Team:Potsdam Bioware

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==Production, Evolutionary Modification, and Selection of Cyclic Peptides for Therapy==
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'''Abstract'''
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One of the most important tasks of biopharmaceuticals is the binding and blocking of deregulated proteins. Towards this goal we mutate and select microviridins, which are tricyclic depsipeptides from cyanobacteria. They are small but stable due to their post- translational side-chain crosslinking and have high therapeutic potential for e.g. blocking proteases linked to diseases. Yet the possibilities of cyclic peptides are largely untapped since genetic systems for evolutionary optimization are not existent or not well established. Thus, we are developing modular systems for the production, mutation, and selection of such peptides. For production, we use the 6.5 kilo base mdn gene cluster cloned in E. coli plasmids. For mutation, we apply error prone PCR in combination with efficient cloning. For selection, we are establishing and testing phage display as well as an in vivo selection device, which links blocking of protease activity to antibiotic resistance. All systems, including the 6.5 kilo base cluster, adhere to the BioBrick standards.
 
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<h2>Modification, Selection and Production of Cyclic Peptides for Therapy</h2>
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<table cellpadding="0"><td><img src="https://static.igem.org/mediawiki/2011/7/7d/UP_micrviridin_movie_final.gif"/></td>
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<td><p style="text-align:justify;">One key task of biopharmaceuticals is the binding and blocking of deregulated proteins. Towards this goal, we mutate and select microviridins, which are tricyclic depsipeptides from cyanobacteria. They are small but stable due to their post-translational side-chain crosslinking. Microviridins have a high potential for therapy as they can block disease-relevant proteases. Yet, the possibilities of cyclic peptides are largely untapped since genetic systems for optimization are not well established. Thus, we developed synthetic systems for the mutation, selection and production of such peptides. We utilized the 6.5 kb microviridin (<i>mdn</i>) gene cluster cloned in <i>E. coli</i> plasmids, established random mutagenesis and generated focused libraries of microviridins. For selection against a panel of proteases, we are applying and testing phage display, and we are constructing a novel in-vivo selection device, which links protease blocking to antibiotic resistance. Our systems adhere to the BioBrick standards. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Project/Summary"><span class="bold">[more]</span></a></p>
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'''Safety and Security Assessment'''
 
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Our iGEM project requires only the handling of the non-pathogenic, non-adherent Escherichia coli K12 and B strains and the well-established filamentous phage. Both, the bacteria and the phage are commonly used chassis in laboratories and pose no risk when handled according to the mandatory rules. As all of us are well briefed about laboratory safety and biohazard regulations we follow these at all times. In Germany, work with genetically modified organisms is regulated by the ‘Law on Gene Technology’ (Gesetz zur Regelung der Gentechnik, GenTG). According to these rules, the responsible governmental authorities of the state of Brandenburg have been notified about our work.
 
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The most important issues we discussed are the consequences of the error-prone PCR we use to modify our parts. We tried to estimate the chances of generating highly toxic proteins. Surveying the literature, we found several reports about natural variants of microviridins and one rational mutational study, but no reports on toxic effects. As cyanobacteria can also produce toxic compounds (non-ribosomal peptides named microcystins) toxicity testing is well established in the cyanobacteria research community, and obviously, testing did not identify toxic effects. Therefore, we assume that our mutations will not have any hazardous effects. Additionally, the obtained, constructed, and planned plasmids contain only previously described parts without any known risk potential. Therefore, as far as we can foresee, our constructed BioBricks will not have or trigger any toxic effects or be critical in any way for the environment. Last but not least, we do not see any particular danger of abuse or other security threat of our work, since it is specifically addresses scientific questions. It is our goal that the health of mankind and the environment benefit from our research.
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<h2>Software</h2>
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<p>
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<b>BioLog</b> – The new allround talent in the lab for your smart phone! Our app combines several features frequently used in the lab. The software stores basic protocols in your pocket - easy, handy and ready to use… <a href="https://2011.igem.org/Team:Potsdam_Bioware/Software"><span class="bold">[more]</span></a></p>
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<a href="https://2011.igem.org/Team:Potsdam_Bioware/Team/Team_2011"><span class="bold">[more]</span></a></p>
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    <p>Nicole Albrecht</p>
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    <p>Katharina Berger</p>
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    <p>Nadja Bjelopoljak</p>
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    <p>Nadine Boehmer</p>
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    <img src="https://static.igem.org/mediawiki/2011/8/82/UP_VanessaB.jpg" alt="Vanessa Boehmer" />
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    <p>Vanessa Boehmer</p>
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    <img src="https://static.igem.org/mediawiki/2011/a/a3/UP_Jessica.jpg" alt="Jessica Eger" />
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    <p>Jessica Eger</p>
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    <img src="https://static.igem.org/mediawiki/2011/e/ed/UP_Niels.jpg" alt="Niels Weisbach" />
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    <p>Niels Weisbach</p>
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    <img src="https://static.igem.org/mediawiki/2011/b/b0/UP_Sebastian.jpg" alt="Sebastian Hanke" />
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    <p>Sebastian Hanke</p>
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    <img src="https://static.igem.org/mediawiki/2011/d/d1/UP_SaschaR.jpg" alt="Sascha Ramm" />
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    <p>Sascha Ramm</p>
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    <img src="https://static.igem.org/mediawiki/2011/8/87/UP_Paul.jpg" alt="Paul Kaufmann" />
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    <p>Paul Kaufmann</p>
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    <img src="https://static.igem.org/mediawiki/2011/6/66/UP_Sandrina.jpg" alt="Sandrina Heyde" />
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    <p>Sandrina Heyde</p>
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    <img src="https://static.igem.org/mediawiki/2011/3/37/UP_Sabine.jpg" alt="Sabine Meyer" />
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    <p>Sabine Meyer</p>
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    <img src="https://static.igem.org/mediawiki/2011/e/eb/UP_Niklas.jpg" alt="Niklas Laasch" />
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    <p>Niklas Laasch</p>
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<img src="https://static.igem.org/mediawiki/2011/c/c0/UP_Oliver.jpg" alt="Oliver Zimmer" />
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    <p>Oliver Zimmer</p>
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    <img src="https://static.igem.org/mediawiki/2011/5/5b/UP_TobiasW.jpg" alt="Tobias Wenzel" />
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    <p>Tobias Wenzel</p>
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<!---Box on the upper right: BioBricks--->
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<img class="right" src="https://static.igem.org/mediawiki/2011/8/84/UP_home_BioBricks.png"/>
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<h2>BioBricks</h2>
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<p class="standard">
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Our datapage displays our systems and BioBricks in a nutshell. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Data_Page"><span class="bold">[more]</a></span><br> <br>
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Our BioBricks are top-down for the <i>mdn</i> gene cluster and botton-up for detection and selection. <a href="https://2011.igem.org/Team:Potsdam_Bioware/BioBricks"><span class="bold">[more]</a></span></p>
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<img class="right" src="https://static.igem.org/mediawiki/2011/1/19/UP_home_Safety.png"/>
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<h2>Safety & Ethics</h2></a>
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<p class="standard">We discussed safety issues and ethic controversies in seminars and polled all members of the German parliament for their opinion on synthetic biology. Learn more about German views. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Safety_Ethics"><span class="bold">[more]</span></a></p>
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<img class="right" src="https://static.igem.org/mediawiki/2011/2/2a/UP_home_Labjournal.png"/>
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<h2>Labjournal</h2>
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<p>
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All the hours spent in the lab - thinking, laughing, sweating and hoping. Here is the tour guide through our lab work. We hope, you enjoy the trip. Please fasten your seat belt and mind the gap. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Labjournal"><span class="bold">[more]</span></a></p>
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<img class="right" src="https://static.igem.org/mediawiki/2011/b/bd/UP_home_Modeling.png"/>
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<h2>Modeling</h2></a>
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<p class="standard">
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This year we focused on systems modeling in which the reaction kinetics of the <i>in vivo</i> selection are analyzed. Read more about the predictions we were able to derive from our model.
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<a href="https://2011.igem.org/Team:Potsdam_Bioware/Project/Summary#Modeling"><span class="bold">[more]</span></a></p>
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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<p style="font-size:xx-small; text-align:center; color:grey">primary contact: Kristian Müller, kristian@syntbio.net, http://www.syntbio.net</p>
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!align="center"|[[Team:Potsdam_Bioware|Home]]
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!align="center"|[[Team:Potsdam_Bioware/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2011&team_name=Potsdam_Bioware Official Team Profile]
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!align="center"|[[Team:Potsdam_Bioware/Project|Project]]
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!align="center"|[[Team:Potsdam_Bioware/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Potsdam_Bioware/Modeling|Modeling]]
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Latest revision as of 13:38, 16 November 2011

Modification, Selection and Production of Cyclic Peptides for Therapy

One key task of biopharmaceuticals is the binding and blocking of deregulated proteins. Towards this goal, we mutate and select microviridins, which are tricyclic depsipeptides from cyanobacteria. They are small but stable due to their post-translational side-chain crosslinking. Microviridins have a high potential for therapy as they can block disease-relevant proteases. Yet, the possibilities of cyclic peptides are largely untapped since genetic systems for optimization are not well established. Thus, we developed synthetic systems for the mutation, selection and production of such peptides. We utilized the 6.5 kb microviridin (mdn) gene cluster cloned in E. coli plasmids, established random mutagenesis and generated focused libraries of microviridins. For selection against a panel of proteases, we are applying and testing phage display, and we are constructing a novel in-vivo selection device, which links protease blocking to antibiotic resistance. Our systems adhere to the BioBrick standards. [more]

Software

BioLog – The new allround talent in the lab for your smart phone! Our app combines several features frequently used in the lab. The software stores basic protocols in your pocket - easy, handy and ready to use… [more]

Team
  • Nicole Albrecht

    Nicole Albrecht

  • Katharina Berger

    Katharina Berger

  • Nadja Bjelopoljak

    Nadja Bjelopoljak

  • Nadine Boehmer

    Nadine Boehmer

  • Vanessa Boehmer

    Vanessa Boehmer

  • Jessica Eger

    Jessica Eger

  • Steffi Sempert

    Steffi Sempert

  • Niels Weisbach

    Niels Weisbach

  • Sebastian Hanke

    Sebastian Hanke

  • Sascha Ramm

    Sascha Ramm

  • Paul Kaufmann

    Paul Kaufmann

  • Stefan Wahlefeld

    Stefan Wahlefeld

  • Sandrina Heyde

    Sandrina Heyde

  • Sabine Meyer

    Sabine Meyer

  • Niklas Laasch

    Niklas Laasch

  • Oliver Zimmer

    Oliver Zimmer

  • Tobias Wenzel

    Tobias Wenzel

BioBricks

Our datapage displays our systems and BioBricks in a nutshell. [more]

Our BioBricks are top-down for the mdn gene cluster and botton-up for detection and selection. [more]

Safety & Ethics

We discussed safety issues and ethic controversies in seminars and polled all members of the German parliament for their opinion on synthetic biology. Learn more about German views. [more]

Labjournal

All the hours spent in the lab - thinking, laughing, sweating and hoping. Here is the tour guide through our lab work. We hope, you enjoy the trip. Please fasten your seat belt and mind the gap. [more]

Modeling

This year we focused on systems modeling in which the reaction kinetics of the in vivo selection are analyzed. Read more about the predictions we were able to derive from our model. [more]


primary contact: Kristian Müller, kristian@syntbio.net, http://www.syntbio.net

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