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Team:Michigan/Modeling
From 2009.igem.org
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<ul> | <ul> | ||
| - | |||
<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> | ||
| - | </ | + | </ul> |
| - | < | + | |
| - | <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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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
