Team:Gothenburg-Sweden/Project

From 2010.igem.org

(Difference between revisions)
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<title>Chalmers University of Technology</title>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#intro">Introduction</a>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#cth">CHALMERS</a></li>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#svs">Supervisors</a></li>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#sts">Students</a>
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                              <div class="Title1">FUSS</div>
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                                            <a href="#">What's all about?</a>
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                                            <a href="#">Background</a>
 +
                                            <a href="#">Protein Fusion</a>
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                                            <a href="#">Methods</a>
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                                            <a href="#">Preliminary Results</a>
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                                  </div>
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<li><a href="http://2010.igem.org/Team:Gothenburg-Sweden">Home</a></li>                 
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<li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project">Project</a></li>
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                  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Lab_Note">Lab Note </a></li>
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                  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Results">Results</a></li>
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  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us">About Us</a></li>
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  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Sponsors">Sponsors</a></li>
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                  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></li>
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<td><span class="text1">The project </span></td>
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<td>Synthetic readout of cellular stress</td>
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<td>&nbsp;</td>
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                            <tr> <td>  <ul>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#aim">Aim</a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#bkg">Theoretic background</a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#method">Methods</a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#tech">Techniques</a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#snf1">SNF1 &amp; AMPK </a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#bricks">Biobricks</a></li>
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                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#app">Possible Applications</a></li>
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<td><p>The conceptual idea is to use the conformational change in the SNF1 protein complex to establish a FRET (Förster Resonance Energy Transfer) system for cellular stress detection. There are two chromophores tagged at  appropriate locations and upon undergoing the conformational change, they come in close  proximity such that the emission energy from one can excite the other, thus  resulting in different emission energy. There are two possibilities to be  tested: <br><br>1. To fuse the chromophores to the subunits  of the Snf1 complex to build an active readout of the conformational change <br>
+
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                      2. To fuse the chromophores to a short  peptide (SAMS peptide) that can be phosphorylated by Snf1 and is commonly used  as a read-out of Snf1 activity. </p> <br></td>
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if(false == $(this).next().is(':visible')) {
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<b>• Working package 1: Find positions for fluorescent markers in SNF1</b> <br>
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$('#accordion > ul').slideUp(300);
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For WP1 all present information about the protein complex is utilized, so that the fluorescent tags do not interfere with active sites or evolutionary conserved regions. Two alternatives should be investigated and presented with regard to present information and distance between fluorophores. The working package is ended with a 3D modeling of the tagging suggestions to further investigate functionality.<br><br>
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}
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<b>• Working Package 2: Decide what fluorescent protein to use</b><br>
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$(this).next().slideToggle(300);
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To apply FRET a compatible fluorphore pair is necessary. Also, efficiency and duration in respect to e.g. photonic bleaching should be taken into consideration.<br><br>
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});
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<b>• Working package 3: Find DNA sequence for SAMS-peptide</b><br>
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Beside the two tagging alternative from WP1 a SAMS-peptide will be used. Both ends will be tagged with fluorophores and conformational change should be indicated with FRET-signal during conformational change at phophorylation by active SNF1.<br><br>
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<b>• Working package 4: Decide on plasmid backbone</b><br>
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The plasmid containing fusion protein should be able to amplify in E.coli and also contain a strong promoter for protein expression in yeast. Use VectorNTI to find good alternatives and locate RE sites.<br><br>
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<b>• Working package 5: Design primers for fusion PCR</b><br>
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When WP 1-4 is finished the primer design can be initiated. Primers should be designed so that they have a high melting temperature, preferably around 60°C, with at least 20 bp homology with each side that should be fused. Primers at utter end of the fusion proteins should include restriction enzyme sites with GGCC repetition at the end. After rigorous proofreading the primers should be ordered together with a primer representing the SAMS peptide.<br><br>
+
-
<b>• Working package 6: Acquire plasmid backbone for transfection with fusion protein</b><br>
+
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Look up how the plasmid backbone from WP4 can be acquired. If it is a common backbone it should be avaible in the plasmid bank at the laboratory, otherwise it should be ordered.<br><br>
+
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<b>• Working package 7: Perform fusion PCR</b><br>
+
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When the primers from WP5 has arrived the fusion PCR can be initiated. As a template for the protein subunits in SNF1 genomic DNA from yeast should be used, this should be avaible at the laboratory, and as template for fluorescent proteins dried DNA provided by iGEM will be used. Create a PCR mastermix that includes all ingredients except the DNA template. Each fusion is run in five steps according to the manual and each step is analyzed on agar gel so that the correct fragments are produced.<br><br>
+
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<b>• Working package 8: Ligate insert into plasmids</b><br>
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$('#accordion > ul:eq(0)').show();
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After WP7 is successful the fusion protein should be inserted into the plasmid backbone. Use restriction enzymes as decided in WP6 and follow ligation protocol. Afterwards the plasmids should be purified with miniprep, they should be cut again and put on a gel to verify that the insert was successful.<br> <br>
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<b>• Working package 9: Amplify transfection plasmids</b><br>
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After WP8 the plasmid need to be amplified before being tranfected into yeast. Tranfect  E.coli and amplify over night. Purify the amplified plasmids with a miniprep kit.<br><br>
+
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<b>• Working package 10: Sporulate diploid yeast strains to acquire Snf1 deletion mutants</b><br>
+
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Grow diploid yeast strains with Snf1 deletions on sporulation plats to acquire haploid deletion mutants. Use protocol to clear the population from diploids and unwanted haploids. <br><br>
+
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<b>• Working package 11: Transfect yeast with tagged fusion protein</b><br>
+
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After WP9-10 the hapoloid yeast deletion strain should be tranfected with the fusion protein plasmid. When the yeast has recovered from transfection the strain should be grown on sucrose overnight to show transfection result.<br><br>
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<b>• Working package 12: Apply FRET and analyze results</b><br>
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By using a microscopy with FRET set up the success of previous WP can be concluded from the presence or absence of a FRET signal. Analyze results and make conclusions together with Marcus Wilhelmsson.<br><br>
+
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<b>• Working package 13:Write report</b><br>
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-
WP 13 is running alongside with the other WPs during the whole project. Initially aims and theory is the major work load and as the project progress results and analysis claims the major part of this WP.<br><br>
+
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<b>• Working package 14: Apply for funding</b><br>
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Also running alongside the other WPs. Funding is initially applied at science funding committees and later, as there are results to be presented, at major companies interested in the possibilities presented by this project. Funding should cover laboratory expenses, travel to Boston and team t-shirts.<br><br></td></tr>
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<td class="text5">safety questions </td>
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  <td> <p><b>Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?</b><br>
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                  No, since the yeast strains we work with are derived from harmless bakers yeast an none of the modifications have unknown or harmful consequences for anything else than the organism itself there is no safety issues with the project organism as such. Plasmid amplification in E.coli requiers a selection marker, ampicillin resistance in our case, which pose a safety issue regarding environmental safety but this is easily avoided by following laboration protocols regarding keeping a clean working environment and sterilization of organic waste.<br><br>
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                <b>Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</b><br>
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                As mentioned above our device contain an ampicillin marker for amplification in E.coli. There could be issues if transfected cells are allowed to be spread outside the controlled laboratory environment. But working with ampicillin resistance as an selection marker is a common procedure and safety protocolls for this kind of work is readilly avaible. This will be regarded when we register our device to iGEM.<br><br>
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                <b>Is there a local biosafety group, committee, or review board at your institution? </b><br>
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                No, when working with synthetic biology at Chalmers we follow regulations set up by the Swedish Work Environment Authority. They set up protocols how chemicals and genetically modified material should be treated and what is demanded from an working environment to be permitted with this kind of labor.<br><br>
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      <p>&nbsp;</p></td>
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    <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden">Home</a></li>
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        onmouseout="mclosetime()"  >Project</a>
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        <a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project">Description</a>
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        <a href="http://2010.igem.org/Team:Gothenburg-Sweden/Lab_Note">Lab Notes</a>
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</table>
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        <a href="http://2010.igem.org/Team:Gothenburg-Sweden/Results">Results</a>
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    <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us"
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<td align="center" class="style1"><a href="http://2010.igem.org/Team:Gothenburg-Sweden">Home</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us">About us </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.chalmers.se/en/">Chalmers</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://2010.igem.org/Team:Gothenburg-Sweden/Sponsors">Sponsors</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></td>
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<a href="#">Chalmers University of Technology</a>
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        <a href="#">Supervisors</a>
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<td align="center" class="style1">Design in Chalmers, Gothenburg, Sweden </td>
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        <a href="#">Students</a>
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    <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Sponsors">Sponsors</a></li>
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    <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></li>
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                  <ul>  
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#aim">Aim</a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#bkg">Theoretic background</a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#method">Methods</a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#tech">Techniques</a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#snf1">SNF1 &amp; AMPK </a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#bricks">Biobricks</a></li>
 +
                                      <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project/more#app">Possible Applications</a></li>  
 +
                  </ul>  
 +
                       
 +
                         
 +
                            <div id="myTitle">Project Description </div>
 +
                           
 +
                            <p>The conceptual idea is to use the conformational change in the SNF1 protein complex to establish a FRET (Förster Resonance Energy Transfer) system for cellular stress detection. There are two chromophores tagged at  appropriate locations and upon undergoing the conformational change, they come in close  proximity such that the emission energy from one can excite the other, thus  resulting in different emission energy. There are two possibilities to be  tested: <br><br>1. To fuse the chromophores to the subunits  of the Snf1 complex to build an active readout of the conformational change <br>
 +
                      2. To fuse the chromophores to a short  peptide (SAMS peptide) that can be phosphorylated by Snf1 and is commonly used  as a read-out of Snf1 activity. </p> <br>
 +
 +
 +
 +
<ul> <li><p> <strong>Working package 1: Find positions for fluorescent markers in SNF1 </strong><br>
 +
For WP1 all present information about the protein complex is utilized, so that the fluorescent tags do not interfere with active sites or evolutionary conserved regions.  Two alternatives should be investigated and presented with regard to present information and distance between fluorophores. The working package is ended with a 3D modeling of the tagging suggestions to further investigate functionality.</p></li>
 +
    <li><p><strong>Working Package 2: Decide what fluorescent protein to use</strong><br>
 +
To apply FRET a compatible fluorphore pair is necessary. Also, efficiency and duration in respect to e.g. photonic bleaching should be taken into consideration.</p></li>
 +
<li><p><strong>Working package 3: Find DNA sequence for SAMS-peptide</strong><br>
 +
Beside the two tagging alternative from WP1 a SAMS-peptide will be used. Both ends will be tagged with fluorophores and conformational change should be indicated with FRET-signal during conformational change at phophorylation by active SNF1.</p></li>
 +
<li><p><strong> Working package 4: Decide on plasmid backbone</strong><br>
 +
The plasmid containing fusion protein should be able to amplify in E.coli and also contain a strong promoter for protein expression in yeast. Use VectorNTI to find good alternatives and locate RE sites.</p></li>
 +
<li><p><strong>Working package 5: Design primers for fusion PCR</strong><br>
 +
When WP 1-4 is finished the primer design can be initiated. Primers should be designed so that they have a high melting temperature, preferably around 60°C, with at least 20 bp homology with each side that should be fused. Primers at utter end of the fusion proteins should include restriction enzyme sites with GGCC repetition at the end. After rigorous proofreading the primers should be ordered together with a primer representing the SAMS peptide.</p></li>
 +
<li><p><strong> Working package 6: Acquire plasmid backbone for transfection with fusion protein</strong><br>
 +
Look up how the plasmid backbone from WP4 can be acquired. If it is a common backbone it should be avaible in the plasmid bank at the laboratory, otherwise it should be ordered.</p></li>
 +
<li><p><strong>  Working package 7: Perform fusion PCR</strong><br>
 +
When the primers from WP5 has arrived the fusion PCR can be initiated. As a template for the protein subunits in SNF1 genomic DNA from yeast should be used, this should be avaible at the laboratory, and as template for fluorescent proteins dried DNA provided by iGEM will be used. Create a PCR mastermix that includes all ingredients except the DNA template. Each fusion is run in five steps according to the manual and each step is analyzed on agar gel so that the correct fragments are produced.</p></li>
 +
 +
<li><p><strong> Working package 8: Ligate insert into plasmids</strong><br>
 +
After WP7 is successful the fusion protein should be inserted into the plasmid backbone. Use restriction enzymes as decided in WP6 and follow ligation protocol. Afterwards the plasmids should be purified with miniprep, they should be cut again and put on a gel to verify that the insert was successful.<br> <br>
 +
<li><p><strong> Working package 9: Amplify transfection plasmids</strong><br>
 +
After WP8 the plasmid need to be amplified before being tranfected into yeast. Tranfect  E.coli and amplify over night. Purify the amplified plasmids with a miniprep kit.</p></li>
 +
<li><p><strong> Working package 10: Sporulate diploid yeast strains to acquire Snf1 deletion mutants</strong><br>
 +
Grow diploid yeast strains with Snf1 deletions on sporulation plats to acquire haploid deletion mutants. Use protocol to clear the population from diploids and unwanted haploids. <br><br>
 +
<li><p><strong> Working package 11: Transfect yeast with tagged fusion protein</strong><br>
 +
After WP9-10 the hapoloid yeast deletion strain should be tranfected with the fusion protein plasmid. When the yeast has recovered from transfection the strain should be grown on sucrose overnight to show transfection result.</p></li>
 +
<li><p><strong> Working package 12: Apply FRET and analyze results</strong><br>
 +
By using a microscopy with FRET set up the success of previous WP can be concluded from the presence or absence of a FRET signal. Analyze results and make conclusions together with Marcus Wilhelmsson.</p></li>
 +
<li><p><strong>Working package 13:Write report</strong><br>
 +
WP 13 is running alongside with the other WPs during the whole project. Initially aims and theory is the major work load and as the project progress results and analysis claims the major part of this WP.</p></li>
 +
<li><p><strong>Working package 14: Apply for funding</strong><br>
 +
Also running alongside the other WPs. Funding is initially applied at science funding committees and later, as there are results to be presented, at major companies interested in the possibilities presented by this project. Funding should cover laboratory expenses, travel to Boston and team t-shirts.</p></li>
 +
                      </ul>
 +
                   
 +
                 
 +
                          <div id="myTitle">Safety Questions </div>
 +
                       
 +
                    <ul>         
 +
                  <li><p><strong>Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?</strong><br>
 +
                  No, since the yeast strains we work with are derived from harmless bakers yeast an none of the modifications have unknown or harmful consequences for anything else than the organism itself there is no safety issues with the project organism as such. Plasmid amplification in E.coli requiers a selection marker, ampicillin resistance in our case, which pose a safety issue regarding environmental safety but this is easily avoided by following laboration protocols regarding keeping a clean working environment and sterilization of organic waste.</p></li>
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 +
                <li><p><strong>Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</strong><br>
 +
                As mentioned above our device contain an ampicillin marker for amplification in E.coli. There could be issues if transfected cells are allowed to be spread outside the controlled laboratory environment. But working with ampicillin resistance as an selection marker is a common procedure and safety protocolls for this kind of work is readilly avaible. This will be regarded when we register our device to iGEM.</p></li>
 +
 +
                <li><p><strong>Is there a local biosafety group, committee, or review board at your institution? </strong><br>
 +
                No, when working with synthetic biology at Chalmers we follow regulations set up by the Swedish Work Environment Authority. They set up protocols how chemicals and genetically modified material should be treated and what is demanded from an working environment to be permitted with this kind of labor.</p></li>
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                                          <p>11</p>
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                                          <div class="newsright"><a href="#">August 11, 2010</a>
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                                          <p> The PCR reaction from yesterday was checked on a gel. α should be ... </p>
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                                    <p>Göteborgs-Posten, a major daily newspaper in Sweden with the second largest national circulation, published an article involving the interview with our team...
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Revision as of 13:39, 1 October 2010

Chalmers University of Technology

Team
FUSS

Project Description

The conceptual idea is to use the conformational change in the SNF1 protein complex to establish a FRET (Förster Resonance Energy Transfer) system for cellular stress detection. There are two chromophores tagged at appropriate locations and upon undergoing the conformational change, they come in close proximity such that the emission energy from one can excite the other, thus resulting in different emission energy. There are two possibilities to be tested:

1. To fuse the chromophores to the subunits of the Snf1 complex to build an active readout of the conformational change
2. To fuse the chromophores to a short peptide (SAMS peptide) that can be phosphorylated by Snf1 and is commonly used as a read-out of Snf1 activity.


  • Working package 1: Find positions for fluorescent markers in SNF1
    For WP1 all present information about the protein complex is utilized, so that the fluorescent tags do not interfere with active sites or evolutionary conserved regions. Two alternatives should be investigated and presented with regard to present information and distance between fluorophores. The working package is ended with a 3D modeling of the tagging suggestions to further investigate functionality.

  • Working Package 2: Decide what fluorescent protein to use
    To apply FRET a compatible fluorphore pair is necessary. Also, efficiency and duration in respect to e.g. photonic bleaching should be taken into consideration.

  • Working package 3: Find DNA sequence for SAMS-peptide
    Beside the two tagging alternative from WP1 a SAMS-peptide will be used. Both ends will be tagged with fluorophores and conformational change should be indicated with FRET-signal during conformational change at phophorylation by active SNF1.

  • Working package 4: Decide on plasmid backbone
    The plasmid containing fusion protein should be able to amplify in E.coli and also contain a strong promoter for protein expression in yeast. Use VectorNTI to find good alternatives and locate RE sites.

  • Working package 5: Design primers for fusion PCR
    When WP 1-4 is finished the primer design can be initiated. Primers should be designed so that they have a high melting temperature, preferably around 60°C, with at least 20 bp homology with each side that should be fused. Primers at utter end of the fusion proteins should include restriction enzyme sites with GGCC repetition at the end. After rigorous proofreading the primers should be ordered together with a primer representing the SAMS peptide.

  • Working package 6: Acquire plasmid backbone for transfection with fusion protein
    Look up how the plasmid backbone from WP4 can be acquired. If it is a common backbone it should be avaible in the plasmid bank at the laboratory, otherwise it should be ordered.

  • Working package 7: Perform fusion PCR
    When the primers from WP5 has arrived the fusion PCR can be initiated. As a template for the protein subunits in SNF1 genomic DNA from yeast should be used, this should be avaible at the laboratory, and as template for fluorescent proteins dried DNA provided by iGEM will be used. Create a PCR mastermix that includes all ingredients except the DNA template. Each fusion is run in five steps according to the manual and each step is analyzed on agar gel so that the correct fragments are produced.

  • Working package 8: Ligate insert into plasmids
    After WP7 is successful the fusion protein should be inserted into the plasmid backbone. Use restriction enzymes as decided in WP6 and follow ligation protocol. Afterwards the plasmids should be purified with miniprep, they should be cut again and put on a gel to verify that the insert was successful.

  • Working package 9: Amplify transfection plasmids
    After WP8 the plasmid need to be amplified before being tranfected into yeast. Tranfect E.coli and amplify over night. Purify the amplified plasmids with a miniprep kit.

  • Working package 10: Sporulate diploid yeast strains to acquire Snf1 deletion mutants
    Grow diploid yeast strains with Snf1 deletions on sporulation plats to acquire haploid deletion mutants. Use protocol to clear the population from diploids and unwanted haploids.

  • Working package 11: Transfect yeast with tagged fusion protein
    After WP9-10 the hapoloid yeast deletion strain should be tranfected with the fusion protein plasmid. When the yeast has recovered from transfection the strain should be grown on sucrose overnight to show transfection result.

  • Working package 12: Apply FRET and analyze results
    By using a microscopy with FRET set up the success of previous WP can be concluded from the presence or absence of a FRET signal. Analyze results and make conclusions together with Marcus Wilhelmsson.

  • Working package 13:Write report
    WP 13 is running alongside with the other WPs during the whole project. Initially aims and theory is the major work load and as the project progress results and analysis claims the major part of this WP.

  • Working package 14: Apply for funding
    Also running alongside the other WPs. Funding is initially applied at science funding committees and later, as there are results to be presented, at major companies interested in the possibilities presented by this project. Funding should cover laboratory expenses, travel to Boston and team t-shirts.

Safety Questions
  • Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?
    No, since the yeast strains we work with are derived from harmless bakers yeast an none of the modifications have unknown or harmful consequences for anything else than the organism itself there is no safety issues with the project organism as such. Plasmid amplification in E.coli requiers a selection marker, ampicillin resistance in our case, which pose a safety issue regarding environmental safety but this is easily avoided by following laboration protocols regarding keeping a clean working environment and sterilization of organic waste.

  • Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?
    As mentioned above our device contain an ampicillin marker for amplification in E.coli. There could be issues if transfected cells are allowed to be spread outside the controlled laboratory environment. But working with ampicillin resistance as an selection marker is a common procedure and safety protocolls for this kind of work is readilly avaible. This will be regarded when we register our device to iGEM.

  • Is there a local biosafety group, committee, or review board at your institution?
    No, when working with synthetic biology at Chalmers we follow regulations set up by the Swedish Work Environment Authority. They set up protocols how chemicals and genetically modified material should be treated and what is demanded from an working environment to be permitted with this kind of labor.

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