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<h4>REACTIONS</h4> | <h4>REACTIONS</h4> | ||
\begin{align*} | \begin{align*} | ||
− | 1) & P_{mNect} & \rightarrow P_{mNect} + mRNA_{mNect} \\ | + | 1) && P_{mNect} & \rightarrow P_{mNect} + mRNA_{mNect} \\ |
− | 2) & P_{sfGFP} & \rightarrow P_{sfGFP} + mRNA_{sfGFP} \\ | + | 2) && P_{sfGFP} & \rightarrow P_{sfGFP} + mRNA_{sfGFP} \\ |
− | 3) & mRNA_{mNect} & \rightarrow mRNA_{mNect} + mNect \\ | + | 3) && mRNA_{mNect} & \rightarrow mRNA_{mNect} + mNect \\ |
− | 4) & mRNA_{sfGFP} & \rightarrow mRNA_{sfGFP} + sfGFP \\ | + | 4) && mRNA_{sfGFP} & \rightarrow mRNA_{sfGFP} + sfGFP \\ |
− | 5) & mRNA_{mNect} & \rightarrow \\ | + | 5) && mRNA_{mNect} & \rightarrow \\ |
− | 6) & mRNA_{sfGFP} & \rightarrow \\ | + | 6) && mRNA_{sfGFP} & \rightarrow \\ |
− | 7) & mNect & \rightarrow \\ | + | 7) && mNect & \rightarrow \\ |
− | 8) & sfGFP & \rightarrow \\ | + | 8) && sfGFP & \rightarrow \\ |
\end{align*} | \end{align*} | ||
</div> | </div> | ||
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<div> | <div> | ||
<div> | <div> | ||
− | <h4> | + | <h4>STOCHASTIC REACTION RATES:</h4> |
\begin{align*} | \begin{align*} | ||
− | + | 1) \quad & k_{mRNAmnect} \cdot P_{mNect} \cdot P_{activity} \\ | |
− | + | 2) \quad & k_{mRNAsfgfp} \cdot P_{sfGFP} \cdot P_{activity} \\ | |
− | + | 3) \quad & k_{mNect} \cdot mRNA_{mNect} \\ | |
− | + | 4) \quad & k_{sfGFP} \cdot mRNA_{sfGFP} \\ | |
− | + | 5) \quad & d_{mRNAmnect} \cdot mRNA_{mNect} \\ | |
− | mRNA_{mNect} | + | 6) \quad & d_{mRNAsfgfp} \cdot mRNA_{sfGFP} \\ |
− | mRNA_{sfGFP} | + | 7) \quad & d_{mNect} \cdot mNect \\ |
− | + | 8) \quad & d_{sfGFP} \cdot sfGFP \\ | |
− | + | ||
\end{align*} | \end{align*} | ||
</div> | </div> | ||
Line 168: | Line 167: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td>P<sub> | + | <td>P<sub>activity</sub></td> |
− | <td> | + | <td>Fraction of the maximal activity of the promoter. This value is computed in the sensor module.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td> | + | <td>k<sub>mRNAmnect</sub></td> |
− | <td> | + | <td>mNectarine mRNA transcription rate.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td> | + | <td>k<sub>mRNAsfgfp</sub></td> |
− | <td>mRNA | + | <td>sfGFP mRNA transcription rate.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td> | + | <td>k<sub>mNect</sub></td> |
− | <td> | + | <td>mNectarine translation rate.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td> | + | <td>k<sub>sfGFP</sub></td> |
− | <td> | + | <td>sfGFP translation rate.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td>sfGFP</td> | + | <td>d<sub>mRNAmnect</sub></td> |
− | <td> | + | <td>mNectarine mRNA degradation rate.</td> |
+ | </tr> | ||
+ | <tr> | ||
+ | <td>d<sub>mRNAsfgfp</sub></td> | ||
+ | <td>sfGFP mRNA degradation rate.</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>d<sub>mNect</sub></td> | ||
+ | <td>mNectarine degradation rate.</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>d<sub>sfGFP</sub></td> | ||
+ | <td>sfGFP degradation rate.</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
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</div> | </div> | ||
</div> | </div> | ||
− | |||
<div class="sec light_grey" id="results"> | <div class="sec light_grey" id="results"> | ||
<div> | <div> |
Revision as of 23:50, 15 October 2016
REPORTER MODULE
OVERVIEW
The reporter is the component of the circuit that enables readout of the stored information. The state of the switch is displayed by two different fluorescent proteins: sfGFP is expressed by DNA that has been switched, while DNA that didn't switch expresses mNectarine.
In order to implement multiplexing, the reporter proteins are expressed only when they are induced by the same candidate marker that triggered the switch.
GOALS
- Assist the design of the reporter.
- Characterize the reporter proteins.
MODEL
Our reporter system consist in two fluorenscent proteins that show the state of the switch. After induction, a switched plasmid expresses GFP, while a plasmid in it's original state expresses mNectarine.
Figure 2: Biological implementation of the integrase reporter. The figure shows both the switched and non switched state. Expression of the reporter proteins is repressed by default and induced in presence of the candidate marker.
The following section describes the species and reactions involved:
REACTIONS
\begin{align*} 1) && P_{mNect} & \rightarrow P_{mNect} + mRNA_{mNect} \\ 2) && P_{sfGFP} & \rightarrow P_{sfGFP} + mRNA_{sfGFP} \\ 3) && mRNA_{mNect} & \rightarrow mRNA_{mNect} + mNect \\ 4) && mRNA_{sfGFP} & \rightarrow mRNA_{sfGFP} + sfGFP \\ 5) && mRNA_{mNect} & \rightarrow \\ 6) && mRNA_{sfGFP} & \rightarrow \\ 7) && mNect & \rightarrow \\ 8) && sfGFP & \rightarrow \\ \end{align*}SPECIES
Name | Description |
---|---|
PmNect | Non switched promoter, facing the mNect gene. |
PsfGFP | Switched promoter, facing the sfGFP gene. |
mRNAmNect | mRNA of the mNectarine protein. |
mRNAsfGFP | mRNA of the sfGFP protein. |
mNect | mNectarine fluorescent protein. |
sfGFP | Superfolder GFP protein. |
STOCHASTIC REACTION RATES:
\begin{align*} 1) \quad & k_{mRNAmnect} \cdot P_{mNect} \cdot P_{activity} \\ 2) \quad & k_{mRNAsfgfp} \cdot P_{sfGFP} \cdot P_{activity} \\ 3) \quad & k_{mNect} \cdot mRNA_{mNect} \\ 4) \quad & k_{sfGFP} \cdot mRNA_{sfGFP} \\ 5) \quad & d_{mRNAmnect} \cdot mRNA_{mNect} \\ 6) \quad & d_{mRNAsfgfp} \cdot mRNA_{sfGFP} \\ 7) \quad & d_{mNect} \cdot mNect \\ 8) \quad & d_{sfGFP} \cdot sfGFP \\ \end{align*}PARAMETERS
Name | Description |
---|---|
Pactivity | Fraction of the maximal activity of the promoter. This value is computed in the sensor module. |
kmRNAmnect | mNectarine mRNA transcription rate. |
kmRNAsfgfp | sfGFP mRNA transcription rate. |
kmNect | mNectarine translation rate. |
ksfGFP | sfGFP translation rate. |
dmRNAmnect | mNectarine mRNA degradation rate. |
dmRNAsfgfp | sfGFP mRNA degradation rate. |
dmNect | mNectarine degradation rate. |
dsfGFP | sfGFP degradation rate. |
RESULTS