Difference between revisions of "Team:EPF Lausanne/Notebook/Yeast"

 
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{{:Team:EPF_Lausanne/Test/Top_Nav}}
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{{:Team:EPF_Lausanne/Top_Nav}}
 
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr">
 
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr">
 
   <head>
 
   <head>
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</div>
 
</div>
  
<!--Protocols have to be added here-->
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<body id="Content" data-spy="scroll" data-target=".scrollspy" data-offset="20">
 
<body id="Content" data-spy="scroll" data-target=".scrollspy" data-offset="20">
   
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<div class="prot-section">
 
<div class="prot-section">
 
     <div class="row">
 
     <div class="row">
         <div class="col col-md-3 scrollspy">
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         <div class="col col-md-2 scrollspy">
 
             <ul id="nav" class="nav hidden-xs hidden-sm" data-spy="affix">
 
             <ul id="nav" class="nav hidden-xs hidden-sm" data-spy="affix">
 
               <li class="active"><a href="#express_dCas9-VP64">Express dCas9-VP64</a>
 
               <li class="active"><a href="#express_dCas9-VP64">Express dCas9-VP64</a>
 
                 <ul class="nav">
 
                 <ul class="nav">
 
                   <li><a href="#integrate_pTPGI_dCas9_VP64">Integrate pTPGI_dCas9_VP64</a></li>
 
                   <li><a href="#integrate_pTPGI_dCas9_VP64">Integrate pTPGI_dCas9_VP64</a></li>
                  <li><a href="#wb_dCas9-VP64">Western Blot of dCas9-VP64</a></li>
 
 
                 </ul>
 
                 </ul>
 
                 </li>
 
                 </li>
  
                 <li><a href="#integrate_reporter_plasmid">Integrate reporter plasmid</a>
+
                 <li><a href="#assemble_reporter_plasmid">Assemble reporter plasmid</a>
 
                 <ul class="nav">
 
                 <ul class="nav">
 
                   <li><a href="#linearise_reporter_plasmid">Linearise the plasmid by PCR</a></li>
 
                   <li><a href="#linearise_reporter_plasmid">Linearise the plasmid by PCR</a></li>
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                   <li><a href="#PCRoverlaps_prom">Add Gibson overlaps to CYC promoters by PCR</a></li>
 
                   <li><a href="#PCRoverlaps_prom">Add Gibson overlaps to CYC promoters by PCR</a></li>
 
                   <li><a href="#gibsonprom">Gibson assembly of promoters in reporter plasmid</a></li>
 
                   <li><a href="#gibsonprom">Gibson assembly of promoters in reporter plasmid</a></li>
                  <li><a href="#integrate_reporters_plasmids">Integrate the reporter plasmids</a></li>
 
 
                 </ul>
 
                 </ul>
 
                 </li>
 
                 </li>
  
                 <li><a href="#Integrate_and_express_gRNAs">Integrate and express gRNAs</a>
+
                 <li><a href="#Assemble_gRNAs">Assemble gRNAs</a>
 
                 <ul class="nav">
 
                 <ul class="nav">
                   <li><a href="#PCR-amplify_the_gRNAs_expressing_cassettes">PCR-amplify the gRNAs expressing cassettes</a></li>
+
                   <li><a href="#Linearize_p405ADH1">Linearize p405ADH1</a></li>
                   <li><a href="#PCR_out_DsRed2">PCR out DsRed2</a></li>
+
                   <li><a href="#synthesize_gRNAs">Synthesize gRNA cassettes</a></li>
                   <li><a href="#PCRoverlaps_gRNAs">Add Gibson overlaps to gRNAs by PCR</a></li>
+
                   <li><a href="#PCRoverlaps_gRNAs">Add Gibson overlaps by PCR</a></li>
 
                   <li><a href="#gibson_gRNAs">Gibson assembly of gRNAs</a></li>
 
                   <li><a href="#gibson_gRNAs">Gibson assembly of gRNAs</a></li>
 
                 </ul>
 
                 </ul>
 
                 </li>
 
                 </li>
 +
 +
                <li><a href="#activation-repression">Test activation-repression</a>
 +
                <ul class="nav">
 +
                  <li><a href="#integrate">Integration</a></li>
 +
                  <li><a href="#test_activ_inhib">Measures</a></li>
 +
                </ul>
 +
                </li>
 +
 +
                <li><a href="#logic_gate">Build the logic gate</a>
 +
                </li>
 +
 
             </ul>
 
             </ul>
  
 
             </nav>
 
             </nav>
         </div>  
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         </div>
         <div class="col-md-9">
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         <div class="col-md-offset-1 col-md-9">
 +
          <p><i>Note that all experiments were done by EPFL iGEM team members.</i></p>
 
<!--Integrate pDCAS9-->
 
<!--Integrate pDCAS9-->
 
             <section id="integrate_pTPGI_dCas9_VP64" class="panel">
 
             <section id="integrate_pTPGI_dCas9_VP64" class="panel">
 
                 <h1><small>Express dCas9-VP64</small></br>Integrate pTPGI_dCas9_VP64</h1>
 
                 <h1><small>Express dCas9-VP64</small></br>Integrate pTPGI_dCas9_VP64</h1>
                 <p>We received plasmid pTPGI_dCas9_VP64 from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas". After glycerol stocks and miniprep, we performed a restriction analysis to check the identity of our plasmid. We linearised the plasmid, in order to integrate it into yeast genome. For more details about our experiments, see <a target="_blank" href="https://static.igem.org/mediawiki/2015/3/30/EPF_Lausanne_Journal_integrate_dCas9-VP64.pdf">here</a>. Only our fourth trial to integrate the plasmid was successful.</p>
+
                 <p>We received plasmid pTPGI_dCas9_VP64 from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas". After glycerol stocks and miniprep, we performed a restriction analysis to check the identity of our plasmid. We linearised the plasmid, in order to integrate it into yeast genome. Only our fourth trial to integrate the plasmid was successful.</p>
  
 
                 <h2>Materials and methods</h2>
 
                 <h2>Materials and methods</h2>
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                     <li>Restriction analysis</li>
 
                     <li>Restriction analysis</li>
 
                     <li>Polymerase Chain Reaction</li>
 
                     <li>Polymerase Chain Reaction</li>
                     <li>Yeast integration A AJOUTER SUR PROTOCOLS</li>
+
                     <li>Yeast integration</li>
 +
                    <li>For more details about our procedures, see <a target="_blank" href="https://static.igem.org/mediawiki/2015/3/30/EPF_Lausanne_Journal_integrate_dCas9-VP64.pdf">here</a>.</li>
 
                 </ul>
 
                 </ul>
  
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                         <figure>
 
                         <figure>
 
                         <a href="https://static.igem.org/mediawiki/2015/3/3e/EPF_Lausanne_Gel_dCas9.png"><img src="https://static.igem.org/mediawiki/2015/3/3e/EPF_Lausanne_Gel_dCas9.png" alt="dCas9 gel" width="75%"></a>
 
                         <a href="https://static.igem.org/mediawiki/2015/3/3e/EPF_Lausanne_Gel_dCas9.png"><img src="https://static.igem.org/mediawiki/2015/3/3e/EPF_Lausanne_Gel_dCas9.png" alt="dCas9 gel" width="75%"></a>
                         <figcaption>Fig.1 - Gel of the dCas9.</figcaption>
+
                         <figcaption>Fig.1a - Restriction analysis of pTPGI_dCas9_VP64.</figcaption>
 
                         </figure>
 
                         </figure>
 
                     </div>
 
                     </div>
 
                     <div class="col-md-6">
 
                     <div class="col-md-6">
                         <p>We used four different sets of enzymes for the restriction analysis. Linearized pTPGI_dCas9_VP64 is expected to be 10'987 bp. We observe that the gel (fig.1) corresponds to the <a target="_blank" href="https://static.igem.org/mediawiki/2015/2/2b/EPF_Lausanne_Expected_Gel_dCas9.pdf">expected one</a>. </br>
+
                         <p>We used four different sets of enzymes for the restriction analysis. Linearized pTPGI_dCas9_VP64 is expected to be 10'987 bp. We observe that the gel (fig.1a) corresponds to the <a target="_blank" href="https://static.igem.org/mediawiki/2015/2/2b/EPF_Lausanne_Expected_Gel_dCas9.pdf">expected one</a>.
                        The plasmid was linearised both with EagI HF and NotI HF prior to integration. We integrated each linearised plasmid to obtain two different yeast strains.
+
                        <br>The plasmid was linearised both with EagI HF and NotI HF prior to integration. We integrated each linearised plasmid to obtain two different yeast strains.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
 
             </section>
 
             </section>
   
 
  
<!--Western Blot pDCAS9-->
 
            <section id="wb_dCas9-VP64" class="panel">
 
                <h1><small>Express dCas9-VP64</small></br>Western Blot of dCas9-VP64</h1>
 
                <p>The Western Blot allows to check the expression of dCas9.</p>
 
  
                <h2>Materials and methods</h2>
 
                <ul>
 
                    <li>Western Blot A AJOUTER SUR PROTOCOLS</li>
 
                </ul>
 
 
                <h2>Results</h2>
 
                <div class="row">
 
                    <div class="col-md-6">
 
                        <figure>
 
                        <a href="Link"><img src="image" alt="name the image" width="75%"></a>
 
                        <figcaption>Insert legend here</figcaption>
 
                        </figure>
 
                    </div>
 
                    <div class="col-md-6">
 
                        <p>Results of Western Blot.</p>
 
                    </div>
 
                </div>
 
            </section>
 
  
 
<!--INTEGRATE REPORTER PLASMID - LINEARISE REPORTER PLASMID-->
 
<!--INTEGRATE REPORTER PLASMID - LINEARISE REPORTER PLASMID-->
             <section id="linearise_reporter_plasmid" class="panel">  
+
             <section id="linearise_reporter_plasmid" class="panel">
 
                 <h1><small>Integrate reporter plasmid</small></br>Linearise reporter plasmid</h1>
 
                 <h1><small>Integrate reporter plasmid</small></br>Linearise reporter plasmid</h1>
                 <p>>We received the plasmid pCYC1m_yeGFP from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas". After glycerol stocks and minipreps. We linearised the plasmid by PCR according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/d/d3/EPF_Lausanne_Linearise_pCYC_yeGFP.pdf">protocol</a>.</p>
+
                 <p>We received the plasmid pCYC1m_yeGFP from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas".</p>
  
 
                 <h2>Materials and methods</h2>
 
                 <h2>Materials and methods</h2>
 
                 <ul>
 
                 <ul>
                     <li>Polymerase Chain Reaction</li>
+
                     <li><b>PCR</b> (cf. Protocols). After glycerol stocks and minipreps. we linearised the plasmid by PCR according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/d/d3/EPF_Lausanne_Linearise_pCYC_yeGFP.pdf">procedure</a>.</li>
 
                 </ul>
 
                 </ul>
  
 
                 <h2>Results</h2>
 
                 <h2>Results</h2>
 
                 <div class="row">
 
                 <div class="row">
                    <div row="col-md-6">
 
                        <figure>
 
                        <a href="Link"><img src="image" alt="name the image" width="75%"></a>
 
                        <figcaption>Insert legend here</figcaption>
 
                        </figure>
 
                    </div>
 
 
                     <div row="col-md-6">
 
                     <div row="col-md-6">
 
                         <p>Linearized pCYC1m_yeGFP is expected to be 5'485 bp. Running an agarose gel electrophoresis allowed to verify that we had linearised the plasmid.</p>
 
                         <p>Linearized pCYC1m_yeGFP is expected to be 5'485 bp. Running an agarose gel electrophoresis allowed to verify that we had linearised the plasmid.</p>
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<!--INTEGRATE REPORTER PLASMID - SYNTHESIZE PROMOTERS-->
 
<!--INTEGRATE REPORTER PLASMID - SYNTHESIZE PROMOTERS-->
             <section id="synthesize_promoters" class="panel">  
+
             <section id="synthesize_promoters" class="panel">
 
             <h1><small>Integrate reporter plasmid</small></br>Synthesize promoters</h1>
 
             <h1><small>Integrate reporter plasmid</small></br>Synthesize promoters</h1>
             <p>From the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas", we learnt that different regions on the promoters could lead to activation or inhibition when dCas9-VP64 was bound. We chose to modify the region of strongest activation, named c3, and the two regions that lead to the strongest inhibition, c6 and c7. We synthesized promoters CYC_0, CYC_1, CYC_2 and CYC_3. The only differences between them are the three regions c3, c6 and c7. The promoter CYC_0 is the original promoter, already present in the plasmid pCYC1m_yeGFP.</p>
+
             <p>From the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas", we learnt that different regions on the promoters could lead to activation or inhibition when dCas9-VP64 was bound. We chose to modify the region of strongest activation, named c3, and the two regions that lead to the strongest inhibition, c6 and c7. We synthesized promoters CYC_0, CYC_1, CYC_2 and CYC_3. They only differ between one another by the three regions c3, c6 and c7. The promoter CYC_0 is the original promoter, already present in the plasmid pCYC1m_yeGFP.</p>
 
+
            <h2>Materials and methods</h2>
+
            <ul>
+
                <li>Synthesis ??</li>
+
            </ul>
+
  
 
             <h2>Results</h2>
 
             <h2>Results</h2>
 
             <div class="row">
 
             <div class="row">
 
                 <div class="col-md-6">
 
                 <div class="col-md-6">
 +
                    <figure>
 
                     <img src="https://static.igem.org/mediawiki/2015/7/72/EPF_Lausanne_CYC_0_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/7/72/EPF_Lausanne_CYC_0_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/9/91/EPF_Lausanne_CYC_1_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/9/91/EPF_Lausanne_CYC_1_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/c/c7/EPF_Lausanne_CYC_2_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/c/c7/EPF_Lausanne_CYC_2_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/c/c6/EPF_Lausanne_CYC_3_IDT.PNG" style="width:80%">
 
                     <img src="https://static.igem.org/mediawiki/2015/c/c6/EPF_Lausanne_CYC_3_IDT.PNG" style="width:80%">
 +
                    <figcaption>Fig. 2 - Synthesized CYC promoters</figcaption>
 +
                    </figure>
 
                 </div>
 
                 </div>
 
                 <div class="col-md-6">
 
                 <div class="col-md-6">
                     <p>Four different promoters according to fig...</p>
+
                     <p>Four different promoters according to Fig. 2.</p>
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
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<!--INTEGRATE REPORTER PLASMID - CYC Gibson overlaps-->
 
<!--INTEGRATE REPORTER PLASMID - CYC Gibson overlaps-->
             <section id="synthesize_promoters" class="panel">  
+
             <section id="PCRoverlaps_prom" class="panel">
 
             <h1><small>Integrate reporter plasmid</small></br>Add Gibson overlaps by PCR</h1>
 
             <h1><small>Integrate reporter plasmid</small></br>Add Gibson overlaps by PCR</h1>
             <p>We amplified the promoters CYC_0, 1, 2, 3 by PCR adding the Gibson overlaps in order to assemble each fragment in the linearised plasmid pCYC1m_yeGFP.The PCR was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/7/74/EPF_Lausanne_Add_Gibson_overlaps_to_CYC-1%2C2%2C3.pdf">protocol</a>.</p>
+
             <p>We amplified the promoters CYC_0, 1, 2, 3 by PCR adding the Gibson overlaps in order to assemble each fragment in the linearised plasmid pCYC1m_yeGFP.</p>
  
 
             <h2>Materials and methods</h2>
 
             <h2>Materials and methods</h2>
 
             <ul>
 
             <ul>
                 <li>Polymerase Chain Reaction</li>
+
                 <li><b>PCR</b> (cf. Protocols). The PCR was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/7/74/EPF_Lausanne_Add_Gibson_overlaps_to_CYC-1%2C2%2C3.pdf">procedure</a>. The PCR for CYC_3 was repeated a <a target="_blank" href="https://static.igem.org/mediawiki/2015/3/3e/EPF_Lausanne_NotebookYeast_AddGibsonOverlapsCYC3_2nd.pdf">second time</a>, and a <a target="_blank" href="https://static.igem.org/mediawiki/2015/9/9a/EPF_Lausanne_NotebookYeast_AddGibsonOverlapsCYC3_3rd.pdf">third time</a>, due to a frameshift detected by sequencing.</li>
 
             </ul>
 
             </ul>
  
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                     <figure>
 
                     <figure>
 
                         <a href="https://static.igem.org/mediawiki/2015/f/fd/EPF_Lausanne_CYC_promoters_with_gbs_overlaps.png"><img src="https://static.igem.org/mediawiki/2015/f/fd/EPF_Lausanne_CYC_promoters_with_gbs_overlaps.png" alt="CYC promoters" width="75%"></a>
 
                         <a href="https://static.igem.org/mediawiki/2015/f/fd/EPF_Lausanne_CYC_promoters_with_gbs_overlaps.png"><img src="https://static.igem.org/mediawiki/2015/f/fd/EPF_Lausanne_CYC_promoters_with_gbs_overlaps.png" alt="CYC promoters" width="75%"></a>
                         <figcaption>Fig.x - CYC promoters with gbs</figcaption>
+
                         <figcaption>Fig.3 - PCR of CYC promoters</figcaption>
 
                     </figure>
 
                     </figure>
 
                 </div>
 
                 </div>
 
                 <div class="col-md-6">
 
                 <div class="col-md-6">
                     <p>On the gel electrophoresis that we ran after PCR, we observe the three CYC fragments at the right height. These fragments are then used for the Gibson assembly in the plasmid pCYC_yeGFP.</p>
+
                     <p>On the gel electrophoresis that we ran after PCR, we observe the three CYC fragments at the right height (Fig.3). These fragments are then used for the Gibson assembly in the plasmid pCYC_yeGFP.</p>
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
 
             </section>
 
             </section>
  
 +
<!--INTEGRATE REPORTER PLASMID - Gibson assembly of CYC promoters-->
 +
            <section id="gibsonprom" class="panel">
 +
            <h1><small>Integrate reporter plasmid</small></br>Gibson assembly of CYC promoters</h1>
 +
            <p>The promoters CYC_0, 1, 2, 3 have overlaps from previous PCR. They were assembled in the linearised plasmid pCYC1m_yeGFP.</p>
  
 +
            <h2>Materials and methods</h2>
 +
            <ul>
 +
                <li><b>Gibson assembly</b> was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/7/74/EPF_Lausanne_NotebookYeast_GibsonAssemblyCYC.pdf">procedure</a>. The Gibson assembly for CYC_3 was repeated a <a target="_blank" href="https://static.igem.org/mediawiki/2015/4/41/EPF_Lausanne_NotebookYeast_GibsonAssemblyCYC3_2nd.pdf">second time</a>, and a <a target="_blank" href="https://static.igem.org/mediawiki/2015/c/c4/EPF_Lausanne_NotebookYeast_GibsonAssemblyCYC3_3rd.pdf">third time</a>.</li>
 +
                <li><b>Colony PCR </b> was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/e/e4/EPF_Lausanne_NotebookYeast_colonyPCR1.pdf">procedure</a>. The colony PCR was repeated a <a target="_blank" href="https://static.igem.org/mediawiki/2015/5/53/EPF_Lausanne_NotebookYeast_colonyPCR2.pdf">second time</a> for CYC1, a <a target="_blank" href="https://static.igem.org/mediawiki/2015/a/a2/EPF_Lausanne_NotebookYeast_colonyPCR3.pdf">third</a>, <a target="_blank" href="https://static.igem.org/mediawiki/2015/b/b9/EPF_Lausanne_NotebookYeast_colonyPCR4.pdf">fourth</a>, <a target="_blank" href="https://static.igem.org/mediawiki/2015/a/aa/EPF_Lausanne_NotebookYeast_colonyPCR5.pdf">fifth</a> and <a target="_blank" href="https://static.igem.org/mediawiki/2015/4/48/EPF_Lausanne_NotebookYeast_colonyPCR6.pdf">sixth</a> time for CYC3. </li>
 +
            </ul>
 +
 +
            <h2>Results</h2>
 +
            <div class="row">
 +
                <div class="col-md-6">
 +
                    <figure>
 +
                        <a href="https://static.igem.org/mediawiki/2015/9/90/EPF_Lausanne_NotebookYeast_colonyPCR1_results.png"><img src="https://static.igem.org/mediawiki/2015/9/90/EPF_Lausanne_NotebookYeast_colonyPCR1_results.png" alt="col PCR 1 results" width="75%"></a>
 +
                        <figcaption>Fig.4 - 1st colony PCR of CYC promoters</figcaption>
 +
                    </figure>
 +
                </div>
 +
                <div class="col-md-6">
 +
                    <p>The results of the Gibson assembly are given by a colony PCR. The amplicon should be 308 bp since we used primers f_Gbs_CYC and r_Gbs_CYC. We observe on Fig. 4 that CYC2 on lane 5 and CYC3 on lanes 8 and 9 migrated at the right height. These colonies can be sent to sequencing. Colony PCR was repeated to find CYC1.
 +
                    <br>After colony PCR, sequencing indicated a frameshift in the CYC3 construct. This is why we repeated the whole process, from the start, for CYC3. </p>
 +
                    <div class="col-md-6"></div>
 +
                </div>
 +
            </div>
 +
            </section>
  
  
<!--Integrate and express gRNAs -->
+
<!--Integrate and express gRNAs - Linearize ADH1 -->
             <section id="PCR-amplify_the_gRNAs_expressing_cassettes" class="panel">
+
             <section id="Linearize_p405ADH1" class="panel">
                 <h1><small>Integrate and express gRNAs</small></br>PCR-amplify the gRNA expressing cassettes</h1>
+
                 <h1><small>Integrate and express gRNAs</small></br>Linearize p405ADH1</h1>
                 <p>The gRNA expressing cassettes c3_0, c3_1, c3_2, c3_3 (activating sequences), c6_0, c6_1, c6_2, c6_3, (inhibiting sequences), c7_0, c7_1, c7_2, c7_3 (inhibiting sequences) were ordered together with the promoters CYC_0, CYC_1, CYC_2, CYC_3 promoters. The c3 gRNA expressing cassettes were synthesized along with their corresponding CYC promoter as individual G-Blocks, all other gRNAs were synthesized as individual G-Blocks. Four primers were used in order to PCR out or amplify the gRNAs and the promoters: f_IDT_tri, f_IDT_squ, r_IDT_dia and r_IDT_cir. For detailed reaction mixes, click here LIEN A INSERER</p>
+
                 <p>In order to test the effects of single gRNAs, we opted for a strong constitutive promoter - ADH1 (coming from our backbone plasmid, p405ADH1) - to be placed just before the gRNA expressing cassette.</p>
  
 
                 <h2>Materials and methods</h2>
 
                 <h2>Materials and methods</h2>
 
                 <ul>
 
                 <ul>
                     <li>Polymerase Chain Reaction</li>
+
                     <li><b>Polymerase Chain Reaction</b> (cf. Protocols). After glycerol stocks and minipreps, the PCR with primers f_Gbs_ADH1 and r_Gbs_ADH1 was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/9/94/EPF_Lausanne_NotebookYeast_linearADH1.pdf">procedure</a>.</li>
 
                 </ul>
 
                 </ul>
  
Line 215: Line 220:
 
                 <div class="row">
 
                 <div class="row">
 
                     <div class="col-md-6">
 
                     <div class="col-md-6">
                         <img src="https://static.igem.org/mediawiki/2015/f/f6/EPF_Lausanne_C6%2C_CYC_0_1_2.png" style="width:75%">
+
                         <figure>
                        <img src="https://static.igem.org/mediawiki/2015/1/1c/EPF_Lausanne_C7_0_1_2.png" style="width:75%">
+
                            <a href="https://static.igem.org/mediawiki/2015/5/56/EPF_Lausanne_NotebookYeast_p405ADH1_linear1.png"><img src="https://static.igem.org/mediawiki/2015/5/56/EPF_Lausanne_NotebookYeast_p405ADH1_linear1.png" alt="ADH1_Linearized" width="60%"></a>
                        <img src="https://static.igem.org/mediawiki/2015/1/10/EPF_Lausanne_C7_3.png" style="width:75%">  
+
                            <figcaption>Fig.6 - ADH1_Linearized</figcaption>
                         <img src="https://static.igem.org/mediawiki/2015/d/dc/EPF_Lausanne_CYC_3_c3_1_2_3.png" style="width:75%">  
+
                         </figure>
                         <img src="https://static.igem.org/mediawiki/2015/6/6a/EPF_Lausanne_C3_0.png" style="width:75%">
+
                    </div>
 +
                    <div class="col-md-6">
 +
                         <p><small> The size of p405ADH1 plasmid is 7.2 kbp. Altough it is not in frame with the ladder, a different migration rate is observed between the PCR products (p405ADH1 linearized) and the circular plasmid on the 10th lane. Therefore, we assumed that the PCR was successful.</small></p>
 +
                    </div>
 +
                </div>
 +
            </section>
  
                          
+
<!--Integrate and express gRNAs - SYNTHESIZE gRNA cassette-->
 +
            <section id="synthesize_gRNAs" class="panel">
 +
            <h1><small>Integrate and express gRNAs</small></br>Synthesize gRNA-expressing cassette</h1>
 +
            <div class="col-md-6">
 +
                <figure>
 +
                  <a href="https://static.igem.org/mediawiki/2015/c/c9/EPF_Lausanne_NotebookYeast_gRNA_designSource.png"><img src="https://static.igem.org/mediawiki/2015/c/c9/EPF_Lausanne_NotebookYeast_gRNA_designSource.png" alt="gRNA source design" width="60%"></a>
 +
                  <figcaption>Fig.7 - Diagram from a reference paper </figcaption>
 +
                </figure>
 +
            </div>
 +
            <p>The design of the gRNA-expressing cassettes is inspired by the article "Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells". The activating gRNA, c3, and the two repressing gRNAs, c6 and c7, were synthesized. Each gRNA is fused to the HH ribozyme on the 5' end, and to the HDV ribozyme on the 3' end.</p>
 +
 
 +
            <h2>Results</h2>
 +
            <div class="row">
 +
                <div class="col-md-6">
 +
                    <figure>
 +
                    <img src="https://static.igem.org/mediawiki/2015/8/84/EPF_Lausanne_NotebookYeast_gRNA_c3_0.png" style="width:60%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/e/e5/EPF_Lausanne_NotebookYeast_gRNA_c3_1.png" style="width:60%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/6/67/EPF_Lausanne_NotebookYeast_gRNA_c3_2.png" style="width:60%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/e/ed/EPF_Lausanne_NotebookYeast_gRNA_c3_3.png" style="width:60%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/2/2f/EPF_Lausanne_NotebookYeast_gRNA_c6_0.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/c/c6/EPF_Lausanne_NotebookYeast_gRNA_c6_1.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/7/7e/EPF_Lausanne_NotebookYeast_gRNA_c6_2.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/c/ca/EPF_Lausanne_NotebookYeast_gRNA_c6_3.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/0/04/EPF_Lausanne_NotebookYeast_gRNA_c7_0.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/7/7f/EPF_Lausanne_NotebookYeast_gRNA_c7_1.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/8/85/EPF_Lausanne_NotebookYeast_gRNA_c7_2.png" style="width:89%">
 +
                    <img src="https://static.igem.org/mediawiki/2015/f/f1/EPF_Lausanne_NotebookYeast_gRNA_c7_3.png" style="width:89%">
 +
                    <figcaption>Fig.8 - Synthesized gRNA-expressing cassettes</figcaption>
 +
                    </figure>
 +
                </div>
 +
                <div class="col-md-6">
 +
                    <p>According to Fig.8, we synthesized the activating gRNA cassette c3 and the two repressing gRNA cassettes c6 and c7. Each of these gRNAs: c3, c6, c7, is in four exemplaries. The numbering 0, 1, 2, 3, corresponds to promoter CYC_0, CYC_1, CYC_2, CYC_3.
 +
                    </p>
 +
                </div>
 +
            </div>
 +
            </section>
 +
 
 +
<!--Integrate and express gRNAs - gRNAs Gibson overlaps -->
 +
            <section id="PCRoverlaps_gRNAs" class="panel">
 +
                <h1><small>Integrate and express gRNAs</small></br>Add Gibson overlaps by PCR</h1>
 +
                <p>The gRNA-expressing cassettes, c3_0, c3_1, c3_2, c3_3, c6_0, c6_1, c6_2, c6_3 and c7_0, c7_1, c7_2, c7_3, were synthesized. In this step, overlaps for Gibson assembly were added by PCR.<br> In order to verify the expression of the gRNAs cassettes, we used fluorescent protein DsRed2 as a reporter gene. In parallel to the gRNA cassettes, the DsRed2 gene was PCR-extracted from plasmid CMVp-dsRed2-Triplex-HHRibo-gRNA1-HDVRibo-pA from Addgene. Overlaps for Gibson assembly were added by PCR. A synthetic polyA tail followed by a part of the Hammerhead ribozyme sequence was included in the reverse primer.</p>
 +
 
 +
                <h2>Materials and methods</h2>
 +
                <ul>
 +
                    <li><b>Polymerase Chain Reaction</b> (cf. Protocols). Gibson overlaps of DsRed2, c3, c6 and c7 cassettes were added according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/2/21/EPF_Lausanne_NotebookYeast_PCRoverlaps_DsRed2_c3_c6_c7.pdf">procedure</a>. As we can see from the gel electrophoresis (Results), we observe no amplicon for c3_0, c3_3 and DsRed2. This PCR had to be repeated (several times) for the three missing fragments.</li>
 +
                    <li>A second PCR was necessary to add specific overlaps to c3 and c6. <a target="_blank" href="https://static.igem.org/mediawiki/2015/e/eb/EPF_Lausanne_NotebookYeast_2ndPCRoverlaps_DsRed2_c3_c6_c7.pdf">Here</a> is the procedure for this second PCR.</li>
 +
                </ul>
 +
 
 +
                <h2>Results</h2>
 +
                <div class="row">
 +
                    <div class="col-md-6">
 +
                         <a href="https://static.igem.org/mediawiki/2015/7/70/EPF_Lausanne_NotebookYeast_1stPCRoverlaps_DsRed2_c3_c6_c7.png"><img src="https://static.igem.org/mediawiki/2015/7/70/EPF_Lausanne_NotebookYeast_1stPCRoverlaps_DsRed2_c3_c6_c7.png" alt="Figure 9a" style="width:30%"></a>
 +
                        <a href="https://static.igem.org/mediawiki/2015/8/89/EPF_Lausanne_NotebookYeast_1stPCRoverlaps_DsRed2_c3_c6_c7_2.png"><img src="https://static.igem.org/mediawiki/2015/8/89/EPF_Lausanne_NotebookYeast_1stPCRoverlaps_DsRed2_c3_c6_c7_2.png" alt="Figure 9b" style="width:30%"></a>
 +
                        <figcaption>Fig.9 - 1st PCR of gRNA cassettes and DsRed2 in order to add Gibson overlaps</figcaption>
 
                     </div>
 
                     </div>
 +
 
                     <div class="col-md-6">
 
                     <div class="col-md-6">
                         <p>Each amplicon (gRNA expressing cassette or CYC promoter) is 250 bp long (the exact length can vary by max two bp depending on the primers used). Several PCRs were required for amplification, we only show the gels corresponding to the PCR products we kept.</br>
+
                         <p>From the gel electrophoresis, we observe that almost every fragment migrated at the right height (207 bp for c3, 208 bp for c6, 308 bp for c7); except c3_0, c3_3 and DsRed2 whose PCR will be repeated.
 +
                        <br>The second PCR produced the amplicons of c3 and c6, that are ready for the Gibson assembly.</p>
  
                        Fig...: c6_0, c6_1, c6_2, c6_3, CYC_0, CYC_1, CYC_2</br>
 
                        Fig...: c7_0, c7_1, c7_2</br>
 
                        Fig...: c7_3</br>
 
                        Fig...: CYC_3, c3_1, c3_2, c3_3</br>
 
                        Fig...: c3_0</br></p>
 
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
 
             </section>
 
             </section>
 +
<!--INTEGRATE and express gRNAs - Gibson assembly of gRNA cassettes-->
 +
            <section id="gibson_gRNAs" class="panel">
 +
            <h1><small>Integrate and express gRNAs</small></br>Gibson assembly of gRNA cassettes</h1>
 +
            <p>The gRNA cassettes c3_0, c3_1, c3_2, c6_0, c6_1, c6_2, c7_0, c7_1, c7_2 have overlaps from previous PCR. They were assembled in the linearised plasmid p405ADH1.
  
 +
            <h2>Materials and methods</h2>
 +
            <ul>
 +
                <li><b>Gibson assembly</b> was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/1/1b/EPF_Lausanne_NotebookYeast_gRNAsGbsAssembly.pdf">procedure</a>. The Gibson assembly was repeated a <a target="_blank" href="https://static.igem.org/mediawiki/2015/8/89/EPF_Lausanne_NotebookYeast_gRNAsGbsAssembly_2nd.pdf">second time</a> for the missing A0, A2 and AI2.</li>
 +
                <li><b>Colony PCR </b> was performed according to the following <a target="_blank" href="https://static.igem.org/mediawiki/2015/b/b4/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs1.pdf">procedure</a>. The colony PCR was repeated a <a target="_blank" href="https://static.igem.org/mediawiki/2015/4/40/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs2.pdf">second time</a>, a <a target="_blank" href="https://static.igem.org/mediawiki/2015/3/3a/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs3.pdf">third</a>, <a target="_blank" href="https://static.igem.org/mediawiki/2015/9/96/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs4.pdf">fourth</a>, <a target="_blank" href="https://static.igem.org/mediawiki/2015/2/27/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs5.pdf">fifth</a>, a <a target="_blank" href="https://static.igem.org/mediawiki/2015/a/a1/EPF_Lausanne_NotebookYeast_colonyPCRgRNAs6.pdf">sixth</a> time and several other times. </li>
 +
            </ul>
  
<!--PCR out DsRed2 -->
+
            <h2>Results</h2>
             <section id="PCR_out_DsRed2" class="panel">
+
            <div class="row">
                 <h1><small>Integrate and express gRNAs</small></br>PCR out DsRed2</h1>
+
                <div class="col-md-6">
                 <p>In order to verify the expression of the gRNAs cassettes, we used fluorescent protein DsRed2 as a reporter gene. It was PCRed out from the plasmid CMVp-dsRed2-Triplex-HHRibo-gRNA1-HDVRibo-pA. A synthetic polyA tail followed by a part of the Hammerhead ribozyme sequence was added on the reverse primer.</p>
+
                    <figure>
 +
                        <a href="https://static.igem.org/mediawiki/2015/e/e5/EPF_Lausanne_NotebookYeast_p405ADH1.png"><img src="https://static.igem.org/mediawiki/2015/e/e5/EPF_Lausanne_NotebookYeast_p405ADH1.png" alt="p405ADH1" width="50%"></a>
 +
                    </figure>
 +
                </div>
 +
                <div class="col-md-6">
 +
                    <div class="row">
 +
                    The results of the Gibson assembly were analysed by colony PCR. Subsequently, the sequencing confirmed we had the desired constructs.
 +
                    <br>A0 stands for DsRed2-polyA-HH ribozyme-c3_0-HDV ribozyme.
 +
                    </div>
 +
                    <div class="row">
 +
                        <a href="https://static.igem.org/mediawiki/2015/f/f7/EPF_Lausanne_NotebookYeast_gRNAsAssemblyA0.png"><img src="https://static.igem.org/mediawiki/2015/f/f7/EPF_Lausanne_NotebookYeast_gRNAsAssemblyA0.png" alt="p405ADH1_DsRed2_A0" width="70%"></a>
 +
                    </div> <div class="row">
 +
                    <br>I0 stands for DsRed2-polyA-HH ribozyme-c6_0-HDV ribozyme-HH ribozyme-c7_0-HDV ribozyme.
 +
                    </div><div class="row">
 +
                        <a href="https://static.igem.org/mediawiki/2015/8/88/EPF_Lausanne_NotebookYeast_gRNAsAssemblyI0.png"><img src="https://static.igem.org/mediawiki/2015/8/88/EPF_Lausanne_NotebookYeast_gRNAsAssemblyI0.png" alt="p405ADH1_DsRed2_I0" width="70%" align="right"></a>
 +
                    </div> <div class="row">
 +
                    <br>AI0 stands for DsRed2-polyA-HH ribozyme-c3_0-HDV ribozyme-HH ribozyme-c6_0-HDV ribozyme-HH ribozyme-c7_0-HDV ribozyme.</p>
 +
                    </div>
 +
                    <div class="row">
 +
                        <a href="https://static.igem.org/mediawiki/2015/7/73/EPF_Lausanne_NotebookYeast_gRNAsAssemblyAI0.png"><img src="https://static.igem.org/mediawiki/2015/7/73/EPF_Lausanne_NotebookYeast_gRNAsAssemblyAI0.png" alt="p405ADH1_DsRed2_AI0" width="70%"></a>
 +
                    </div>
 +
                </div>
 +
            </div>
 +
            </section>
 +
 
 +
 
 +
            <!--INTEGRATE REPORTER PLASMID - Integration-->
 +
             <section id="integrate" class="panel">
 +
                 <h1 id = "activation-repression"> <small>Measure activation - repression </small></br>Integrate CYC promoters and gRNAs</h1>
 +
                 <p>Each reporter sequence CYC_0, CYC_1, CYC_2, CYC_3 was integrated together with :
 +
                    <ul>
 +
                        <li> the corresponding A (activation), I (inhibition), AI (activation and inhibition) among exemplary 0, 1, 2, 3. This was to test activation and inhibition of the appropriate promoter CYC.</li>
 +
                        <li> any gRNA that doesn't correspond to the appropriate promoter, for example CYC_1 and A_0. This was to test orthogonality.</li>
 +
                        <li> no gRNA. This was to measure the basal level of the promoters. </li>
 +
                    </ul>
 +
                </p>
 +
                <p><font color="red">F</font><font color="ff3399">U</font><font color="9900cc">N</font> <font color="3333cc">F</font><font color="00cc66">A</font><font color="009900">C</font><font color="ff9900">T</font>: on September 8, ten days before wiki freeze, we changed our strain of yeast. The strain we used previously, YM4271, had a mutation on GAL4 gene, preventing its growth in galactose supplemented medium and preventing induction of GAL1 promoter.The new strain is W303.</p>
 +
                <p>We present our methods, both for the former strain and the more recent one. </p>
  
 
                 <h2>Materials and methods</h2>
 
                 <h2>Materials and methods</h2>
 
                 <ul>
 
                 <ul>
                     <li>Miniprep</li>
+
                     <li>Integration (cf. Protocols)</li>
                     <li>Polymerase Chain Reaction</li>
+
                     <ol>
 +
                        <li>Plasmids were linearized with restriction enzyme EagI-HF, according to a <a target="_blank" href="https://static.igem.org/mediawiki/2015/0/0f/EPF_Lausanne_NotebookYeast_integ_linear1.pdf">first</a>, <a target="_blank" href="https://static.igem.org/mediawiki/2015/0/01/EPF_Lausanne_NotebookYeast_integ_linear2.pdf">second</a> and <a target="_blank" href="https://static.igem.org/mediawiki/2015/e/ef/EPF_Lausanne_NotebookYeast_integ_linear3.pdf">third</a> procedure.
 +
                        <br>With the former strain YM4271, we executed three different integrations. Here are the descriptions of the <a target="_blank" href="https://static.igem.org/mediawiki/2015/4/47/EPF_Lausanne_NotebookYeast_integ1.pdf">first</a> integration of CYC_0, the<a target="_blank" href="https://static.igem.org/mediawiki/2015/0/00/EPF_Lausanne_NotebookYeast_integ2.pdf"> second</a> for CYC_1 and CYC_2, and the <a target="_blank" href="https://static.igem.org/mediawiki/2015/b/b0/EPF_Lausanne_NotebookYeast_integ3.pdf"> third</a> for CYC_3.
 +
                        <br>After integration, the yeasts were spread on selection plates. Single colonies were prepared for analysis at the plate reader, untill we realized there was a galactose mutation in the yeast strain.</li>
 +
 
 +
                        <li>With strain W303, plasmids were linearized (<a target="_blank" href="https://static.igem.org/mediawiki/2015/6/6c/EPF_Lausanne15_NotebookYeast_integW303linear.pdf">procedure</a>). All the integration were as described <a target="_blank" href="https://static.igem.org/mediawiki/2015/3/34/EPF_Lausanne15_NotebookYeast_integW303.pdf"> here</a>.</li>
 +
                    </ol>
 
                 </ul>
 
                 </ul>
  
 
                 <h2>Results</h2>
 
                 <h2>Results</h2>
 
                 <div class="row">
 
                 <div class="row">
 +
 +
                <div class="col-md-6">
 +
                    <figure>
 +
                        <a href="https://static.igem.org/mediawiki/2015/5/5b/EPF_Lausanne_NotebookYeast_integCYC0_plates.jpeg"><img src="https://static.igem.org/mediawiki/2015/5/5b/EPF_Lausanne_NotebookYeast_integCYC0_plates.jpeg" alt="platesCYC0" width="75%"></a>
 +
                        <a href="https://static.igem.org/mediawiki/2015/f/f3/EPF_Lausanne_NotebookYeast_integCYC1_plates.jpeg"><img src="https://static.igem.org/mediawiki/2015/f/f3/EPF_Lausanne_NotebookYeast_integCYC1_plates.jpeg" alt="platesCYC1" width="75%"></a>
 +
 +
                    </figure>
 +
                </div>
 +
 
                     <div class="col-md-6">
 
                     <div class="col-md-6">
 +
                        <p>After integration, the yeasts were spread on selection plates.</p>
 
                         <figure>
 
                         <figure>
                            <a href="https://static.igem.org/mediawiki/2015/5/5f/EPF_Lausanne_DsRed2_polyA_HH1.png"><img src="https://static.igem.org/mediawiki/2015/5/5f/EPF_Lausanne_DsRed2_polyA_HH1.png" alt="DsRed2 polyA" width="75%"></a>
+
                        <a href="https://static.igem.org/mediawiki/2015/7/77/EPF_Lausanne_NotebookYeast_integCYC2_plates.jpeg"><img src="https://static.igem.org/mediawiki/2015/7/77/EPF_Lausanne_NotebookYeast_integCYC2_plates.jpeg" alt="platesCYC2" width="75%"></a>
                            <figcaption>Fig.x - DsRed2 polyA HH1</figcaption>
+
                        <a href="https://static.igem.org/mediawiki/2015/4/4e/EPF_Lausanne_NotebookYeast_integCYC3_plates.jpeg"><img src="https://static.igem.org/mediawiki/2015/4/4e/EPF_Lausanne_NotebookYeast_integCYC3_plates.jpeg" alt="platesCYC3" width="45%"></a>
                        </figure> 
+
                         </figure>
                    </div>
+
                    <div class="col-md-6">
+
                        <p><small> The size of the DsRed2_polyA_HH1 amplicon is 750 bp. The plasmid on the gel is CMVp-dsRed2-Triplex-HHRibo-gRNA1-HDVRibo-pA.</br>
+
                         </small></p>
+
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
 
             </section>
 
             </section>
 +
 +
            <section id="integrate" class="panel">
 +
                <h1 id = "test_activ_inhib"> <small>Measure activation - repression </small></br>Test Activation/Inhibition</h1>
 +
 +
                <p>Once each construct was integrated, we prepared the 96-well plate for the measurement at the plate reader. The first step was to centrifuge the cells at 1800 rpm for 5 minutes. Once the supernatant was thrown, we washed it with water and centrifuge at 1800 rpm for 5 minutes again. The pellet was finally resuspended in 10 ml yeast minimal media (SD medium) and 100 µl was put in each well (the disposition of the plate is shown <a href="https://static.igem.org/mediawiki/2015/3/3d/EPF_Lausanne_protocol_measure.pdf" target="blank">here</a>. Anhydro tetracycline (aTc) was added at different concentrations to induce the production of dCas9.</p>
 +
 +
            </section>
 +
 +
            <section id="integrate" class="panel">
 +
                <h1 id = "test_activ_inhib">Build logic gate</h1>
 +
 +
                <p>Now that transistors were created and characterized, we can link them to build a (bio)-logical gate. The assembly is separated in two steps: the building of the inputs, and the building of the gates. The design of the NAND gate is shown here:</p>
 +
 +
                <center>
 +
                    </br>
 +
                <figure>
 +
                  <img src="https://static.igem.org/mediawiki/2015/5/5d/EPF_Lausanne_NAND_Design.png" style="height:70%;width:70%;" />
 +
                  <figcaption>NAND gate design with three biological transistors.</figcaption>
 +
                </figure>
 +
                    </br>
 +
                </center>
 +
 +
                <h3>Assembly of the gate </h3>
 +
                <p>The building blocks of the gate (gRNAs under the control of CYC) were ordered on IDT and assemble using  <a href="https://static.igem.org/mediawiki/2015/9/96/EPF_Lausanne_Gibson_gates.pdf" target="blank">Gibson assembly</a>. We then made a colony PCR to find the gate and achieve to have a band at the desired height (1745 bp with primers f_Seq_gate and r_Seq_gate). Once the sequencing confirmed that the plasmid contains every fragments assembled, we integrated the gate into the yeast genome and focused on the inputs building.</p>
 +
 +
                <h3>Assembly of the inputs</h3>
 +
 +
                <p>As the NAND gate requires 2 inputs, we will need to change the selection marker for the ADH1 plasmid in order to have the same backbone with different markers. We chose to insert the KanMX marker (resistance to geneticin) in  <a href="https://static.igem.org/mediawiki/2015/f/f7/EPF_Lausanne_Gibson_Kana.pdf" target="blank">p405 ADH1 plasmid</a>. After PCRs and <a href="https://static.igem.org/mediawiki/2015/b/bd/EPF_Lausanne_Gibson_inputs.pdf" target="blank">Gibson assemblies</a> for the inputs, we did a colony PCR to find every expected inputs (as we planned to build two gates, the NAND and the NOR, we have 4 different inputs named as A1, A2, A1I2 and A2I1. A refers to an activation, I to an inhibition and 1/2 refers to the promoter CYC1/2). After this step, the inputs were integrated into the yeast genome. Unfortunately, due to a lack of time, we didn’t achieve to measure the ratios of the gate).</p>
 +
 +
            </section>
 +
 
         </div>
 
         </div>
    </div>
+
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Latest revision as of 03:57, 19 September 2015

EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits

saccharomyces cerevisiae

Note that all experiments were done by EPFL iGEM team members.

Express dCas9-VP64
Integrate pTPGI_dCas9_VP64

We received plasmid pTPGI_dCas9_VP64 from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas". After glycerol stocks and miniprep, we performed a restriction analysis to check the identity of our plasmid. We linearised the plasmid, in order to integrate it into yeast genome. Only our fourth trial to integrate the plasmid was successful.

Materials and methods

  • Glycerol stocks
  • Miniprep
  • Restriction analysis
  • Polymerase Chain Reaction
  • Yeast integration
  • For more details about our procedures, see here.

Results

dCas9 gel
Fig.1a - Restriction analysis of pTPGI_dCas9_VP64.

We used four different sets of enzymes for the restriction analysis. Linearized pTPGI_dCas9_VP64 is expected to be 10'987 bp. We observe that the gel (fig.1a) corresponds to the expected one.
The plasmid was linearised both with EagI HF and NotI HF prior to integration. We integrated each linearised plasmid to obtain two different yeast strains.

Integrate reporter plasmid
Linearise reporter plasmid

We received the plasmid pCYC1m_yeGFP from Addgene. The plasmid was found from the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas".

Materials and methods

  • PCR (cf. Protocols). After glycerol stocks and minipreps. we linearised the plasmid by PCR according to the following procedure.

Results

Linearized pCYC1m_yeGFP is expected to be 5'485 bp. Running an agarose gel electrophoresis allowed to verify that we had linearised the plasmid.

Integrate reporter plasmid
Synthesize promoters

From the article "Tunable and multifunctional eukaryotic transcription factors based on Crispr/Cas", we learnt that different regions on the promoters could lead to activation or inhibition when dCas9-VP64 was bound. We chose to modify the region of strongest activation, named c3, and the two regions that lead to the strongest inhibition, c6 and c7. We synthesized promoters CYC_0, CYC_1, CYC_2 and CYC_3. They only differ between one another by the three regions c3, c6 and c7. The promoter CYC_0 is the original promoter, already present in the plasmid pCYC1m_yeGFP.

Results

Fig. 2 - Synthesized CYC promoters

Four different promoters according to Fig. 2.

Integrate reporter plasmid
Add Gibson overlaps by PCR

We amplified the promoters CYC_0, 1, 2, 3 by PCR adding the Gibson overlaps in order to assemble each fragment in the linearised plasmid pCYC1m_yeGFP.

Materials and methods

  • PCR (cf. Protocols). The PCR was performed according to the following procedure. The PCR for CYC_3 was repeated a second time, and a third time, due to a frameshift detected by sequencing.

Results

CYC promoters
Fig.3 - PCR of CYC promoters

On the gel electrophoresis that we ran after PCR, we observe the three CYC fragments at the right height (Fig.3). These fragments are then used for the Gibson assembly in the plasmid pCYC_yeGFP.

Integrate reporter plasmid
Gibson assembly of CYC promoters

The promoters CYC_0, 1, 2, 3 have overlaps from previous PCR. They were assembled in the linearised plasmid pCYC1m_yeGFP.

Materials and methods

Results

col PCR 1 results
Fig.4 - 1st colony PCR of CYC promoters

The results of the Gibson assembly are given by a colony PCR. The amplicon should be 308 bp since we used primers f_Gbs_CYC and r_Gbs_CYC. We observe on Fig. 4 that CYC2 on lane 5 and CYC3 on lanes 8 and 9 migrated at the right height. These colonies can be sent to sequencing. Colony PCR was repeated to find CYC1.
After colony PCR, sequencing indicated a frameshift in the CYC3 construct. This is why we repeated the whole process, from the start, for CYC3.

Integrate and express gRNAs
Linearize p405ADH1

In order to test the effects of single gRNAs, we opted for a strong constitutive promoter - ADH1 (coming from our backbone plasmid, p405ADH1) - to be placed just before the gRNA expressing cassette.

Materials and methods

  • Polymerase Chain Reaction (cf. Protocols). After glycerol stocks and minipreps, the PCR with primers f_Gbs_ADH1 and r_Gbs_ADH1 was performed according to the following procedure.

Results

ADH1_Linearized
Fig.6 - ADH1_Linearized

The size of p405ADH1 plasmid is 7.2 kbp. Altough it is not in frame with the ladder, a different migration rate is observed between the PCR products (p405ADH1 linearized) and the circular plasmid on the 10th lane. Therefore, we assumed that the PCR was successful.

Integrate and express gRNAs
Synthesize gRNA-expressing cassette

gRNA source design
Fig.7 - Diagram from a reference paper

The design of the gRNA-expressing cassettes is inspired by the article "Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells". The activating gRNA, c3, and the two repressing gRNAs, c6 and c7, were synthesized. Each gRNA is fused to the HH ribozyme on the 5' end, and to the HDV ribozyme on the 3' end.

Results

Fig.8 - Synthesized gRNA-expressing cassettes

According to Fig.8, we synthesized the activating gRNA cassette c3 and the two repressing gRNA cassettes c6 and c7. Each of these gRNAs: c3, c6, c7, is in four exemplaries. The numbering 0, 1, 2, 3, corresponds to promoter CYC_0, CYC_1, CYC_2, CYC_3.

Integrate and express gRNAs
Add Gibson overlaps by PCR

The gRNA-expressing cassettes, c3_0, c3_1, c3_2, c3_3, c6_0, c6_1, c6_2, c6_3 and c7_0, c7_1, c7_2, c7_3, were synthesized. In this step, overlaps for Gibson assembly were added by PCR.
In order to verify the expression of the gRNAs cassettes, we used fluorescent protein DsRed2 as a reporter gene. In parallel to the gRNA cassettes, the DsRed2 gene was PCR-extracted from plasmid CMVp-dsRed2-Triplex-HHRibo-gRNA1-HDVRibo-pA from Addgene. Overlaps for Gibson assembly were added by PCR. A synthetic polyA tail followed by a part of the Hammerhead ribozyme sequence was included in the reverse primer.

Materials and methods

  • Polymerase Chain Reaction (cf. Protocols). Gibson overlaps of DsRed2, c3, c6 and c7 cassettes were added according to the following procedure. As we can see from the gel electrophoresis (Results), we observe no amplicon for c3_0, c3_3 and DsRed2. This PCR had to be repeated (several times) for the three missing fragments.
  • A second PCR was necessary to add specific overlaps to c3 and c6. Here is the procedure for this second PCR.

Results

Figure 9a Figure 9b
Fig.9 - 1st PCR of gRNA cassettes and DsRed2 in order to add Gibson overlaps

From the gel electrophoresis, we observe that almost every fragment migrated at the right height (207 bp for c3, 208 bp for c6, 308 bp for c7); except c3_0, c3_3 and DsRed2 whose PCR will be repeated.
The second PCR produced the amplicons of c3 and c6, that are ready for the Gibson assembly.

Integrate and express gRNAs
Gibson assembly of gRNA cassettes

The gRNA cassettes c3_0, c3_1, c3_2, c6_0, c6_1, c6_2, c7_0, c7_1, c7_2 have overlaps from previous PCR. They were assembled in the linearised plasmid p405ADH1.

Materials and methods

  • Gibson assembly was performed according to the following procedure. The Gibson assembly was repeated a second time for the missing A0, A2 and AI2.
  • Colony PCR was performed according to the following procedure. The colony PCR was repeated a second time, a third, fourth, fifth, a sixth time and several other times.

Results

p405ADH1
The results of the Gibson assembly were analysed by colony PCR. Subsequently, the sequencing confirmed we had the desired constructs.
A0 stands for DsRed2-polyA-HH ribozyme-c3_0-HDV ribozyme.
p405ADH1_DsRed2_A0

I0 stands for DsRed2-polyA-HH ribozyme-c6_0-HDV ribozyme-HH ribozyme-c7_0-HDV ribozyme.
p405ADH1_DsRed2_I0

AI0 stands for DsRed2-polyA-HH ribozyme-c3_0-HDV ribozyme-HH ribozyme-c6_0-HDV ribozyme-HH ribozyme-c7_0-HDV ribozyme.

p405ADH1_DsRed2_AI0

Measure activation - repression
Integrate CYC promoters and gRNAs

Each reporter sequence CYC_0, CYC_1, CYC_2, CYC_3 was integrated together with :

  • the corresponding A (activation), I (inhibition), AI (activation and inhibition) among exemplary 0, 1, 2, 3. This was to test activation and inhibition of the appropriate promoter CYC.
  • any gRNA that doesn't correspond to the appropriate promoter, for example CYC_1 and A_0. This was to test orthogonality.
  • no gRNA. This was to measure the basal level of the promoters.

FUN FACT: on September 8, ten days before wiki freeze, we changed our strain of yeast. The strain we used previously, YM4271, had a mutation on GAL4 gene, preventing its growth in galactose supplemented medium and preventing induction of GAL1 promoter.The new strain is W303.

We present our methods, both for the former strain and the more recent one.

Materials and methods

  • Integration (cf. Protocols)
    1. Plasmids were linearized with restriction enzyme EagI-HF, according to a first, second and third procedure.
      With the former strain YM4271, we executed three different integrations. Here are the descriptions of the first integration of CYC_0, the second for CYC_1 and CYC_2, and the third for CYC_3.
      After integration, the yeasts were spread on selection plates. Single colonies were prepared for analysis at the plate reader, untill we realized there was a galactose mutation in the yeast strain.
    2. With strain W303, plasmids were linearized (procedure). All the integration were as described here.

Results

platesCYC0 platesCYC1

After integration, the yeasts were spread on selection plates.

platesCYC2 platesCYC3

Measure activation - repression
Test Activation/Inhibition

Once each construct was integrated, we prepared the 96-well plate for the measurement at the plate reader. The first step was to centrifuge the cells at 1800 rpm for 5 minutes. Once the supernatant was thrown, we washed it with water and centrifuge at 1800 rpm for 5 minutes again. The pellet was finally resuspended in 10 ml yeast minimal media (SD medium) and 100 µl was put in each well (the disposition of the plate is shown here. Anhydro tetracycline (aTc) was added at different concentrations to induce the production of dCas9.

Build logic gate

Now that transistors were created and characterized, we can link them to build a (bio)-logical gate. The assembly is separated in two steps: the building of the inputs, and the building of the gates. The design of the NAND gate is shown here:


NAND gate design with three biological transistors.

Assembly of the gate

The building blocks of the gate (gRNAs under the control of CYC) were ordered on IDT and assemble using Gibson assembly. We then made a colony PCR to find the gate and achieve to have a band at the desired height (1745 bp with primers f_Seq_gate and r_Seq_gate). Once the sequencing confirmed that the plasmid contains every fragments assembled, we integrated the gate into the yeast genome and focused on the inputs building.

Assembly of the inputs

As the NAND gate requires 2 inputs, we will need to change the selection marker for the ADH1 plasmid in order to have the same backbone with different markers. We chose to insert the KanMX marker (resistance to geneticin) in p405 ADH1 plasmid. After PCRs and Gibson assemblies for the inputs, we did a colony PCR to find every expected inputs (as we planned to build two gates, the NAND and the NOR, we have 4 different inputs named as A1, A2, A1I2 and A2I1. A refers to an activation, I to an inhibition and 1/2 refers to the promoter CYC1/2). After this step, the inputs were integrated into the yeast genome. Unfortunately, due to a lack of time, we didn’t achieve to measure the ratios of the gate).

EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits