Team:SJTU-BioX-Shanghai/Modeling/Report gene prediction

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__NOTOC__
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<!----------------------------------------------------从这里开始写wiki--------------------------------->
<!----------------------------------------------------从这里开始写wiki--------------------------------->
=Report Gene Prediction=
=Report Gene Prediction=
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We choose constitutive RFP as our preliminary report gene. Cph8 has been choosen as the light control system combined with dCas9 system. When we raise the red light intensity, Cph8 will inhibit the sgRNA transcription. With the decrease of the combination between sgRNA and dCas9, the expression of RFP will be up-regulated. So we expect that the red light intensity should be positive correlation with the RFP expression.
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We choose constitutive RFP as our preliminary report gene. Cph8 has been choosen as the light control system combined with dCas9 system.When we rise the red light intensity, Cph8 will inhibit the sgRNA expression. With the decrease of the combination between sgRNA and dCas9, the expression of RFP will be up-regulated. So we expect that the red light intensity should be positive correlation with the RFP expression.
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----
=Circuit=
=Circuit=
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[[File:13sjtumzfSensor cph8.JPG]]
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[[File:Aabbccdd1.png|center|500px]]
=Modeling Hypothesis=
=Modeling Hypothesis=
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'''light sensor efficiency'''
'''light sensor efficiency'''
<br>Due to our previous hypothesis, we consider Cph8 efficiency as the ODE as follows:
<br>Due to our previous hypothesis, we consider Cph8 efficiency as the ODE as follows:
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<br>[[File:13sjtumzf0.JPG|150px]]
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<br>[[File:0.JPG|150px]]
'''Cph8 expression balance'''
'''Cph8 expression balance'''
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<br>[[File:13sjtumzf1.JPG|300px]]‎
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<br>[[File:1.JPG|300px]]‎
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<br>[[File:13sjtumzf2.JPG|300px]]‎
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<br>[[File:2.JPG|300px]]‎
'''sgRNA expression ratio'''
'''sgRNA expression ratio'''
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<br>[[File:13sjtumzf3.JPG|300px‎]]
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<br>[[File:3.JPG‎]]
<br><br>KM[Cph8]: The value of [Cph8] when the variation of [sgRNA] get its max degree.
<br><br>KM[Cph8]: The value of [Cph8] when the variation of [sgRNA] get its max degree.
<br>ncph8: The Hill coefficient related to Cph8.
<br>ncph8: The Hill coefficient related to Cph8.
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'''RFP expression ratio due to the variation of [sgRNA]'''
'''RFP expression ratio due to the variation of [sgRNA]'''
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<br>[[File:13sjtumzf4.JPG|250px‎]]
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<br>[[File:4.JPG‎]]
<br>α： The original strength of the RFP promoter Pm (J23110).
<br>α： The original strength of the RFP promoter Pm (J23110).
<br>ζ： The leakage of the RFP promoter.
<br>ζ： The leakage of the RFP promoter.
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=Results=
=Results=
We run our equations with basic parameters under Matlab environment and get results as follows:
We run our equations with basic parameters under Matlab environment and get results as follows:
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<br>[[File:13sjtumzfResult1.jpg]]
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<br>[[File:Result1.jpg]]
<br>The results matches our prediction: as the intensity of red light increasing, the expression level of sgRNA will be up regurgitated, and the RFP expression amount will decrease.
<br>The results matches our prediction: as the intensity of red light increasing, the expression level of sgRNA will be up regurgitated, and the RFP expression amount will decrease.
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Revision as of 03:45, 29 October 2013

Report Gene Prediction

We choose constitutive RFP as our preliminary report gene. Cph8 has been choosen as the light control system combined with dCas9 system.When we rise the red light intensity, Cph8 will inhibit the sgRNA expression. With the decrease of the combination between sgRNA and dCas9, the expression of RFP will be up-regulated. So we expect that the red light intensity should be positive correlation with the RFP expression.


Circuit

Aabbccdd1.png

Modeling Hypothesis

In order to figure out the typical properties of our system, the model should be visualized and controllable. For this, a number of hypotheses and approximations have been set.

  • Cph8 and dCas9 are conserved as the system will be steady in most case anyway. We mainly aim at optimization instead of measuring degradation rate (Kdeg) of light sensor or the promoter strength (KP) .
  • Degradation rates of normal proteins are easily got (Kdeg are easy to measured but not mentioned in most literature).
  • All photoconversion processes are treated as irreversible processes.
  • The expression amount of dCas9 is sufficient (the key factor which determines the inhibition ratio of report gene is sgRNA expression amount) .


PDEs

light sensor efficiency
Due to our previous hypothesis, we consider Cph8 efficiency as the ODE as follows:
150px

Cph8 expression balance
300px‎
300px‎

sgRNA expression ratio
3.JPG

KM[Cph8]: The value of [Cph8] when the variation of [sgRNA] get its max degree.
ncph8: The Hill coefficient related to Cph8.
We can set this equation because the inhibitory ratio of sgRNA is not related to the dCas9 proteins expression amount.

RFP expression ratio due to the variation of [sgRNA]
File:4.JPG
α： The original strength of the RFP promoter Pm (J23110).
ζ： The leakage of the RFP promoter.

Results

We run our equations with basic parameters under Matlab environment and get results as follows:
Result1.jpg
The results matches our prediction: as the intensity of red light increasing, the expression level of sgRNA will be up regurgitated, and the RFP expression amount will decrease.

Bio-X Institutions
Shanghai Jiao Tong University
800, Dongchuan Road
200240 Shanghai, China
igemsjtu2013@gmail.com

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