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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.
"
