Team:CIDEB-UANL Mexico/Wet-lab/Planning

From 2012hs.igem.org

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           <a name="Construction"></a>Construction maps
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           <a name="General"></a>General Planning
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     <p>We decided to follow a deterministic approach for the mathematical representation of our genetic circuits. The simulations were made using MATLAB’s Simulink, according to the following general expressions for the genetic inhibition and activation elements present in the ODE systems. These expressions were adapted from Mendes, P, <i>et al</i>., (2003).</p>
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     <p>To work in the laboratory we made a plan about how to build the circuit. The principal processes are cut and ligate. To cut the biobricks we need restriction enzymes type II. These enzymes cut in a specific place. Here we hace an example about how to cut and ligate the pieces 1-6M and 3-12M:</p>
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<p>The effect of an inhibitor was modeled as follows:</p>
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<p>The part 1-6M is in the left side and is cut with the EcoRI and SpeI enzymes.</p>
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<p><a href="http://openwetware.org/wiki/Image:3AAssembly.gif">http://openwetware.org/wiki/Image:3AAssembly.gif</a></p>
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<a href="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif" rel="lightbox">
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<img src="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif"width="126px" height="44px" align="center">
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<p>where α is the maximum transcription rate of a gene, K is the dissociation constant of the inhibitor, I represents its concentration and n is its Hill coefficient.</p>
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<p>In the other hand, the effect of an activator was expressed as follows:</p>
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<p>The part 3-12M is in the right side and is cut with XbaI and PstI enzymes.</p>
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<p><a href="http://openwetware.org/wiki/Image:3AAssembly.gif">http://openwetware.org/wiki/Image:3AAssembly.gif</a></p>
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<a href="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif" rel="lightbox" >
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<img src="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif"width="130px" height="44px" align="center">
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<a href="https://static.igem.org/mediawiki/2012hs/0/04/Green001c.png" rel="lightbox">
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<img src="https://static.igem.org/mediawiki/2012hs/0/04/Green001c.png" width="140px" height="170px" align="center">
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<p>where α is also the maximum transcription rate of a gene, K is the dissociation constant of the activator, A represents its concentration and n is its Hill coefficient.</p>
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<p>To cut a vector we need the EcoRI and PstI enzymes in order to ligate the parts 1-6M and 3-12M in the correct order.</p>
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<p>The maximum transcription rate is used instead of the basal transcription rate under the assumption that inducible promoters should not present significant basal activity and that repressible promoters are active at this maximum rate in the absence of an inhibitor. The maximum transcription rate was calculated according to the Team Beijing iGEM 2009 (<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a>).</p>
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<p>The general form of the differential equations used to model the change of the mRNA concentration of a gene is as follows:</p>
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<p><a href="http://openwetware.org/wiki/Image:3AAssembly.gif">http://openwetware.org/wiki/Image:3AAssembly.gif</a></p>
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<img src="https://static.igem.org/mediawiki/2011/a/ad/3_mRNA_concentration_change.gif"width="482px" height="44px" alt="" align="center">
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<a href="https://static.igem.org/mediawiki/2012hs/4/4b/Red001c2.png" rel="lightbox">
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<p>This general form represents an hypothetical gene, whose transcription is affected by an inhibitor I and an activator A. Different Hill Coefficients (n1 and n2) are used for the inhibitor and activator. The equation includes also the degradation rate, µ, for which we used the same numerical value for all the genes included in our circuits, cell division rate (1/30 min) plus substance degradation rate (1/4.4 min), as suggested by the Team Beijing iGEM 2009.</p>
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<p>In this way, when the 2 parts that were removed  are inserted in a new vector, the part 1 (the left one) will attach to the EcoRI side and the part 2 (the right one) will be attached in the PstI side. XbaI and SpeI take the place in the way that they finish in the initial order but instead of having one biobrick inside, there are 2 biobricks ligated. The enzymes will have this order:</p>
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<p>For the protein concentration differential equations we took into consideration the maximum translation rate, α<sub>T </sub>, (also calculated as suggested also by the Team Beijing iGEM), the degradation rate, µ<sub>T</sub> , and the rate of postranslational modifications, specifically, phosphorylations of some transcription factors.</p>
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<p>Because all the genes in our circuits have been modified with a LVA tag, unless it is otherwise stated, all the protein degradation rates were considered to be equal to the cell division rate (1/30 min) plus the substance degradation rate (1/40 min, as suggested by Team Leuven iGEM 2008, <a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2008.igem.org/Team:KULeuven/Model/Inverter</a>)</p>
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<p>The general form for the differential equation of protein concentration change the following:</p>
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<a href="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif" rel="lightbox">
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<a href="https://static.igem.org/mediawiki/2012hs/2/29/Et2001.png" rel="lightbox">
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<img src="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif"width="346px" height="39px" alt="" align="center">
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          <a name="References"></a>References
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<p>After cutting the parts we attach the two parts  joining them together. For example the parts 1-6M and 3-12M are cut. Then 1-6M  has ampiciline resistance and the part 3-12M has ampiciline and kanamicine  resistance. We have to use a vector with a different resistance to see if the bacteria  have the complete new vector when tested. Following this factor is how we chose  the vector that we will use and in this case we chose tetracycline and the vector  with this resistance is the PSB1T3 (1-7A).</p>
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<p>Once the parts are together they are transformed  in bacteria.</p>
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<p>After that we culture in tubes with broth medium and the process is repeated until all the circuit is complete.</p>
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          <a name="Construction"></a>Circuit Construction
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<p>In a general way, the steps followed in the laboratory were:</p>
<ol>
<ol>
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  <li>Mendes, P, et al., (2003), Artificial gene networks for objective comparison of analysis algorithms, BIOINFORMATICS, Vol. 19 Suppl. 2, pages ii122–ii129</li>
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            <li>The  first step is to hydrate all the biobricks of the list.</li>
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  <li>Team Beijing iGEM 2009 (<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a>).</li>
+
            <li>Then  they must be transformed into bacteria. </li>
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  <li>Team Leuven iGEM 2008,<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2008.igem.org/Team:KULeuven/Model/Inverter</a>)</li>
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            <li>After  that, we add the bacteria into Petri dishes with agar-based growth medium. </li>
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</ol>
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            <li>The  next step was to resemble in test tubes. </li>
 +
            <li>Do  MiniPreparation of plasmid DNA with all the biobricks</li>
 +
            <li>Check  the quality of the DNAs by running </li>
 +
          </ol>
 +
          <p>Then the biobricks will follow a  different process divided by sections: Stand-by, High concentration, Low  concentration</p>
 +
<p> In order to build the section of Stand-by the following steps must be  followed: </p>
 +
       
 +
          <ol>
 +
            <li>Cut  the pieces 1-6M with EcoRI and SpeI, and the part 3-12M with XbaI and PstI.</li>
 +
            <li>Ligate  them into the plasmid pSB1T3 (1-7A).</li>
 +
          </ol>
 +
          <p>&nbsp;</p>
 +
       
 +
          <p> In order to build the section of High concentration the following  steps must be followed: </p>
 +
       
 +
          <ol>
 +
            <li> Cut the part 1-6E with EcoRI and SpeI, and the part 1-10E with XbaI  and PstI.</li>
 +
            <li>Ligate  them into the plasmid PBB1K3 (1-5A) and we obtain the part pBAD-RBS</li>
 +
            <li>Cut  the part 1-14N with EcoRI and SpeI , and the part 1-2M </li>
 +
            <li>Ligate  them into the plasmid PSB1T3 (1-7A) and we obtain the part YFP-cI434.</li>
 +
            <li>Cut  the part pBAD-RBS with EcoRI and SpeI and the part YFP-cI434 with XbaI and  PstI.</li>
 +
            <li>Ligate  them into the the plasmid PSB1A3 (1-1G).</li>
 +
          </ol>
 +
         
 +
          <p> In order to build the section of High concentration the following  steps must be followed: </p>
 +
       
 +
          <ol>
 +
            <li> Cut the part 2-11J with EcoRI and SpeI, and the part 3-12O with XbaI  and PstI.</li>
 +
            <li>Ligate  them into the plasmid PSB1T3 (1-7A) and we obtain the part PRM-RFP.</li>
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            <li> Cut the part 2-14A with EcoRI and SpeI, and the part 1-10C with XbaI  and PstI.</li>
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            <li>Ligate  them into the plasmid PSB1K3 (1-5A) and we obtain the part pLL-cI.</li>
 +
            <li>Cut  the part 2-12G with EcoRI and SpeI, and the part 1-10G with XbaI and PstI.</li>
 +
            <li>Ligate  them into the plasmid PSB1K3 (1-5A) and we obtain the part phiR73-c22.</li>
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            <li>Cut  the part pLL-cI with EcoRI and SpeI, and the part pRM-RFPwith XbaI and PstI.</li>
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            <li>Ligate  them into the plasmid PSB1A3 (1-1G) and we obtain the part pLL-cI-pRM-RFP.</li>
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            <li>Cut  the part 1-14N with EcoRI and SpeI, and the part phiR73-c22 with XbaI and PstI.</li>
 +
            <li>Ligate  them into the plasmid PSB1T3 (1-7A) and we obtain the part pBad-phiR73-c22.</li>
 +
            <li>Cut  the part pBad-phiR73-c22 with EcoRI and SpeI, and the part pLL-cI-pRM-RFP with  XbaI and PstI.</li>
 +
            <li>Ligate  them into the plasmid PSB1K3 (1-5A) and we obtain the low concentration circuit.</li>
 +
          </ol>
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          <p>&nbsp;</p>
 +
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<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
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          <a name="Now"></a>Until now
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          <ul>
 +
            <li>We  had some problems transforming the part 1-14N. We ran out of DNA of this  biobrick so we contacted with the IGEM team from the iGEM-UANL Team  and they gave us some DNA. But it didn’t work when we try to transform it.</li>
 +
            <li>We  have DNA in tubes stored and others in the refrigerator of the lab to use them  continuously.</li>
 +
           
 +
            <li>We  have cut all the biobricks but after certain time they tend to degradate so we  have to do it continuously.</li>
 +
           
 +
            <li>The  Ligation 3 is already done. This is composed by the parts: 2-12G and 1-10G.</li>
 +
          </ul>
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Overview#Overview">Overview</a></div>
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     <div class="lateral-button"><a href="https://2012hs.igem.org/Team:CIDEB-UANL_Mexico/Wet-lab/Planning#General">General</a></div>
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    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Overview#References">References</a></div>
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<div class="lateral-button"><a href="https://2012hs.igem.org/Team:CIDEB-UANL_Mexico/Wet-lab/Planning#Construction">Construction</a></div>
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<div class="lateral-button"><a href="https://2012hs.igem.org/Team:CIDEB-UANL_Mexico/Wet-lab/Planning#Now">Until now</a></div>
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Latest revision as of 05:26, 17 June 2012

banner-main iGEM-logo
Team: UANL_Mty-Mexico

Team: CIDEB-UANL Mexico

Wet-lab: Planning
General Planning

To work in the laboratory we made a plan about how to build the circuit. The principal processes are cut and ligate. To cut the biobricks we need restriction enzymes type II. These enzymes cut in a specific place. Here we hace an example about how to cut and ligate the pieces 1-6M and 3-12M:

The part 1-6M is in the left side and is cut with the EcoRI and SpeI enzymes.

http://openwetware.org/wiki/Image:3AAssembly.gif

The part 3-12M is in the right side and is cut with XbaI and PstI enzymes.

http://openwetware.org/wiki/Image:3AAssembly.gif

To cut a vector we need the EcoRI and PstI enzymes in order to ligate the parts 1-6M and 3-12M in the correct order.

http://openwetware.org/wiki/Image:3AAssembly.gif

In this way, when the 2 parts that were removed are inserted in a new vector, the part 1 (the left one) will attach to the EcoRI side and the part 2 (the right one) will be attached in the PstI side. XbaI and SpeI take the place in the way that they finish in the initial order but instead of having one biobrick inside, there are 2 biobricks ligated. The enzymes will have this order:

After cutting the parts we attach the two parts joining them together. For example the parts 1-6M and 3-12M are cut. Then 1-6M has ampiciline resistance and the part 3-12M has ampiciline and kanamicine resistance. We have to use a vector with a different resistance to see if the bacteria have the complete new vector when tested. Following this factor is how we chose the vector that we will use and in this case we chose tetracycline and the vector with this resistance is the PSB1T3 (1-7A).

Once the parts are together they are transformed in bacteria.

After that we culture in tubes with broth medium and the process is repeated until all the circuit is complete.

Circuit Construction

In a general way, the steps followed in the laboratory were:

  1. The first step is to hydrate all the biobricks of the list.
  2. Then they must be transformed into bacteria.
  3. After that, we add the bacteria into Petri dishes with agar-based growth medium.
  4. The next step was to resemble in test tubes.
  5. Do MiniPreparation of plasmid DNA with all the biobricks
  6. Check the quality of the DNAs by running

Then the biobricks will follow a different process divided by sections: Stand-by, High concentration, Low concentration

In order to build the section of Stand-by the following steps must be followed:

  1. Cut the pieces 1-6M with EcoRI and SpeI, and the part 3-12M with XbaI and PstI.
  2. Ligate them into the plasmid pSB1T3 (1-7A).

 

In order to build the section of High concentration the following steps must be followed:

  1. Cut the part 1-6E with EcoRI and SpeI, and the part 1-10E with XbaI and PstI.
  2. Ligate them into the plasmid PBB1K3 (1-5A) and we obtain the part pBAD-RBS
  3. Cut the part 1-14N with EcoRI and SpeI , and the part 1-2M
  4. Ligate them into the plasmid PSB1T3 (1-7A) and we obtain the part YFP-cI434.
  5. Cut the part pBAD-RBS with EcoRI and SpeI and the part YFP-cI434 with XbaI and PstI.
  6. Ligate them into the the plasmid PSB1A3 (1-1G).

In order to build the section of High concentration the following steps must be followed:

  1. Cut the part 2-11J with EcoRI and SpeI, and the part 3-12O with XbaI and PstI.
  2. Ligate them into the plasmid PSB1T3 (1-7A) and we obtain the part PRM-RFP.
  3. Cut the part 2-14A with EcoRI and SpeI, and the part 1-10C with XbaI and PstI.
  4. Ligate them into the plasmid PSB1K3 (1-5A) and we obtain the part pLL-cI.
  5. Cut the part 2-12G with EcoRI and SpeI, and the part 1-10G with XbaI and PstI.
  6. Ligate them into the plasmid PSB1K3 (1-5A) and we obtain the part phiR73-c22.
  7. Cut the part pLL-cI with EcoRI and SpeI, and the part pRM-RFPwith XbaI and PstI.
  8. Ligate them into the plasmid PSB1A3 (1-1G) and we obtain the part pLL-cI-pRM-RFP.
  9. Cut the part 1-14N with EcoRI and SpeI, and the part phiR73-c22 with XbaI and PstI.
  10. Ligate them into the plasmid PSB1T3 (1-7A) and we obtain the part pBad-phiR73-c22.
  11. Cut the part pBad-phiR73-c22 with EcoRI and SpeI, and the part pLL-cI-pRM-RFP with XbaI and PstI.
  12. Ligate them into the plasmid PSB1K3 (1-5A) and we obtain the low concentration circuit.

 

Until now
  • We had some problems transforming the part 1-14N. We ran out of DNA of this biobrick so we contacted with the IGEM team from the iGEM-UANL Team and they gave us some DNA. But it didn’t work when we try to transform it.
  • We have DNA in tubes stored and others in the refrigerator of the lab to use them continuously.
  • We have cut all the biobricks but after certain time they tend to degradate so we have to do it continuously.
  • The Ligation 3 is already done. This is composed by the parts: 2-12G and 1-10G.