Latest revision as of 02:14, 27 October 2007

Infector Detector: Testing

Summary

The key results of the testing were:

The optimum DNA concentration for [http://partsregistry.org/Part:BBa_T9002 pTet-LuxR-pLux-GFPmut3b] in our Commcercial S30 Cell extract is 4µg.
Several of the specifications have been tested and met:
- Input:Sensitivity to 5-50nM AHL
- Operating Conditions:25^oC
- Response Time:Response time to of visual threshold not determined, but peak fluorescence is reached at ~300 minutes.

Aims

From the initial testing we determined that the construct worked in both in vivo and in vitro. Now we were concerned with:

Optimization - To test and obtain the optimal DNA concentration for construct 1 in vitro to reach the full potential of our infecter detector system.
Test our specifications - To test the range 5-50nM AHL defined in our specifications and characterise the output of GFPmut3b for a range of AHL inputs. We aimed to measure fluorescence and using our calibration curve convert to molecules of GFPmut3b, click here for our calibration curve and for how we used it to convert

Results

DNA Concentrations

Fig.1.1:Molecules of GFPmut3b synthesised over time, for each DNA Concentration in vitro at 25^oC - The fluorescence was measured over time for each experiment and converted into molecules of GFPmut3b in vitro using our calibration curve Click here for results and protocol.

Fig.1.2:Molecules of GFPmut3b synthesised for each DNA Concentration in vitro, after 360 minutes at 25^oC.

The Results above show that the optimum DNA concentration for in vitro is 4µg for 50nM AHL. From figure 1.1. and 1.2 it can be seen that as DNA concentration increases above 4µg the GFPmut3b molecules synthesised decrease. Interestingly for figure 1.2 the graph can be split into several regions of how the DNA concentration changes the output of GFPmut3b synthesis:

Linear phase - The DNA Concentration is proportional to synthesis of GFP molecules
Saturation phase - The expressional machinary is saturated i.e. RNA polymerases and ribosomes, and so the synthesis is no longer affected by DNA concentration. The maximum synthesis of GFP is at 4µg.
Inhibition phase- Increasing the DNA concentration actually inhibits the rate of protein synthesis.

The fact that increasing DNA concentration above 4µg causes a decrease in rate of protein synthesis is very interesting. The reason for this is thought to be that increasing DNA concentration causes problems with premature translational termination.

Although there is only a limited number of data points and there is a lot of error we feel that the results do show that 4µg was taken as the maximum and used for the rest of the testing. This agrees with the instructions provided by Promega which state that above 4µg the rate of protein synthesis is inhibited.

AHL Testing

Fig.1.3: Molcules of GFPmut3b synthesised vs AHL concentrations at 25^oC. The Testing was carried out for the 4µg of DNA. Again the fluorescence reading was converted into GFPmut3b molecules via the calibration curve. Click for full results and protocols can be found on the links results and protocol pages.

Fig.1.4:Molecules of GFPmut3b synthesised for each DNA Concentration in vitro, after 360 minutes at 25^oC. The data is from the fluorescence measurement at 360minutes which was converted to GFPmut3b molecules and plotted against [AHL]. The scale on the X axis is a logarithmic scale.

Figure 1.3 shows us the following:

Functional at 25^oC
The output of GFPmut3b increases with input of AHL
The system is sensitive to a range of 5-1000nM AHL
The GFPmut3b molecules synthesis stops at ~300minutes. This could be due to steady state or due to no synthesis of GFPmut3b. It is known not to be steady state because the degradation experiment proved degradation is negligible. Interestingly this time at which synthesis stops is independent of the GFPmut3b molecules produced as all the [AHL] level off at the same time. This shows that the LuxR under the control of pTet is the major source of energy consumption. The pTet is a very strong promoter and is a big consumer of the energy of the chassis. This highlights the advantages of using the construct 2 [http://partsregistry.org/Part:BBa_J37032 pLux-GFPmut3b] that does not have the energetic burden of producing LuxR under pTet.

Figure 1.4 shows us the following:

The shape of the Transfer function shows a linear range of response between 5nM and 100nM AHL. This defines the thresholds of response.
The lower threshold of response is the AHL concentration that the construct will respond
The upper threshold of response is the value of AHL the system is saturated and increasing AHL will not increase the rate of GFP synthesis.

<< Implementation | Testing | F2620 Comparison >>

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      <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Modelling" title=""><span>Modelling</span></a></li>
      <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Implementation" title=""><span>Implementation</span></a></li>
-     <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Testing" title=""><span>Testing</span></a></li>
+     <li><a class="current" href="https://2007.igem.org/Imperial/Infector_Detector/Testing" title=""><span>Testing</span></a></li>
-    <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Future" title=""><span>Future Work</span></a></li>
+     <li><a href="https://2007.igem.org/Imperial/Infector_Detector/F2620 Comparison" title=""><span>F2620</span></a></li>
-     <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Notes" title=""><span>Notes</span></a></li>
+     <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Conclusion" title=""><span>Conclusion</span></a></li>
-     <li><a href="https://2007.igem.org/Imperial/Infector_Detector/References" title=""><span>References</span></a></li>
    </ul>
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+<hr />
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 __NOTOC__
+= Infector Detector: Testing =
+==Summary==
+The key results of the testing were:
+*The optimum DNA concentration for [http://partsregistry.org/Part:BBa_T9002 '''pTet-LuxR-pLux-GFPmut3b'''] in our Commcercial S30 Cell extract is 4&micro;g.
+*Several of the specifications have been tested and met:
+**'''Input''':Sensitivity to 5-50nM AHL
+**'''Operating Conditions''':25<sup>o</sup>C
+**'''Response Time''':Response time to of visual threshold not determined, but peak fluorescence is reached at ~300 minutes.
-== Aims ==
+== Aims==
-The sensitivity of the system is to be determined through this experiment. To do this, we induce the system with known concentrations of AHL. We then record the change in GFP, such that we can calculate the rate of GFP production relative to concentration of AHL in solution.
+From the initial testing we determined that the construct worked in both ''in vivo'' and ''in vitro''. Now we were concerned with:
-* To determine the rate of protein production relative to concentration of AHL
+*'''Optimization''' - To test and obtain the '''optimal DNA concentration for construct 1 ''in vitro'' to reach the full potential of our infecter detector system.
-* To determine the response time relative to concentration of AHL
+*'''Test our specifications''' - To test the range 5-50nM AHL defined in our specifications and characterise the '''output of GFPmut3b for a range of AHL inputs'''.  We aimed to measure fluorescence and using our calibration curve convert to molecules of GFPmut3b, click here for our [[Imperial/Wet_Lab/Results/Res1.3 |calibration curve]] and for how we [[Imperial/Wet Lab/Results/Res1.3/Converting_Units| used it to convert]]
-* To determine the steady state response of protein relative to concentration of AHL
-== Materials and Methods ==
-==== AHL Dilutions ====
-concentrations of AHL were tested - 0, 5, 10, 15, 20, 50, 100, 1000 nM. These concentrations of AHL were produced by serial dilutions. Indepth protocols of these dilutions are documented at [[Imperial/Infector_Detector/Testing/Dilutions|AHL dilutions]] page.
-==== Preparing Cell Extract ====
-The following mixture was made
-* 20µl Premix Solution
-* 15µl S30 Cell Extract
-* 2.5µl Amino Acid Mixture 1
-* 2.5µl Amino Acid Mixture 2
-* 10.2µl DNA (4 µg)
-* 9.8µl Nuclease-Free Water
-==== Recording Results ====
-[A little about when and how to read the plates, maybe...]
-== Testing and Results ==
-==== Determine AHL sensitivity ====
-We first induced the system with varying concentrations of AHL to determine the output of the system. From the results, we were able to determine that the sensitivity range of the system was indeed between 5-50 nM, which is what was specified earlier. We can thus calibrate the system to give a visual output at this range of AHL concentrations.
-[[Image:Imperial ID testing transient1.png|thumb|left|430px|Transient reponse of the system at different AHL concentrations. There is a clear trend that with increasing amount of AHL concentration, the GFP output of the system also increases.]]
-[[Image:Imperial ID testing transfer1.png|thumb|right|430px|The transfer function of our system - with the output of GFP at 3 hours af varying AHL inputs. This curve behaves similiarly as it would ''in vivo'', with the highest sensitivity at around 5-50nM.]]
+==Results==
+===DNA Concentrations===
+<br clear=all>
+{|align="center" style="text-align: center; border-top:1px solid #000077; border-right:1px solid #000077; border-bottom:1px solid #000077; border-left:1px solid #000077;"
+|<br><center>[[Image:IC 2007 DNA Concentration.PNG|thumb|420px|left|Fig.1.1:Molecules of GFPmut3b synthesised over time, for each DNA Concentration ''in vitro'' at 25<sup>o</sup>C - The fluorescence was measured over time for each experiment and converted into molecules of GFPmut3b ''in vitro''
+[[Imperial/Wet Lab/Results/Res1.3/Converting_Units| using our calibration curve]] Click here for [[Imperial/Wet_Lab/Results/ID2.1| results]] and [[Imperial/Wet_Lab/Protocols/ID2.1| protocol]].]]
+[[image:IC 2007 DNA Concentration 360mins.PNG|thumb|420px|right|Fig.1.2:Molecules of GFPmut3b synthesised for each DNA Concentration ''in vitro'', after 360 minutes at 25<sup>o</sup>C.<br><br><br>]] </center>
+|-
+|style="text-align: left;" |<br>The Results above show that the optimum DNA concentration for ''in vitro'' is 4&micro;g for 50nM AHL. From figure 1.1. and 1.2 it can be seen that as DNA concentration increases above 4&micro;g the GFPmut3b molecules synthesised decrease. Interestingly for figure 1.2 the graph can be split into several regions of how the DNA concentration changes the output of GFPmut3b synthesis:
+*'''Linear phase''' - The DNA Concentration is proportional to synthesis of GFP molecules
+*'''Saturation phase''' - The expressional machinary is saturated i.e. RNA polymerases and ribosomes, and so the synthesis is no longer affected by DNA concentration. The maximum synthesis of GFP is at 4&micro;g.
+*'''Inhibition phase'''- Increasing the DNA concentration actually inhibits the rate of protein synthesis.
+The fact that increasing DNA concentration above 4&micro;g causes a decrease in rate of protein synthesis is very interesting. The reason for this is thought to be that increasing DNA concentration causes problems with premature translational termination. <br>
+<br>
+Although there is only a limited number of data points and there is a lot of error we feel that the results do show that 4&micro;g was taken as the maximum and used for the rest of the testing. This agrees with the instructions provided by Promega which state that above 4&micro;g the rate of protein synthesis is inhibited.
+|}
+<br clear=all><br>
-== Discussion and Validation ==
+===AHL Testing===
+<br clear=all>
+{|align="center" style="text-align: center; border-top:1px solid #000077; border-right:1px solid #000077; border-bottom:1px solid #000077; border-left:1px solid #000077;"
+|<br><center>[[Image:GFPMolecule syn ID2 Final.PNG|thumb|center|420px|left|Fig.1.3: Molcules of GFPmut3b synthesised vs AHL concentrations at 25<sup>o</sup>C. The Testing was carried out for the 4&micro;g of DNA. Again the fluorescence reading was converted into GFPmut3b molecules via the calibration curve. Click for full results and protocols can be found on the links [[Imperial/Wet Lab/Results/ID3.1| results]] and [[Imperial/Wet_Lab/Protocols/ID3.1|protocol]] pages.]]
+[[Image:Titrations curve - molecules.PNG|thumb|440px|right|Fig.1.4:Molecules of GFPmut3b synthesised for each DNA Concentration ''in vitro'', after 360 minutes at 25<sup>o</sup>C. The data is from the fluorescence measurement at 360minutes which was converted to GFPmut3b molecules and plotted against [AHL]. The scale on the X axis is a logarithmic scale.]]</center>
+|-
+|style="text-align: left;" |<br>
+Figure 1.3 shows us the following:
+*Functional at 25<sup>o</sup>C
+*The output of '''GFPmut3b increases with input of AHL'''
+*The system is sensitive to a range of '''5-1000nM AHL'''
+*The GFPmut3b molecules synthesis stops at '''~300minutes'''. This could be due to steady state or due to no synthesis of GFPmut3b. It is known not to be steady state because the [[Imperial/Wet_Lab/Results/Res1.4| degradation experiment]] proved degradation is negligible. Interestingly this time at which synthesis stops is independent of the GFPmut3b molecules produced as all the [AHL] level off at the same time. This shows that the LuxR under the control of pTet is the major source of energy consumption. The pTet is a very strong promoter and is a big consumer of the energy of the chassis. This highlights the advantages of using the construct 2 [http://partsregistry.org/Part:BBa_J37032 pLux-GFPmut3b] that does not have the energetic burden of producing LuxR under pTet. <br><br>
+Figure 1.4 shows us the following:
+*The shape of the '''Transfer function''' shows a linear range of response between 5nM and 100nM AHL. This defines the thresholds of response.
+*The '''lower threshold of response''' is the AHL concentration that the construct will respond
+*The '''upper threshold of response''' is the value of AHL the system is saturated and increasing AHL will not increase the rate of GFP synthesis.<br><br>
+|}
-<center>  [https://2007.igem.org/Imperial/Infector_Detector/Implementation << Implementation] | Testing/Validation | [https://2007.igem.org/Imperial Home >>]
+<center>  [https://2007.igem.org/Imperial/Infector_Detector/Implementation<< Implementation] | Testing | [https://2007.igem.org/Imperial/Infector_Detector/F2620_Comparison F2620 Comparison >>]
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