in the original model.
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The model created was similar to that described previously except with the addition of a second tet operon (tetO2):<br><br>
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{| class="wikitable" style="text-align:center" border = "1"
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|-
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! Rxn #
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! Reaction
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! Forward Kinetic Constant
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! Reverse Kinetic Constant
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|-
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|1/2||RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP||1E+07|| 1
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|-
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|3||RNA:lacP -> RNAp:lacP* || .01 ||
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|-
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|4||RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp||30||
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|-
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|5||RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
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|-
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|6||gfp_mRNA + rib -> rib:gfp_mRNA||100000||
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|-
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|7||rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA||33||
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|-
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|8||rib:gfp_mRNA_1 -> rib + gfp||33||
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|-
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|9||gfp_mRNA -> Ø||1.16E-03||
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|-
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|10||gfp -> Ø||3.21E-05||
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|-
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|11\12||tetR2 + aTc ↔ tetR2:aTc||1E+08||1E-03
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|-
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|13\14||tetR2:aTc + aTc  ↔ tetR2:aTc2||1E+08||1E-03
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|-
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|15\16||tetR2 + tetO1 ↔ tetR2:tetO1||1E+08||1E-03
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|-
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|17\18||tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1
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|-
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|19\20||tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+05
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|-
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|21\22||tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03
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|-
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|23\24||tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2||1E+08||1E-03
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|-
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|25\26||tetR2 + tetO2 ↔ tetR2:tetO2||1E+08||1E-03
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|-
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|27\28||tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc||1E+08||1
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|-
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|29\30||tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc2||1E+08||1E+05
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|-
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|31\32||tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc||1E+08||1E-03
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|-
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|33\34||tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc2||1E+08||1E-03
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|-
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|35||tetR2 -> Ø||2.89E-04||
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|-
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|36||tetR2:aTc -> aTc||2.89E-04||
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|-
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|37||tetR2:aTc2 -> 2 aTc||2.89E-04||
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|-
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|38\39||tetR2 + nsDNA ↔  tetR2:nsDNA||1000||3.2409
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|-
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|40\41||tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA||1000||3.2409
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|-
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|42||tetR2:aTc:nsDNA -> aTc + nsDNA||1.93E-04||
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|-
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|43||tetR2:nsDNA -> nsDNA||1.93E-04||
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|-
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|44||Ø -> tetR2||1E-11||
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|-
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|45||Ø -> aTc||3.3E-04||
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|}
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<br>Since we needed to have the aTc concentration constant both of the models created eliminated the aTc in all the equations and physically set each kinetic constant according to the desired aTc concentration.

Latest revision as of 16:26, 2 August 2009

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Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.
The model created was similar to that described previously except with the addition of a second tet operon (tetO2):

Rxn # Reaction Forward Kinetic Constant Reverse Kinetic Constant
1/2RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP1E+07 1
3RNA:lacP -> RNAp:lacP* .01
4RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp30
5RNAp:DNAgfp -> RNAp + gfp_mRNA30
6gfp_mRNA + rib -> rib:gfp_mRNA100000
7rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA33
8rib:gfp_mRNA_1 -> rib + gfp33
9gfp_mRNA -> Ø1.16E-03
10gfp -> Ø3.21E-05
11\12tetR2 + aTc ↔ tetR2:aTc1E+081E-03
13\14tetR2:aTc + aTc ↔ tetR2:aTc21E+081E-03
15\16tetR2 + tetO1 ↔ tetR2:tetO11E+081E-03
17\18tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc1E+081
19\20tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc21E+081E+05
21\22tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc1E+081E-03
23\24tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc21E+081E-03
25\26tetR2 + tetO2 ↔ tetR2:tetO21E+081E-03
27\28tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc1E+081
29\30tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc21E+081E+05
31\32tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc1E+081E-03
33\34tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc21E+081E-03
35tetR2 -> Ø2.89E-04
36tetR2:aTc -> aTc2.89E-04
37tetR2:aTc2 -> 2 aTc2.89E-04
38\39tetR2 + nsDNA ↔ tetR2:nsDNA10003.2409
40\41tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA10003.2409
42tetR2:aTc:nsDNA -> aTc + nsDNA1.93E-04
43tetR2:nsDNA -> nsDNA1.93E-04
44Ø -> tetR21E-11
45Ø -> aTc3.3E-04


Since we needed to have the aTc concentration constant both of the models created eliminated the aTc in all the equations and physically set each kinetic constant according to the desired aTc concentration.

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