Team:Michigan/Modeling

From 2009.igem.org

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<ul>
<ul>
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<li>
 
<li> This is in order to balance antiholin and holin levels without repression </li>
<li> This is in order to balance antiholin and holin levels without repression </li>
<li> ''This can be tuned so that timing of cell death works out'' </li>
<li> ''This can be tuned so that timing of cell death works out'' </li>
<li> Set antiholin production rate to that of holin in the absence of repression </li>
<li> Set antiholin production rate to that of holin in the absence of repression </li>
<li> Put this through the transcription and translation equations to obtain production rate </li>
<li> Put this through the transcription and translation equations to obtain production rate </li>
-
</li>
+
</ul>
-
<li>
+
 
-
<li>Can directly search for these rates in literature</li>
+
Assume degradation rates of all mRNAs are the same
-
</li>
+
 
 +
<ul>
 +
<li>Can directly search for these rates in literature </li>
 +
<li>Can use half life to calculate rate </li>
 +
</ul>
 +
 
 +
For protein degradation rate:
 +
 
 +
'''Case 1: Proteins are stable:'''
 +
 
 +
<ul>
 +
<li>Degradation rates equal reproduction rate of cell </li>
 +
<li>This is due to dilution of proteins across daughter cells </li>
 +
</ul>
 +
 
 +
'''Case 2: Proteins are unstable:'''
 +
<ul>
 +
<li>If not other degradation rate information is provided, can possibly assume that the degradation rates are a few orders of magnitude above the reproduction rate of cell</li>
 +
<li>Will have to look into this further</li>
</ul>
</ul>

Revision as of 22:19, 20 October 2009


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HOME THE TEAM THE PROJECT MODELING REGISTRY PARTS NOTEBOOK SAFETY

Kill switch topology for modeling.jpg


Cell Growth/Death

Transcription of Repressor:

Transcription of Lysozyme and Holin:

Repression of Lysozyme and Holin Transcription

Production of Repressor

Production of Proteins

Assumptions

Can set γA equal to rate of production of holin in the case that all operating sites are free

  • This is in order to balance antiholin and holin levels without repression
  • This can be tuned so that timing of cell death works out
  • Set antiholin production rate to that of holin in the absence of repression
  • Put this through the transcription and translation equations to obtain production rate

Assume degradation rates of all mRNAs are the same

  • Can directly search for these rates in literature
  • Can use half life to calculate rate

For protein degradation rate:

Case 1: Proteins are stable:

  • Degradation rates equal reproduction rate of cell
  • This is due to dilution of proteins across daughter cells

Case 2: Proteins are unstable:

  • If not other degradation rate information is provided, can possibly assume that the degradation rates are a few orders of magnitude above the reproduction rate of cell
  • Will have to look into this further