Team:LCG-UNAM-Mexico/Experiments/Design

From 2008.igem.org

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           <br>
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     </table>
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        <a href="#Devices">
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      <p align="justify" class="calHeader style13"><a href="#Devices"><u>System</u></a></p>
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        <p align="justify" class="calHeader style1">System</p>
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       <p align="justify" class="calHeader style12"><span class="style16"><a href="#Sensing"><u>Sensing dispositive</u></span></a></span><br>
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      </a>
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      </p>
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       <p><a href="#Sensing"><span class="calHeader style1">Sensing dispositive</span><br>
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        </a></p>
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         <div align="center">
         <div align="center">
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           <p><span class="calHeader"><a name="Devices"></a>System</span></p>
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           <p><span class="calHeader"><a name="Devices"></a>System</span></p><br>
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           <p align="justify"> &nbsp; First of all, we needed a system that could <span dir="ltr" id=":1s">cause a change in a medium's conductivity</span>. An extrusion pump seemed to be the best scheme to achieve this. Once this was devised, we needed a mechanism to regulate the system. <span dir="ltr" id=":1s">We  decided to use a negative regulator because it's the only way to  transcriptionally regulate the expression of a gene in a definitive way.</span></p>
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           <p align="justify"> &nbsp; First of all, we needed a system that could <span dir="ltr" id=":1s">cause a change in its medium  conductivity</span>. An extrusion pump seemed to be the best scheme to achieve this. Once this was devised, we needed a mechanism to regulate the system. <span dir="ltr" id=":1s">We  decided to use a negative regulator because it's the only way to  transcriptionally regulate the expression of a gene in a definitive way.</span></p>
           <p align="justify"><br>
           <p align="justify"><br>
   &nbsp; We had to be able to restart our system, so we could add a signal at  anytime. This could be accomplished with an induction signal that  disappears rapidly after its involvement. The need of a link between  the inductor signal and the repressor, lead  us to include a little regulation cascade. This cascade allows us to  add new steps which might increase our system’s complexity.<br><br>
   &nbsp; We had to be able to restart our system, so we could add a signal at  anytime. This could be accomplished with an induction signal that  disappears rapidly after its involvement. The need of a link between  the inductor signal and the repressor, lead  us to include a little regulation cascade. This cascade allows us to  add new steps which might increase our system’s complexity.<br><br>
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           <p class="style4">&nbsp;</p>
           <p class="style4">&nbsp;</p>
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           <p align="left" class="calHeader style1">Primer design</p>
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           <p align="left" class="calHeader style1">Primer design</p><br>
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          <p align="left" class="calHeader style1">&nbsp;</p>
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           <p align="center" ><span class="bodyText"><img src="https://static.igem.org/mediawiki/2008/a/a0/Oligo_design_LCG_UNAM.png" width="500" border="0" /></span></p>
           <p align="center" ><span class="bodyText"><img src="https://static.igem.org/mediawiki/2008/a/a0/Oligo_design_LCG_UNAM.png" width="500" border="0" /></span></p>
           <p align="justify" ><span class="bodyText"><br>
           <p align="justify" ><span class="bodyText"><br>
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           </ul>
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           <p align="center">&nbsp;</p>
           <p align="center">&nbsp;</p>
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           <p align="left" class="calHeader style1">Devices</p>
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           <p align="left" class="calHeader">Devices</p>
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           <p align="left"><img src="https://static.igem.org/mediawiki/2008/2/28/Device3_2.png" width="150" border="0" /></p>
           <p align="left"><img src="https://static.igem.org/mediawiki/2008/2/28/Device3_2.png" width="150" border="0" /></p>
           <p align="left">&nbsp;</p>
           <p align="left">&nbsp;</p>
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             <span class="bodyText">The propose of this device is to manipulate the transcription of rcnA  by an inhibitory signal while maintaining the natural regulation of  rcnA through RcnR. To achieve this the device contains a CI  dependent  promoter, RcnR binding site  and the RcnA extrusion pump inserted in the vector <a href="https://static.igem.org/mediawiki/2008/9/94/PBB1MCS-5.PNG">pBBR1MCS-5.</a></span></p>
             <span class="bodyText">The propose of this device is to manipulate the transcription of rcnA  by an inhibitory signal while maintaining the natural regulation of  rcnA through RcnR. To achieve this the device contains a CI  dependent  promoter, RcnR binding site  and the RcnA extrusion pump inserted in the vector <a href="https://static.igem.org/mediawiki/2008/9/94/PBB1MCS-5.PNG">pBBR1MCS-5.</a></span></p>
           <p align="justify" class="style3">&nbsp;</p>
           <p align="justify" class="style3">&nbsp;</p>
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           <p align="justify" class="style3">Devices <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119010</a>/<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119011</a>: <em>The  regulatory device</em></p>
+
           <p align="justify" class="style3">Devices <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119010</a>/<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119011</a>: <em>The  regulatory device</em></p><br>
           <p align="justify" class="bodyText">In order to control the RcnA activity this device includes  the gene encoding LuxR  under the regulation TetR constitutive promoter followed by  cI, which will repress RcnA in the prescence of AHL:LuxR. The last component of the device is the gene encoding AiiA. In  <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119010</a> lacZ promoter is upstream of AiiA, while <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119011</a> carries a mutated version of it. The plasmid carrying this device will be <a href="https://static.igem.org/mediawiki/2008/5/5e/PRK415.png">PRK415</a>.</p>
           <p align="justify" class="bodyText">In order to control the RcnA activity this device includes  the gene encoding LuxR  under the regulation TetR constitutive promoter followed by  cI, which will repress RcnA in the prescence of AHL:LuxR. The last component of the device is the gene encoding AiiA. In  <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119010</a> lacZ promoter is upstream of AiiA, while <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K119010">BBa_K119011</a> carries a mutated version of it. The plasmid carrying this device will be <a href="https://static.igem.org/mediawiki/2008/5/5e/PRK415.png">PRK415</a>.</p>
           <p align="left">&nbsp;</p>
           <p align="left">&nbsp;</p>
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          <p align="left">&nbsp;</p>
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           <p><span class="calHeader"><a name="Sensing"></a><span class="style11">Sensing dispositive</span></span></p>
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          <p align="left">&nbsp;</p>
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          <p align="left" class="calHeader">&nbsp;</p>
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          <p>&nbsp;</p>
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          <p>&nbsp;</p>
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           <p><span class="calHeader"><a name="Sensing"></a><span class="style1">Sensing dispositive</span></span><br>
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          </p>
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           <p><br>
           <p><br>
           </p>
           </p>
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           <p align="justify" class="bodyText">We intend to measure variations in resistivity in a medium with a bacteria culture. This is achieved using an electronic system. </p>
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           <p align="left"> <span class="bodyText">We intend to measure variations in resistivity in a bacteria culture which has been exposed to nickel . This is achieved through an electronic system. <br>
-
           <p align="justify" class="bodyText">First of all we need a dispositive capable of detecting small resistivity variations. To achieve this, a resistive array in a Wheatstone bridge configuration is implemented. </p>
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          </span></p>
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           <p align="justify" class="bodyText">To process the signal a Digital-Analogical  capture card with an USB communication interface will be used. This will allow analogical  data acquisition and its transfer to a computer on a binary format.</p>
+
           <p align="left" class="bodyText"> First of all we need a dispositive capable of detecting small resistivity variations. To achieve this, a resistive array in a Wheatstone bridge configuration is implemented. <br>
-
           <p align="justify">&nbsp;</p>
+
          </p>
 +
           <p align="left" class="bodyText"> To process the signal an Analogical-Digital capture card with an USB communication interface will be used. This will allow analogical  data acquisition and its transfer to a computer on a binary format.<br>
 +
          </p>
 +
           <p align="left" class="bodyText"> Detection of conductivity variations in the bacterial culture is  achieved by introducing two platinum-covered chrome electrodes into the  medium. Since high medium resistivity is expected, we use four  resistances of 100 kΩ, one of them is variable.<span class="bodyText"><br>
 +
            </span></p>
 +
          <p align="left" class="style10"> </p>
 +
          <p align="left" class="bodyText"> <span class="calHeader style1">Efflux and internalization parameters</span> <span class="bodyText"><br>
 +
          </span></p>
 +
          <p align="left" class="bodyText"> In order to determine the nickel internalization and extrusion parameters a gradient of NiSO4 concentrations from 1x10-3 to 1X10-10 was tested. The growth inhibitory and the minimum RcnR inhibitory concentrations were included in the analysis as well. </p>
 +
          <p align="left" class="bodyText"> Before to start with the measurements the electronic system’s  sensitivity should be tested. In order to achieve this and get a  reference signal which would let us eliminate noise, measurements where  done with just LB, LB with NiSO4 and LB with cells. </p>
 +
          <p align="left"> <span class="bodyText"><br>
 +
          </span></p>
 +
          <p align="left" class="bodyText"> <span class="style3">Internalization</span></p><br>
 +
          <p align="left" class="bodyText"> In order to  determine the nickel internalization parameter liquid cultures of the  YohM- strain will be needed at an O.D. (Optical density) 0.5 at a  lambda of 600nm, where resistivity will be measured for different  concentrations of NiSO4. YohM- strain was selected because  as it lacks RcnA, so it will be internalizing nickel all the time. This  may facilitate to get the wished parameter as the changes in the  resistivity medium might be caused by the internalization pump alone. </p>
 +
          <p align="left" class="bodyText">  </p>
 +
          <p align="left" class="style3"> Extrusion </p><br>
 +
          <p align="left" class="bodyText"> The following steps were performed in order to  prove the RcnA activity, and to get the enough data to calculate  conductivity  from the resistivity measurements. These data will be  used to get the extrusion rate of RcnA by a relation between the  conductivity and divalent ions concentration.</p>
 +
          <p align="left"><br>
 +
          </p>
 +
          <p>  <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Notebook/2008-October#11"> Further details on notebook</a></p>
           <p align="justify">&nbsp;</p>
           <p align="justify">&nbsp;</p>
           <p align="justify">&nbsp;</p>
           <p align="justify">&nbsp;</p>
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<p align="left"><strong>4.-</strong><span class="bodyText">Parsek MR,</span>(1999) <span class="bodyText"><strong>Acyl homoserine-lactone quorum-sensing signal generation.</strong></span>Apr 13;96(8):4360-5.
<p align="left"><strong>4.-</strong><span class="bodyText">Parsek MR,</span>(1999) <span class="bodyText"><strong>Acyl homoserine-lactone quorum-sensing signal generation.</strong></span>Apr 13;96(8):4360-5.
<p align="left"><strong>5.-http://partsregistry.org/Part:BBa_I729006</strong>
<p align="left"><strong>5.-http://partsregistry.org/Part:BBa_I729006</strong>
-
                  <p align="left"><strong>6.-</strong>Whiteheada N.A., Barnada A.M.L., Slaterra  H.(2001)<strong> &quot;Quorum-sensing in Gram-negative bacteria&quot; .</strong><br>
+
          <p align="left"><strong>6.-</strong>Whiteheada N.A., Barnada A.M.L., Slaterra  H.(2001)<strong> &quot;Quorum-sensing in Gram-negative bacteria&quot; .</strong><br>
                         <strong><br>
                         <strong><br>
           7.-</strong>Fuqua, W.C., Winans, S.C., Greenber,  E.P.(2001).<strong>”Quorum sensing in bacteria: The LuxR-LuxI family of cell  densisty-responsive transcriptional regulators”.</strong><br><br>
           7.-</strong>Fuqua, W.C., Winans, S.C., Greenber,  E.P.(2001).<strong>”Quorum sensing in bacteria: The LuxR-LuxI family of cell  densisty-responsive transcriptional regulators”.</strong><br><br>

Revision as of 01:54, 30 October 2008

LCG-UNAM-Mexico:Experiments

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Design

System

Sensing dispositive

System


  First of all, we needed a system that could cause a change in its medium conductivity. An extrusion pump seemed to be the best scheme to achieve this. Once this was devised, we needed a mechanism to regulate the system. We decided to use a negative regulator because it's the only way to transcriptionally regulate the expression of a gene in a definitive way.


  We had to be able to restart our system, so we could add a signal at anytime. This could be accomplished with an induction signal that disappears rapidly after its involvement. The need of a link between the inductor signal and the repressor, lead us to include a little regulation cascade. This cascade allows us to add new steps which might increase our system’s complexity.

The components selected to fulfill the system requirements are enlisted in the next table:



* All the references for this table are included at the end of the design section.

 

 

Primer design



For the assembly of the devices, the oligos contain restriction sites that are compatible to each vector or subsequent part. The synthesized primers were designed to carry the following operators and promoters in order to introduce them in the devices.


  • The upper primer of the RcnA contain the cI and RcnR promoters in the BBa_K119009 part.
  • For the BBa_K119010/BBa_119011 the upper primer of AiiA contain the LacZ promoter and the modified LacZ promoter.

 

Devices

 

Device BBa_K119009: The extrusion pump.


The propose of this device is to manipulate the transcription of rcnA by an inhibitory signal while maintaining the natural regulation of rcnA through RcnR. To achieve this the device contains a CI dependent promoter, RcnR binding site and the RcnA extrusion pump inserted in the vector pBBR1MCS-5.

 

Devices BBa_K119010/BBa_K119011: The regulatory device


In order to control the RcnA activity this device includes the gene encoding LuxR under the regulation TetR constitutive promoter followed by cI, which will repress RcnA in the prescence of AHL:LuxR. The last component of the device is the gene encoding AiiA. In BBa_K119010 lacZ promoter is upstream of AiiA, while BBa_K119011 carries a mutated version of it. The plasmid carrying this device will be PRK415.

 

Sensing dispositive


We intend to measure variations in resistivity in a bacteria culture which has been exposed to nickel . This is achieved through an electronic system.

First of all we need a dispositive capable of detecting small resistivity variations. To achieve this, a resistive array in a Wheatstone bridge configuration is implemented.

To process the signal an Analogical-Digital capture card with an USB communication interface will be used. This will allow analogical data acquisition and its transfer to a computer on a binary format.

Detection of conductivity variations in the bacterial culture is achieved by introducing two platinum-covered chrome electrodes into the medium. Since high medium resistivity is expected, we use four resistances of 100 kΩ, one of them is variable.

Efflux and internalization parameters

In order to determine the nickel internalization and extrusion parameters a gradient of NiSO4 concentrations from 1x10-3 to 1X10-10 was tested. The growth inhibitory and the minimum RcnR inhibitory concentrations were included in the analysis as well.

Before to start with the measurements the electronic system’s sensitivity should be tested. In order to achieve this and get a reference signal which would let us eliminate noise, measurements where done with just LB, LB with NiSO4 and LB with cells.


Internalization


In order to determine the nickel internalization parameter liquid cultures of the YohM- strain will be needed at an O.D. (Optical density) 0.5 at a lambda of 600nm, where resistivity will be measured for different concentrations of NiSO4. YohM- strain was selected because as it lacks RcnA, so it will be internalizing nickel all the time. This may facilitate to get the wished parameter as the changes in the resistivity medium might be caused by the internalization pump alone.

Extrusion


The following steps were performed in order to prove the RcnA activity, and to get the enough data to calculate conductivity from the resistivity measurements. These data will be used to get the extrusion rate of RcnA by a relation between the conductivity and divalent ions concentration.


Further details on notebook

 

 

References


1.-Koch, D., Nies, D.H., Grass G.”.(2006) "The RcnR (YohLM) system of Escherichia coli: A connection between nickel cobalt and iron homeostasis"

2.-Rodrigue A. Et al. (2005) "Identification of rcnA (yohM), a Nickel and Cobalt Resistance Gene in Esherichia coli"

3.-Kovach et al.(1994), "pBBR1MCS: a broad-host-range cloning vector".

4.-Parsek MR,(1999) Acyl homoserine-lactone quorum-sensing signal generation.Apr 13;96(8):4360-5.

5.-http://partsregistry.org/Part:BBa_I729006

6.-Whiteheada N.A., Barnada A.M.L., Slaterra H.(2001) "Quorum-sensing in Gram-negative bacteria" .

7.-
Fuqua, W.C., Winans, S.C., Greenber, E.P.(2001).”Quorum sensing in bacteria: The LuxR-LuxI family of cell densisty-responsive transcriptional regulators”.

8.-Salmond, G.P.C., Bycroft, B.W., Stewart, G.S.A.B., Williams, P.(1995).”The bacterial 'enigma': Crackin the code of cell-cell communication”.

9.-Y. Dong and L. Zhang,(2005). “Quorum sensing and quorum-quenching enzymes”.

10.-Atsumi, S., Little, J.W.(2006). “A synthetic phage λ regulatory circuit”.

11.- Karzai, A.W.(2000)."The Ssra-SmpB system for protein tagging, directed degradation and ribosome rescue".

12.-
Keiler, K.C.et al.(1996)."Role of a peptide-tagging system in degradation of proteins synthesized from damaged messenger RNA" .

13.-Malan, T. P., A. Kolb, H. Buc, and W. R. McClure (1984). Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter. J. Mol. Biol. 180:881–909.

14.-J. Togashi, K. Ueda and T. Namai,(2001). “Overwintering of Erwinia carotovora subsp. carotovora in diseased tissues in soil and its role as inoculum for soft rot of Chinese cabbage”

15.-Y. Dong and L. Zhang,(2005). “Quorum sensing and quorum-quenching enzymes”.

16.- (1998). N.T. Keen, S. Tamaki, D. Kobayashi, and D. Trollinger.

 




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