Team:DTU-Denmark

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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<h2>The wiki is super live!!</h2>
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<p>How does that make you feel?</br>
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<input type='radio' name='group1'>Awesome</input>
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                <h2><b>Problem</b></h2>How can we quantify promoter activity?</br>
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<input type='radio' name='group1'>Mega good</input>
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                <p>When characterising promoters today it is done by proxy of protein. This can result in unwanted variations caused by translation and folding efficiency or excess cellular stress. Another important issue is the lack of a standard for measurements of fluorescence as most characterisations are done using fluorescent proteins such as GFP. As a result, most characterisations are done in relative units making it complicated or impossible to compare measurements between labs, strains and growth conditions. <a href="/Team:DTU-Denmark/Overview/Background"> <b>READ MORE</b> </a> </p>
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    <img class="background-epopi" style="display:block;margin:auto;" width="45%" src=https://static.igem.org/mediawiki/2014/9/96/DTU-Denmark-E-popi-PROBLEM.png />
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                <h2><b>Solution</b></h2>Spinach RNA allows us to measure RNA concentration using fluorometry</br>
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                <p>The Spinach RNA is an aptamer, which can bind to DFHBI to create a fluorophore that resembles GFP in spectral properties. This provides a way to easily quantify RNA concentration and allows promoter activities to be <b><a href="/Team:DTU-Denmark/Achievements/Calculator">calculated</a></b> in units Polymerases Per Second. The possibility of measuring promoter activity in absolute terms will enable researchers to share and compare results obtained in different labs, and better characterise the function of promoters. <a href="/Team:DTU-Denmark/Overview/Strategy"> <b>READ MORE</b> </a></p>
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    <img class="background-epopi" style="display:block;margin:auto;" width="45%" src=https://static.igem.org/mediawiki/2014/2/22/DTU-Denmark-E-popi-SOLUTION.png />
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                <h2><b>Results</b></h2>We have developed a method that can be used to measure absolute promoter activity</br>
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                <p>Using RNA transcribed <i>in vitro</i> we created a standard series which can be used to determine the concentration of Spinach given a fluorescence intensity. We also designed an experiment to determine the degradation rate of the Spinach RNA <i>in vivo</i>. Combining these two experiments with the growth rate and fluorescence of a Spinach-expressing culture it is possible to determine the promoter activity using our derived formulas or our online calculator. <a href="/Team:DTU-Denmark/Achievements/Experimental_Results"> <b>READ MORE</b> </a></p>
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    <img class="background-epopi" style="display:block;margin:auto;" width="45%" src=https://static.igem.org/mediawiki/2014/4/47/DTU-Denmark-E-popi-RESULTS.png />
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<h3>Try Our PoPS Calculator!</h3>
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<p>Have you measured promoter activity but is data analysis a drag? Use our PoPS calculator to calculate promoter activity based on Spinach measurements!</p>
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<p> Please be sure to keep these links, your audience will want to find your: </p>
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<!-- Links to other team pages -->
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<li><a href="https://2014.igem.org/Team:DTU-Denmark">Home</a> </li>     
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<li><a href="https://2014.igem.org/Team:DTU-Denmark/Team">Team</a> </li>
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<li><a href="https://2014.igem.org/Team:DTU-Denmark/Modeling">Modeling</a> </li>
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<li><a href="https://2014.igem.org/Team:DTU-Denmark/Notebook">Notebook</a> </li>
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<li><a href="https://2014.igem.org/Team:DTU-Denmark/Safety">Safety</a> </li>
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<li><a href="https://2014.igem.org/Team:DTU-Denmark/Attributions">Attributions</a> </li>
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<p>We are currently working on providing teams with some easy to use design templates.
 
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<br> In the meantime you can also view other team wikis for inspiration! Here are some very good examples</p>
 
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<li> <a href="https://2013.igem.org/Team:SDU-Denmark/"> 2013 SDU Denmark </a> </li>
 
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<li> <a href="https://2013.igem.org/Team:SYSU-China">2013 SYSU China</a> </li>
 
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<li> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_ATCG"> 2013 Shenxhen BGIG ATCG </a></li>
 
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<li> <a href="https://2013.igem.org/Team:Colombia_Uniandes">2013 Colombia Unianades </a></li>
 
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<li> <a href="https://2013.igem.org/Team:Lethbridge">2013 Lethbridge</a></li>
 
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<p>For a full wiki list, you can visit <a href="https://igem.org/Team_Wikis?year=2013">iGEM 2013 web sites </a> and <a href="https://igem.org/Team_Wikis?year=2012">iGEM 2012 web sites</a>  lists. </p>
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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Latest revision as of 08:32, 7 February 2015

Technical University of Denmark

Problem

How can we quantify promoter activity?

When characterising promoters today it is done by proxy of protein. This can result in unwanted variations caused by translation and folding efficiency or excess cellular stress. Another important issue is the lack of a standard for measurements of fluorescence as most characterisations are done using fluorescent proteins such as GFP. As a result, most characterisations are done in relative units making it complicated or impossible to compare measurements between labs, strains and growth conditions. READ MORE

Solution

Spinach RNA allows us to measure RNA concentration using fluorometry

The Spinach RNA is an aptamer, which can bind to DFHBI to create a fluorophore that resembles GFP in spectral properties. This provides a way to easily quantify RNA concentration and allows promoter activities to be calculated in units Polymerases Per Second. The possibility of measuring promoter activity in absolute terms will enable researchers to share and compare results obtained in different labs, and better characterise the function of promoters. READ MORE

Results

We have developed a method that can be used to measure absolute promoter activity

Using RNA transcribed in vitro we created a standard series which can be used to determine the concentration of Spinach given a fluorescence intensity. We also designed an experiment to determine the degradation rate of the Spinach RNA in vivo. Combining these two experiments with the growth rate and fluorescence of a Spinach-expressing culture it is possible to determine the promoter activity using our derived formulas or our online calculator. READ MORE



Try Our PoPS Calculator!

Have you measured promoter activity but is data analysis a drag? Use our PoPS calculator to calculate promoter activity based on Spinach measurements!



Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
+45 45 25 25 25
dtuigem14@gmail.com .

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