Team:Potsdam Bioware

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<b>Hallo liebes iGEM Potsdam Team :P , auch wenn ihr unser Wiki gemopst habt, wünschen wir euch viel Erfolg beim Endspurt ;)</b>
 
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<h2>Modification, Selection and Production of Cyclic Peptides for Therapy</h2>
<h2>Modification, Selection and Production of Cyclic Peptides for Therapy</h2>
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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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<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 use 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, including the 6.5 kb cluster, adhere to the BioBrick standards.
 
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<h2>Project</h2>
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<h2>Software</h2>
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Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Project/Results"><span class="bold">[more]</span></a></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/NoteBook/Statistics" style="z-index:20;position:relative;"><h2>Statistics - In a Minute</h2></a>
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<a href="https://2011.igem.org/Team:Potsdam_Bioware/Team" style="z-index:20;position:relative;"><h2>Team</h2></a>
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   <img src="https://static.igem.org/mediawiki/2011/6/67/UP_Nicole.jpg" alt="Nicole Albrecht"/>
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     <p>Nicole Albrecht</p>
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    <p>Katharina Berger</p>
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    <img src="https://static.igem.org/mediawiki/2011/0/0e/UP_Nadja.jpg" alt="Nadja Bjelopoljak" />
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    <p>Nadja Bjelopoljak</p>
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<h2>BioBricks</h2>
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    <p>Nadine Boehmer</p>
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<p class="standard">Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.<a href="https://2011.igem.org/Team:Potsdam_Bioware/BioBricks"><span class="bold">[more]</a></span></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 class="standard">Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. <a href="https://2011.igem.org/Team:Potsdam_Bioware/Safety_ethics"><span class="bold">[more]</span></a></p>
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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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Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.<a href="https://2011.igem.org/Team:Potsdam_Bioware/journal/journal"><span class="bold">[more]</span></a></p>
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    <img src="https://static.igem.org/mediawiki/2011/b/b1/UP_Steffi.jpg" alt="Steffi Sempert" />
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    <p>Steffi Sempert</p>
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<a href="https://2011.igem.org/Team:Potsdam_Bioware/software"><span class="bold">[more]</span></a></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/c/cb/UP_Stefan.jpg" alt="Stefan Wahlefeld" />
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    <p>Stefan Wahlefeld</p>
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===Abstract===
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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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<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 use 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, including the 6.5 kb cluster, adhere to the BioBrick standards.</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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[[File:UP_poster_project_overview.PNG|500px|centre]]<br>
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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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===Safety and Security Assessment===
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<p style="text-align:justify;">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. Following these rules, there should not be a significant danger neither to the environment nor to team members.<br>
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<h2>BioBricks</h2>
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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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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. This means that only a negligible risk arises from our used methods and constructs to the environment, the public and the team members. 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.</p>
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'''Safety Questions'''
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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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* 1. Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?
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** No, our project is not raising any of these safety issues.
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* 2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes, did you document these issues in the Registry? how did you manage to handle the safety issue? How could other teams learn from your experience?
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** No, our BioBrick parts or devices are not going to raise any safety issues.
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* 3. Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?
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** 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. Our work was classified as biosafety level 1.
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* 4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?
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** So far biosafety assessment is primarily based on the characterization of wild-type devices or systems. For Synthetic Biology these rules should be extended to better represent the variations made by synthetic biology approaches. In addition to the continuous evaluation of safety and security, a section on technological impact assessment should be added.  
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<h2>Labjournal</h2>
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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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<h2>Modeling</h2></a>
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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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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2009.igem.org/Help:Template/Examples">HERE</a>.
 
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<div id="clustrmaps-widget"></div><script type="text/javascript">var _clustrmaps = {'url' : 'https://2011.igem.org/Team:Potsdam_Bioware', 'user' : 910340, 'server' : '2', 'id' : 'clustrmaps-widget', 'version' : 1, 'date' : '2011-07-15', 'lang' : 'en', 'corners' : 'square' };(function (){ var s = document.createElement('script'); s.type = 'text/javascript'; s.async = true; s.src = 'http://www2.clustrmaps.com/counter/map.js'; var x = document.getElementsByTagName('script')[0]; x.parentNode.insertBefore(s, x);})();</script><noscript><a href="http://www2.clustrmaps.com/user/239de404"><img src="http://www2.clustrmaps.com/stats/maps-no_clusters/2011.igem.org-Team-Potsdam_Bioware-thumb.jpg" alt="Locations of visitors to this page" /></a></noscript>
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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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