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/Implementation" title=""><span>Implementation</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/F2620 Comparison" title=""><span>F2620</span></a></li>
      <li><a href="https://2007.igem.org/Imperial/Infector_Detector/Conclusion" title=""><span>Conclusion</span></a></li>
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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 of Testing==
+== Aims==
-To test and characterise the key characteristics of our system such as the sensitivity of the system to AHL. To do this, we induce the system with known concentrations of AHL input and measure the fluorescence output. Then using a calibration curve the fluorescence was converted into the number of GFPmut3b molecules synthesised, click on the following link for an explaination about how to [http://www.openwetware.org/wiki/IGEM:IMPERIAL/2007/new_pages/Data_anaylsis#Conversion_of_Datause use the calibration curve]. The full results and protocols can be found on the links [http://openwetware.org/wiki/IGEM:Imperial/2007/Wet_Lab/results/ID3.1 results] and [[Imperial/Wet_Lab/Protocols/ID3.1|protocol]] pages.
+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 [[Imperial/Wet_Lab/Results/Res1.3 |calibration curve]] and for how we [[Imperial/Wet Lab/Results/Res1.3/Converting_Units| used it to convert]]
-=Results=
+==Results==
-{|align="left"
+===DNA Concentrations===
-|<center><br>[[Image:GFPMolecule syn ID2 Final.PNG|500px]]</center>
+<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>
 |-
-|The results show us the following:
+|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>
+===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 degradation experiment(link) proved degradation is negligible. Interestingly this time is independent of the GFPmut3b molecules produced, showing that the LuxR under the control of pTet is the major source of energy consumption. 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
+*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:
-In addition the results ''in vitro'' have been compared to the work on [http://partsregistry.org/Part:BBa_F2620 BBa_F2620]('''pTet-LuxR-pLux-GFPmut3b''' ''in vivo'' which is the same as the construct 1 used for infecter detector. To do this we investigated the comparison between ''in vitro'' and ''in vivo.''
+*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
-<br clear=all>
+*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>
-{|align="center"
-| width="200px"|<br><center>[[Image:IC2007_,,BF_stage1_construct.PNG|thumb|500px]]</center>
 |}
-Normalise the in vitro on the plasmids to give a platform for comparison:
-*''In Vitro'' - 4&micro;g of DNA was added which for [http://partsregistry.org/Part:BBa_T9002 '''pTet-LuxR-pLux-GFPmut3b'''] is 904823007 plasmids
-*''In Vivo'' - Each cell has ~30 plasmids per cell
-To compare we normalised the data of ''in vitro'' '''GFPmut3b molecules synthesised per 30 plasmids''' to allow some comparison to the ''in vivo'' data.
-===Rate of GFPmut3b Synthesis for 100nM AHL===
-{|align="center"
-|width="100%"|<br>[[image:In vitro in vivo comp.png|thumb|800px|Comparison between ''in vivo'' and ''in vitro'' for rate of GFPmut3b at 100nM AHL. The rate for in vitro and in vivo was taken for the maximum rate for each chassis. <br>
-*''in vivo'' has a maximal rate of 400-500 molecules of GFP synthesised per second per cell. The ''in vivo'' reaches steady state ~30minutes.<br>
-*''in vitro'' has the equivalent of 220 molecules of GFP synthesised per second per cell equivalent. This is based upon the normalization on DNA plasmids. The ''in vitro'' chassis decreases in rate of synthesis after 90 minutes and keeps decreasing until rate is zero at around 360 minutes <br>
-]]
-|}
-===Transfer Function===
-{|align="center"
-|width="100%"|<br>[[image:In_vivo_in_vitro_comp2.png|thumb|800px|The graph above shows the transfer function of '''AHL input''' vs '''rate of GFP synthesis output'''. The blue line on ''in vivo'' corresponds to the range of AHL on ''in vitro''<br>
-*''in vitro'' shows a similar shape to the ''in vivo'' transfer function, however rate of GFP synthesis  lower in the ''in vitro'' chassis. e.g. for 1000nM the rate ''in vivo'' is ~450 GFP molecules per sec per cell,'' in vitro has an equivalent value of 220 GFP molecules per second.<br>
-*The ''in vitro'' chassis looks as if the rate is very low for low AHL inputs being <10 molecules of GFP per second.]]
-|}
-==Summary==
-Below is list of which of the orginial Specifications that our infecter detector achieved:
-{|border="1" width="80%" align="center"
-|-
-|width="20%" style="background:#ffffcc"|<center>'''Property'''</center>
-|width="--"|<center>'''Value'''</center>
-|'''Achievements'''
-|-
-|style="background:#ffffcc"|Inputs
-|<center>System must be sensitive to AHL concentration between 5-50nM</center>
-|'''<font color=green>Sensitive to 5-1000nM</font>'''
-|-
-|style="background:#ffffcc"|Outputs
-|<center>System must give a visual signal if bacteria is present</center>
-|'''<font color=red>Future work - Using Stronger fluorescent protein such as DsRed express</font>'''
-|-
-|style="background:#ffffcc"|Response Time
-|<center>System needs to have a response time under 3 hour</center>
-|'''<font color=green>Systems responds <30minutes</font>'''
-|-
-|style="background:#ffffcc"|Operating Conditions
-|<center>System must operate within temperature 20-30&deg;C</center>
-|'''<font color=green>System works at 25&deg;C</font>'''
-|-
-|style="background:#ffffcc"|Health & Safety
-|<center>System Must not be living replicating bacteria, and in any way harmful or infectious.</center>
-|'''<font color=green>Cell Free ''in vitro'' chassis</font>'''
-|-
-|style="background:#ffffcc"|Lifespan
-|<center>System must have a shelf life of 7 days</center>
-|'''<font color=green>Can be stored in freezer for prolonged periods</font>'''
-|-
-|style="background:#ffffcc"|Packaging
-|<center>System must be portable and convenient to use</center>
-|'''<font color=red>Future Work - Using our chassis in a spray</font>'''
-|}
-<br clear="all">
-<center>  [https://2007.igem.org/Imperial/Infector_Detector/Implementation<< Implementation] | Testing | [https://2007.igem.org/Imperial/Infector_Detector/Conclusion Conclusions >>]
+<center>  [https://2007.igem.org/Imperial/Infector_Detector/Implementation<< Implementation] | Testing | [https://2007.igem.org/Imperial/Infector_Detector/F2620_Comparison F2620 Comparison >>]
 </center>

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