Team:Carnegie Mellon/Modeling

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'''Intracellular model'''
'''Intracellular model'''
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The intracellular model attempts to simulate the synthesis and action of KillerRed using ordinary differential equations. It includes:
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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:
mRNA synthesis and degradation
mRNA synthesis and degradation
 +
KillerRed synthesis, maturation, and degradation
KillerRed synthesis, maturation, and degradation
 +
KillerRed states: singlet, singlet excited, triplet excited, and deactivated
KillerRed states: singlet, singlet excited, triplet excited, and deactivated
 +
Superoxide production (by KillerRed)
Superoxide production (by KillerRed)
 +
Superoxide elimination (by superoxide dismutase)
Superoxide elimination (by superoxide dismutase)

Revision as of 19:26, 26 September 2013


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Intracellular model

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:

mRNA synthesis and degradation

KillerRed synthesis, maturation, and degradation

KillerRed states: singlet, singlet excited, triplet excited, and deactivated

Superoxide production (by KillerRed)

Superoxide elimination (by superoxide dismutase)

Parameters:

mRNA synthesis: adapted from Kennell and Riezman 1977.

mRNA degradation: Bernstein, Lin, Cohen, and Lin-Chao 2002.

KillerRed synthesis: from Kennell and Riezman 1977 and our own fluorescence data

Superoxide production: adapted from Tsien and Waggoner 1995; Song, Hennink, Young, and Tanke 1995; and our own fluorescence data.