Team:Heidelberg/Tour

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   <h1><span style="font-size:150%;color:#666666;">Take the Tour!</span><span class="text-muted" style="font-size:90%"> Have a quick look at our Project. </span></h1>
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  <img src="https://static.igem.org/mediawiki/2013/9/92/Heidelberg_tour_bike.png" style="width:200px; float: right; margin-right: 4%">
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   <h1><span style="font-size:150%;color:#666666;">Take the Tour!</span><span class="text-muted" style="font-size:80%"> Take Your Chance and Join Our Quest!  </span></h1>
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                 <div class="jumbotron" id="overview">
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                 <div class="jumbotron" id="overview" style="background-image:url(https://static.igem.org/mediawiki/2013/8/8b/Heidelberg_Tour_Overview.png); background-repeat:no-repeat; background-size:115%; background-position:25% 30%">
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                      <h2>Overview</h2>
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                         <p style="font-size:14px; align:left">
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                                 The iGEM Team Heidelberg introduces NRPS to the iGEM community:
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<ul>
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<li style="font-size:14px">Proved modular principle of <b>N</b>on-<b>R</b>ibosomal <b>P</b>eptide <b>S</b>ynthetase by successful shuffling domains and modules</li> 
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<li style="font-size:14px">Developed a method for easy <b>N</b>on-<b>R</b>ibosomal <b>P</b>eptide-detection</li>
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<li style="font-size:14px">Employed and tested a concept for the recycling of gold from electronic waste using <b>N</b>on-<b>R</b>ibosomal <b>P</b>eptides </li>
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<li style="font-size:14px">Implemented a software which enables everyone to design synthetic <b>N</b>on-<b>R</b>ibosomal <b>P</b>eptides</li>
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</ul>
                         </p>
                         </p>
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<a href="/Team:Heidelberg/Project" style="margin-bottom:5%"><button typ="button" class="btn btn-default">Find out more!</button></a>
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                        <img src="https://static.igem.org/mediawiki/2013/3/3a/Heidelberg_GRAPHICAL_ABSTRACT_small.png" style="width:100%; margin-top:-20%">
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                          Recycling of gold from electronic waste using recombinant delftibactin
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<h2>Recycling Gold from Electronic Waste Using the NRP Delftibactin</h2>
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Undoubtedly, gold is one of the most precious materials on earth. Besides its common use in art and jewelry, gold is also an essential component of our modern computers and cell-phones. Due to the fast turn-over of today’s high-tech equipment, millions of tons of electronic waste accumulate each year containing tons of this valuable metal. The main approach nowadays to recycle gold from electronic waste is by electrolysis. Unfortunately, this is a highly inefficient and expensive procedure, preventing most of the gold from being recovered.
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                          <p style="font-size:14px; text-align:justify">
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Due to the fast turn-over of today’s high-tech equipment, millions of tons of electronic waste accumulate each year. It contains tons of gold which is very valuable to the society, not only because of its use in jewelry but also for medical applications. The main approach nowadays is to recycle gold by electrolysis which is highly inefficient and expensive, preventing most of the gold from being recovered.  
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This year a paper was published in Nature Chemical Biology by Johnsston <i>et al.</i> which described a small peptide produced by <i>Delftia acidovorans</i> which has the astonishing property to precipitate gold from solution- delftibactin. The aim of the gold recycling project was to use this non-ribosomal peptide to precipitate gold from electronic waste. This would provide a more natural way of recovery.
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In our project we worked on finding a more efficient and environmentally friendly method to recover this precious metal:
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Furthermore another goal is the introduction of the pathway for delftibactin production and additionally needed enzymes, which means about 70 kb of DNA in total, into <i>E. coli</i>. We want to show that these large constructs can be potentially inserted and expressed by E. coli with the promising perspective that delftibactin could readily be used as an efficient way of gold recycling from electronic waste.  
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<ul>
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<li style="font-size:14px"> We managed to recover gold from electronic waste using delftibactin, a NRP produced by <i>Delftia acidovorans</i> </li>
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<li style="font-size:14px"> We managed to clone all genes needed for delftibactin production into <i>E. coli</i> </li>
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<li style="font-size:14px"> We managed to recombinantly express the NRPS responsible for delftibactin production in <i>E. coli</i> </li>
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</ul>
                         </p>
                         </p>
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<a href="/Team:Heidelberg/Project/Delftibactin"><button typ="button" class="btn btn-default">Read more!</button></a>
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<a href="/Team:Heidelberg/Project/Delftibactin" style="margin-bottom:5%"><button typ="button" class="btn btn-default">Find out more!</button></a>
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                         <h2 >Synthetic Peptides</h2>
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                            <p style="font-size:14px; text-align:justify">
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Non-Ribosomal Peptide Synthetases are composed of building blocks, which are called modules. Each module shows a distinct specificity for a large variety of different monomers assembling them chain-like to a protein. Therefore, the order of modules determines the sequence of the final proteins. We used the tyrocidine synthetase from <i>Brevibacillus parabrevis</i> to:</p>
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<ul>
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<li style="font-size:14px">Employ this modularity to investigate the interchangeability and therefore compatibility of modules</li>
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<li style="font-size:14px">Engineer custom synthetic peptides <i>in vivo</i> by shuffling modules</li>
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<li style="font-size:14px">Demonstrate the broad variety of possible products</li>
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</ul>
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<p style="font-size:14px; text-align:justify">
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Understanding this modularity could provide new insights into combinatorial biology and approaches for creating compound libraries for screening purposes.</p>
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                              <a href="/Team:Heidelberg/Project/Tyrocidine" style="margin-bottom:5%"><button typ="button" class="btn btn-default">Discover more!</button></a>
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                    <h2>Indigoidine-Tag</h2>
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                                 <ul>
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<li style="font-size:14px">
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Creation of fusion NRPS producing peptides labelled with the <a href="https://2013.igem.org/Team:Heidelberg/Project/Indigoidine-Tag">Indigoidine-Tag</a>
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</li>
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<li style="font-size:14px">
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High-throughput protocols for design, construction and evaluation of combinatorial NRPS libraries (<a href="https://2013.igem.org/Team:Heidelberg/RFCs">RFC99 and RFC100</a>)
 +
</li>
 +
<li style="font-size:14px">
 +
<a href="https://2013.igem.org/Team:Heidelberg/Project/Tag-Optimization">Optimization</a> of the indigoidine synthetase by domain exchanges and coexpression with different PPTases
 +
</li>
 +
<li style="font-size:14px">
 +
Creation of functional synthetic NRPS domains based on multiple sequence alignments
 +
</li>
 +
                                </ul>
 +
                            </p>
 +
                            <a href="/Team:Heidelberg/Project/Indigoidine-Tag" style="margin-bottom:5%"><button typ="button" class="btn btn-default">Read more!</button></a>
 +
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                 </div>
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                 <div class="jumbotron" id="model">
+
            </div>
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                         <p style="font-size:14px; text-aling:justify">
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                                This text show only be displayed under model.
+
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                      </div>
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                 <div class="jumbotron hpouter" id="soft" style="background-image:url(https://static.igem.org/mediawiki/2013/d/dc/Heidelberg_oftware1.png); background-repeat:no-repeat; background-size:130%;">
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                      <div class="container hpinner" style="background-color:rgba(255,255,255,0.90)">
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                        <div class="col-md-6">
 +
                        <h2 style="padding-left:45px; padding-top:45px">Software: NRPSDesigner</h2>
 +
                        <p style="font-size:14px; text-align:justify; padding-left:45px">
 +
Features:</p>
 +
<ul>
 +
<li style="font-size:14px; margin-left:45px">Computer aided design of fully synthetic NRPS determined to produce a user-defined short peptide</li>
 +
<li style="font-size:14px; margin-left:45px">Optimal domain assembly based on evolutionary distance</li>
 +
<li style="font-size:14px; margin-left:45px">The curated database stores information of 658 Domains encoded on 99 DNA sequences</li>
 +
<li style="font-size:14px; margin-left:45px">Automated domain recognition for newly entered NRPS sequences</li>
 +
<li style="font-size:14px; margin-left:45px">Integration of Gibthon to facilitate implementation of cloning strategy</li>
 +
<li style="font-size:14px; margin-left:45px">Parts registry interface and SBOL output format</li>
 +
</ul>
 +
 
 +
                        <a href="/Team:Heidelberg/Project_Software"><button typ="button" class="btn btn-default" style="margin-bottom:45px; margin-left:45px">Find out more!</button></a>
 +
                      </div>
 +
                      <div class="col-md-6">
 +
<img src="https://static.igem.org/mediawiki/2013/1/1c/Graphical_abstract_nrps_designer.png" style="width:100%; margin-top:20%">
 +
                      </div>
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                    </div>
 +
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 +
                <div class="jumbotron hpouter" id="model" style="background-image:url(https://static.igem.org/mediawiki/2013/2/28/Heidelberg_fit.png); background-repeat:no-repeat; background-size:150%;">
 +
                    <div class="container hpinner">
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<div class="row" >
 +
                        <h2 style="padding-left:50px; text-align:left">Modeling the Feasibility of Gold Recycling with Delftibactin</h2>
 +
<div class="col-sm-12 col-md-6">
 +
 
 +
                         <p style="font-size:14px; text-align:justify; padding-left:45px">
 +
<br/>
 +
                    Non-ribosomal peptide synthetases expressed in natural organisms help to develop evolutionary advantages over competitors. This ability has been recognized at the industrial level for example, by pharmaceutical companies. Of course, we were also fascinated by the idea to elevate our system to a larger scale and to test its industrial feasibility. Accompanying our experimental results confirming the ability of delftibactin to precipitate gold, we attempt to use theoretical considerations and metabolic modeling to show the realistic potential of our idea. </p>
 +
<a href="/Team:Heidelberg/Modelling/Gold_Recovery" style="margin-bottom:5%; padding-left:45px"><button typ="button" class="btn btn-default">Read more!</button></a>
 +
</div>
 +
<div class="col-sm-12 col-md-6">
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2013/a/a2/Heidelberg_Modeldelftibactin.png" style="width:300px; margin-top:0%">
 +
</center>
 +
</div>
 +
</div>
 +
<div class="row" >
 +
<div class="col-sm-12 col-md-6">
 +
                        <h2 style="padding-left:50px; text-align:left">Modeling the Indigoidine Production</h2>
 +
                        <p style="font-size:14px; text-align:justify; padding-left:45px">
 +
                                A challenge we had to face during the characterization and optimization of indC was to identify the production kinetics of indigoidine. In order to disentangle the underlying mechanisms of bacterial growth and peptide synthesis, we decided to set up a mathematical model based on coupled ordinary differential equations. Calibrated with our experimental time-resolved data, the mathematical model could potentially not only elucidate how indigoidine production influences growth of bacteria but also provide a more quantitative understanding of the synthesis efficiency of the different T domains and PPTases that were tested.  
                         </p>
                         </p>
 +
<a href="/Team:Heidelberg/Modelling/Ind_Production" style="margin-bottom:5%; padding-left:45px"><button typ="button" class="btn btn-default">Discover more!</button></a>
 +
</div>
 +
<div class="col-sm-12 col-md-6">
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2013/f/f1/Heidelberg_IndModeling_Overview.png" style="width:400px; margin-top:20%">
 +
</center>
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</div>
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                         <h2> Human Practice:</h2>           
+
                         <h2> Human Practice</h2>
-
                         <p style="font-size:14px; text-aling:justify">
+
                      <div class="row">
-
                                The aim of science and synthetic biology in particular is to <b>improve lives by solving problems</b>. We as researchers (-to-be) are therefore working for society. Yet, we can only offer solutions, which have to be approved and applied by the public. Moreover, national and international legal frameworks limit every scientific action, which again, lie in the hand of the people. Thus, synthetic biology in general and our project in particular have implications for every individual, as we are all <b>interdependent</b>. Everyone, may he or she be a scientist or not, has an equally valuable opinion on synthetic biology.
+
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 +
                         <p style="font-size:14px; text-align:justify">The aim of science and synthetic biology in particular is to <b>improve lives by solving problems</b>. We as researchers are therefore working for society. Yet, we can only offer solutions, which have to be approved and applied by the public.
 +
</p>
 +
<p style="font-size:14px; text-align:justify">
 +
We as iGEM Team Heidelberg have therefore put great effort in communicating with many groups within society to open minds, broaden horizons as well as minimize prejudices and concerns by:
 +
</p>
 +
<ul style="padding-left:45px">
 +
<li style="font-size:14px">Involving experts</li>
 +
<li style="font-size:14px">Engaging the broad public</li>
 +
<li style="font-size:14px">Getting inspired by artists</li>
 +
<li style="font-size:14px">Intruiging the next generation of scientists</li>
 +
</ul>
 +
<p style="font-size:14px">
 +
And finally bringing them all together to an open talk evening addressing the question <b>"On the Way to a Synthetic Future?"</b>
-
We as iGEM Team Heidelberg have therefore put great effort in communicating with various groups within society and to <b>engage the broad public</b> as well as <b>artists</b> and of course <b>the next generation of scientists</b> into our project. We hope to open minds, broaden horizons as well as minimize prejudices and concerns. Additionally, we discussed our ideas with various <b>experts in science and society</b> right from the start. Finally, we invited them all these great people to an open talk evening addressing the question <b>"On the Way to a Synthetic Future?"</b> in cooperation with the <b>Biotechnological Students Initiative e.V.</b> and the <b>Helmholtz-Initiative for Synthetitic Biology</b>.
 
                         </p>
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-
                         <a href="/Team:Heidelberg/HumanPractice" style="margin-bottom:5%"><button typ="button" class="btn btn-default">Read more!</button></a>
+
                         <a href="/Team:Heidelberg/HumanPractice" style="margin-bottom:5%"><button typ="button" class="btn btn-default">See more!</button></a>
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 +
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                              <img src="https://static.igem.org/mediawiki/2013/6/69/Heidelberg_IMG_5231new.png" style="max-height:187px" alt="" />
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 +
 
 +
                    <a class="left carousel-control" href="#myCarouselC" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a>
 +
                    <a class="right carousel-control" href="#myCarouselC" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a>
 +
 
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                      </div>
 +
                    </div>
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                 </div>
                 </div>
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                 <div class="jumbotron" id="results" style="background-image:url(https://static.igem.org/mediawiki/2013/a/a9/Heidelberg_BG_Beyond_Science.JPG); background-size:100%; background-position:25% 30%">
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                 <div class="jumbotron" id="results" style="background-image:url(https://static.igem.org/mediawiki/2013/a/a9/Heidelberg_BG_Beyond_Science.JPG); background-repeat:no-repeat; background-size:105%; background-position:25% 30%">
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                         <h2> Results:</h2>
+
 
-
                         <p style="font-size:14px; text-aling:justify">
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<a href="http://igem2013.bioquant.uni-heidelberg.de/NRPSDesigner/" style="float:right"  target="_blank"><img src="https://static.igem.org/mediawiki/2013/1/1a/Heidelberg_nrps_des_btn.png" style="width:60px"></a>
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<a href="/Team:Heidelberg/RFCs" style="float:right"  target="_blank"><img src="https://static.igem.org/mediawiki/2013/6/67/Heidelberg_rfc100_btn.png" style="width:60px"></a>
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<a href="/Team:Heidelberg/RFCs#rfc99" style="float:right"  target="_blank"><img src="https://static.igem.org/mediawiki/2013/8/88/Heidelberg_rfc99_btn.png" style="width:60px"></a>
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<a href="http://parts.igem.org/Part:BBa_K1152007" style="float:right"  target="_blank"><img src="https://static.igem.org/mediawiki/2013/c/cc/Heidelberg_ind_tag_btn.png" style="width:60px"></a>
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                         <h2> Results</h2>
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                         <p style="font-size:14px; text-align:justify">
                           <ul>
                           <ul>
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                               <li style="font-size:14px">We opened up the usage of NRPS to the iGEM community</li>
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                               <li style="font-size:14px">Automated Design of <b>Custom Non-Ribosomal Peptide Synthetases</b></li>
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                               <li style="font-size:14px">We proved modularity of NRPS on different hierachical layers</li>
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                               <li style="font-size:14px">Production of <b>Synthetic Peptides</b> in different engineered E. coli Hosts</li>
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                               <li style="font-size:14px">We established a <a href="">universal and specific Tag for the labeling of NRPs</a></li>
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                               <li style="font-size:14px">Invention of a Universal Tag for Non-Ribosomal Peptide labeling in vivo </li>
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                               <li style="font-size:14px">We submitted a standardized assembly line production procedure for synthetic NRPs: <a href="">RFC 99 and RFC 100</a></li>
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                              <li style="font-size:14px">Using the Tag for peptide characterization and quantification of production </a></li>
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                              <li style="font-size:14px">We had a great summer with lots of <a href="/Team:Heidelberg/Team/Gallery">fun and new experiences!</a></li>
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                               <li style="font-size:14px">Introducing our standardized Framework for Production of Synthetic Peptides to the Synbio Community: <a href="/Team:Heidelberg/RFCs">RFC 99 and RFC 100</a></li>
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                              <li style="font-size:14px">Having lots of <a href="/Team:Heidelberg/Team/Gallery">fun</a> and very much looking forward to the Jamboree in Boston</a></li>
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                           </ul>
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Latest revision as of 03:55, 29 October 2013

Take the Tour! Take Your Chance and Join Our Quest!

Overview

The iGEM Team Heidelberg introduces NRPS to the iGEM community:

  • Proved modular principle of Non-Ribosomal Peptide Synthetase by successful shuffling domains and modules
  • Developed a method for easy Non-Ribosomal Peptide-detection
  • Employed and tested a concept for the recycling of gold from electronic waste using Non-Ribosomal Peptides
  • Implemented a software which enables everyone to design synthetic Non-Ribosomal Peptides

Recycling Gold from Electronic Waste Using the NRP Delftibactin

Due to the fast turn-over of today’s high-tech equipment, millions of tons of electronic waste accumulate each year. It contains tons of gold which is very valuable to the society, not only because of its use in jewelry but also for medical applications. The main approach nowadays is to recycle gold by electrolysis which is highly inefficient and expensive, preventing most of the gold from being recovered. In our project we worked on finding a more efficient and environmentally friendly method to recover this precious metal:

  • We managed to recover gold from electronic waste using delftibactin, a NRP produced by Delftia acidovorans
  • We managed to clone all genes needed for delftibactin production into E. coli
  • We managed to recombinantly express the NRPS responsible for delftibactin production in E. coli

Synthetic Peptides

Non-Ribosomal Peptide Synthetases are composed of building blocks, which are called modules. Each module shows a distinct specificity for a large variety of different monomers assembling them chain-like to a protein. Therefore, the order of modules determines the sequence of the final proteins. We used the tyrocidine synthetase from Brevibacillus parabrevis to:

  • Employ this modularity to investigate the interchangeability and therefore compatibility of modules
  • Engineer custom synthetic peptides in vivo by shuffling modules
  • Demonstrate the broad variety of possible products

Understanding this modularity could provide new insights into combinatorial biology and approaches for creating compound libraries for screening purposes.

Indigoidine-Tag

  • Creation of fusion NRPS producing peptides labelled with the Indigoidine-Tag
  • High-throughput protocols for design, construction and evaluation of combinatorial NRPS libraries (RFC99 and RFC100)
  • Optimization of the indigoidine synthetase by domain exchanges and coexpression with different PPTases
  • Creation of functional synthetic NRPS domains based on multiple sequence alignments

Software: NRPSDesigner

Features:

  • Computer aided design of fully synthetic NRPS determined to produce a user-defined short peptide
  • Optimal domain assembly based on evolutionary distance
  • The curated database stores information of 658 Domains encoded on 99 DNA sequences
  • Automated domain recognition for newly entered NRPS sequences
  • Integration of Gibthon to facilitate implementation of cloning strategy
  • Parts registry interface and SBOL output format

Modeling the Feasibility of Gold Recycling with Delftibactin


Non-ribosomal peptide synthetases expressed in natural organisms help to develop evolutionary advantages over competitors. This ability has been recognized at the industrial level for example, by pharmaceutical companies. Of course, we were also fascinated by the idea to elevate our system to a larger scale and to test its industrial feasibility. Accompanying our experimental results confirming the ability of delftibactin to precipitate gold, we attempt to use theoretical considerations and metabolic modeling to show the realistic potential of our idea.

Modeling the Indigoidine Production

A challenge we had to face during the characterization and optimization of indC was to identify the production kinetics of indigoidine. In order to disentangle the underlying mechanisms of bacterial growth and peptide synthesis, we decided to set up a mathematical model based on coupled ordinary differential equations. Calibrated with our experimental time-resolved data, the mathematical model could potentially not only elucidate how indigoidine production influences growth of bacteria but also provide a more quantitative understanding of the synthesis efficiency of the different T domains and PPTases that were tested.

Human Practice

The aim of science and synthetic biology in particular is to improve lives by solving problems. We as researchers are therefore working for society. Yet, we can only offer solutions, which have to be approved and applied by the public.

We as iGEM Team Heidelberg have therefore put great effort in communicating with many groups within society to open minds, broaden horizons as well as minimize prejudices and concerns by:

  • Involving experts
  • Engaging the broad public
  • Getting inspired by artists
  • Intruiging the next generation of scientists

And finally bringing them all together to an open talk evening addressing the question "On the Way to a Synthetic Future?"

Results

  • Automated Design of Custom Non-Ribosomal Peptide Synthetases
  • Production of Synthetic Peptides in different engineered E. coli Hosts
  • Invention of a Universal Tag for Non-Ribosomal Peptide labeling in vivo
  • Using the Tag for peptide characterization and quantification of production
  • Introducing our standardized Framework for Production of Synthetic Peptides to the Synbio Community: RFC 99 and RFC 100
  • Having lots of fun and very much looking forward to the Jamboree in Boston

Thanks to