Team:Carnegie Mellon/Modeling

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.