REPORTER MODULE

OVERVIEW

Figure 1: Schematic of the reporter of our circuit.

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

MODEL

RESULTS

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
$P_{mNect}$	Non switched promoter, facing the mNectarine gene.
$P_{sfGFP}$	Switched promoter, facing the sfGFP gene.
$mRNA_{mNect}$	mRNA of the mNectarine protein.
$mRNA_{sfGFP}$	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
$P_{activity}$	Fraction of the maximal activity of the promoter. This value is computed in the sensor module.
$k_{mRNAmnect}$	mNectarine mRNA transcription rate.
$k_{mRNAsfgfp}$	sfGFP mRNA transcription rate.
$k_{mNect}$	mNectarine translation rate.
$k_{sfGFP}$	sfGFP translation rate.
$d_{mRNAmnect}$	mNectarine mRNA degradation rate.
$d_{mRNAsfgfp}$	sfGFP mRNA degradation rate.
$d_{mNect}$	mNectarine degradation rate.
$d_{sfGFP}$	sfGFP degradation rate.

CHARACTERIZATION

The reporter has been characterized by placing the fluorescent proteins under an aTc-inducible promoter. In this case the activity of the promoter is modeled as:

\begin{align*} P_{activity}=l_{pTet}+(1-l_{pTet})\cdot\frac{[aTc]^{n}}{K_m^n+[aTc]^{n}} \end{align*}

Where aTc is the tetracycline variant used for induction, $l_{pTet}$ is the leakiness of the promoter, $n$ the sensitivity to aTc and $K_m$ the affinity.

RESULTS

REFERENCES

[1] -

Team:ETH Zurich/Detector Module