Team:Carnegie Mellon/KRModel

From 2013.igem.org

(Difference between revisions)
Line 2: Line 2:
-
<h1>Intracellular model</h1>
+
<h1>Intracellular model overview</h1>
<p>
<p>
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 37ºC, storage at 4ºC to allow for protein maturation, and photobleaching at room temperature. It includes:
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 37ºC, storage at 4ºC to allow for protein maturation, and photobleaching at room temperature. It includes:
Line 17: Line 17:
<li>KillerRed synthesis: Normal translation rates from Kennell and Riezman<sup>2</sup>. The maximum translation rate  in the model is three orders of magnitude lower to reflect the presents of several rare codons. This adjustment is suggested by comparisons of our fluorescence data for KillerRed and mRFP, which have nearly identical brightness.</li>
<li>KillerRed synthesis: Normal translation rates from Kennell and Riezman<sup>2</sup>. The maximum translation rate  in the model is three orders of magnitude lower to reflect the presents of several rare codons. This adjustment is suggested by comparisons of our fluorescence data for KillerRed and mRFP, which have nearly identical brightness.</li>
<li>Superoxide production: Given by photophysical calculations adapted from Tsien and Waggoner<sup>3</sup>; Song ''et. al.''<sup>4</sup>; and our own fluorescence data.</li></ul></p>
<li>Superoxide production: Given by photophysical calculations adapted from Tsien and Waggoner<sup>3</sup>; Song ''et. al.''<sup>4</sup>; and our own fluorescence data.</li></ul></p>
 +
 +
 +
<h1>Superoxide production</h1>
 +
 +
<h2>References</h2>
<h2>References</h2>
-
<p><sup>1</sup> Kennel, D. and Riezman, H. Transcription and translation initiation frequencies of the ''Escherichia coli'' ''lac'' operon. ''J. Mol. Biol.'' 1977 114: 1-21.
+
<p><sup>1</sup> Kennel D and Riezman H. Transcription and translation initiation frequencies of the ''Escherichia coli'' ''lac'' operon. ''J. Mol. Biol.'' 1977 114: 1-21.
</p>
</p>
-
<p><sup>2</sup> Bernstein, J.A., Lin, P.-H., Cohen, S.N. and Lin-Chao, S. Global analysis of ''Escherichia coli'' RNA degradosome function using DNA microarrays. ''Proc. Natl. Acad. Sci. U.S.A.'' 2004 101: 2758–2763.
+
<p><sup>2</sup> Bernstein JA, Lin P-H, Cohen SN and Lin-Chao S. Global analysis of ''Escherichia coli'' RNA degradosome function using DNA microarrays. ''Proc. Natl. Acad. Sci. U.S.A.'' 2004 101: 2758–2763.
</p>
</p>
-
<p><sup>3</sup> Tsien, R.Y., Ernst, L. and Waggoner A. Fluorophores for Confocal Microscopy: Photophysics and
+
<p><sup>3</sup> Tsien RY, Ernst L and Waggoner A. Fluorophores for Confocal Microscopy: Photophysics and
Photochemistry. ''Handbook of Biological Confocal Microscopy,'' 3rd ed. SpringerScience+Business Media, New York, 2006.
Photochemistry. ''Handbook of Biological Confocal Microscopy,'' 3rd ed. SpringerScience+Business Media, New York, 2006.
</p>
</p>
-
<p><sup>4</sup>Song, L., Hennink, E.J., Young, I.T. and Tanke, H.J. Photobleaching Kinetics of Fluorescein in Quantitative Fluorescence Microscopy. ''Biophys. J.'' 1995 68: 2588-2600.
+
<p><sup>4</sup>Song L, Hennink EJ, Young IT and Tanke HJ. Photobleaching Kinetics of Fluorescein in Quantitative Fluorescence Microscopy. ''Biophys. J.'' 1995 68: 2588-2600.

Revision as of 02:24, 27 September 2013

Killer Red



Intracellular model overview

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 37ºC, storage at 4ºC 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 and assumptions:

  • mRNA synthesis: adapted from Kennell's and Riezman's studies of the lac operon1. Our construct uses a wild-type lac promoter, so we assume that its transcription rates are similar to the lac operon.
  • mRNA degradation: Characteristic half-life from Bernstein et. al.2
  • KillerRed synthesis: Normal translation rates from Kennell and Riezman2. The maximum translation rate in the model is three orders of magnitude lower to reflect the presents of several rare codons. This adjustment is suggested by comparisons of our fluorescence data for KillerRed and mRFP, which have nearly identical brightness.
  • Superoxide production: Given by photophysical calculations adapted from Tsien and Waggoner3; Song et. al.4; and our own fluorescence data.


Superoxide production



References

1 Kennel D and Riezman H. Transcription and translation initiation frequencies of the Escherichia coli lac operon. J. Mol. Biol. 1977 114: 1-21.

2 Bernstein JA, Lin P-H, Cohen SN and Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 2004 101: 2758–2763.

3 Tsien RY, Ernst L and Waggoner A. Fluorophores for Confocal Microscopy: Photophysics and Photochemistry. Handbook of Biological Confocal Microscopy, 3rd ed. SpringerScience+Business Media, New York, 2006.

4Song L, Hennink EJ, Young IT and Tanke HJ. Photobleaching Kinetics of Fluorescein in Quantitative Fluorescence Microscopy. Biophys. J. 1995 68: 2588-2600.

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