Team:Carnegie Mellon/Modeling

From 2013.igem.org

(Difference between revisions)
 
(10 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:Carnegie_Mellon/Templates/header}}
{{:Team:Carnegie_Mellon/Templates/header}}
 +
<html>
 +
<br><br>
-
'''Intracellular model'''
+
<h1>Modeling</h1>
-
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:
+
<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.
-
mRNA synthesis and degradation
+
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.
 +
</p>
 +
<br><br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2013/d/db/Stevens.png" width="640" height="386" alt="Project"> </center>
-
KillerRed synthesis, maturation, and degradation
+
</html>
-
KillerRed states: singlet, singlet excited, triplet excited, and deactivated
 
-
Superoxide production (by KillerRed)
 
-
Superoxide elimination (by superoxide dismutase)
+
<br><br><br>
-
 
+
-
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.
+

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





Retrieved from "http://2013.igem.org/Team:Carnegie_Mellon/Modeling"