Team:Carnegie Mellon/Modeling

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<h1>Modeling</h1>
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<p> We developed two models, each of which characterizes our experimental system on a different scale. The <a href="https://2013.igem.org/Team:Carnegie_Mellon/KRModel">intracellular model</a> uses chemical kinetics to model transcription and translation of the KillerRed gene, maturation of KillerRed, and the photochemistry of superoxide radical production.
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The <a href="https://2013.igem.org/Team:Carnegie_Mellon/HostPhageDynamics">host-phage dynamics model</a> examines the external interactions between <i>E. coli</i> and $\lambda$ and characterizes the effect of KillerRed (or control mRFP) on the system.
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!align="center"|[[Team:Carnegie_Mellon|Home]]
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</p>
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!align="center"|[[Team:Carnegie_Mellon/Team|Team]]
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<br><br>
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!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Carnegie_Mellon Official Team Profile]
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!align="center"|[[Team:Carnegie_Mellon/Project|Project]]
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<img src="https://static.igem.org/mediawiki/2013/d/db/Stevens.png" width="640" height="386" alt="Project"> </center>
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!align="center"|[[Team:Carnegie_Mellon/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Carnegie_Mellon/Modeling|Modeling]]
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!align="center"|[[Team:Carnegie_Mellon/Notebook|Notebook]]
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!align="center"|[[Team:Carnegie_Mellon/Safety|Safety]]
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!align="center"|[[Team:Carnegie_Mellon/Attributions|Attributions]]
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'''Intracellular model'''
 
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The intracellular model attempts to simulate the synthesis and action of KillerRed using ordinary differential equations over three stages of a typical photobleaching expeiment: induction at 37degC, storage at 4degC to allow for protein maturation, and photobleaching at room temperature. It includes:
 
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mRNA synthesis and degradation
 
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KillerRed synthesis, maturation, and degradation
 
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KillerRed states: singlet, singlet excited, triplet excited, and deactivated
 
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Superoxide production (by KillerRed)
 
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Superoxide elimination (by superoxide dismutase)
 
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Parameters:
 
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mRNA synthesis: adapted from Kennell and Riezman 1977.
 
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mRNA degradation: Bernstein, Lin, Cohen, and Lin-Chao 2002.
 
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KillerRed synthesis: from Kennell and Riezman 1977 and our own fluorescence data
 
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Superoxide production: adapted from Tsien and Waggoner 1995; Song, Hennink, Young, and Tanke 1995; and our own fluorescence data.
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<br><br><br>

Latest revision as of 20:41, 27 September 2013

Killer Red




Modeling

We developed two models, each of which characterizes our experimental system on a different scale. The intracellular model uses chemical kinetics to model transcription and translation of the KillerRed gene, maturation of KillerRed, and the photochemistry of superoxide radical production. The host-phage dynamics model examines the external interactions between E. coli and $\lambda$ and characterizes the effect of KillerRed (or control mRFP) on the system.



Project





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