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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After submitting the model from yesterday, we got the results from the supercomputer.  
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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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We compared the gfp that was produced by the model to the experimental results that were found by other members of our group.
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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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Here are the graphs:<br>
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{| class="wikitable" style="text-align:center" border = "1"
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[[Image:Tnnatcvaries4.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br>
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|-
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<br>
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! Rxn #
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From these graphs, it is possible to see that the model is not really very correct. There is no GFP production at an aTC concentration of 0, when the experiments show a lot of production. This phenomenon is called leakiness and it is something that will need to be dealt with in future models.<br>
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! Reaction
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Also, the model seems to peak at 3 hours or so, and then slowly decreases. This is not what we want to see. Instead the model should peak at 6 hours and then level off to a steady state.<br>
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! Forward Kinetic Constant
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The next model will hopefully improve on this effort and fix some of the problems.
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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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